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Merge branch 'thermo-energy' of github.com:lammps/lammps into thermo-energy

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Stan Gerald Moore
2021-02-08 14:15:00 -07:00
parent 6909cf9dd5 33939a0e26
commit 0797d15219
1318 changed files with 36902 additions and 51251 deletions
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47
.github/workflows/codeql-analysis.yml vendored Normal file
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@ -0,0 +1,47 @@
# GitHub action to run static code analysis on C++ and Python code
name: "CodeQL Code Analysis"
on:
push:
branches: [master]
jobs:
analyze:
name: Analyze
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
language: ['cpp', 'python']
steps:
- name: Checkout repository
uses: actions/checkout@v2
with:
fetch-depth: 2
- name: Setup Python
uses: actions/setup-python@v2
with:
python-version: '3.x'
- name: Initialize CodeQL
uses: github/codeql-action/init@v1
with:
languages: ${{ matrix.language }}
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
- name: Building LAMMPS via CMake
if: ${{ matrix.language == 'cpp' }}
shell: bash
working-directory: ${{github.workspace}}/build
run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
cmake --build . --parallel 2
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v1

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.github/workflows/unittest-macos.yml vendored Normal file
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@ -0,0 +1,34 @@
# GitHub action to build LAMMPS on MacOS and run unit tests
name: "Unittest for MacOS"
on:
push:
branches: [master]
jobs:
build:
name: MacOS Unit Test
if: ${{ github.repository == 'lammps/lammps' }}
runs-on: macos-latest
steps:
- name: Checkout repository
uses: actions/checkout@v2
with:
fetch-depth: 2
- name: Create Build Environment
run: cmake -E make_directory ${{github.workspace}}/build
- name: Building LAMMPS via CMake
shell: bash
working-directory: ${{github.workspace}}/build
run: |
cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \
-DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
cmake --build . --parallel 2
- name: Run Tests
working-directory: ${{github.workspace}}/build
shell: bash
run: ctest -V

16
cmake/CMakeLists.txt
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@ -107,13 +107,15 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION
USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF)
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
option(PKG_${PKG} "Build ${PKG} Package" OFF)
endforeach()

9
cmake/Modules/Packages/KOKKOS.cmake
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@ -1,4 +1,7 @@
########################################################################
# As of version 3.3.0 Kokkos requires C++14
set(CMAKE_CXX_STANDARD 14)
########################################################################
# consistency checks and Kokkos options/settings required by LAMMPS
if(Kokkos_ENABLE_CUDA)
message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
@ -35,8 +38,8 @@ if(DOWNLOAD_KOKKOS)
list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
include(ExternalProject)
ExternalProject_Add(kokkos_build
URL https://github.com/kokkos/kokkos/archive/3.2.01.tar.gz
URL_MD5 ba72440e285ccde05b403694ea0c92e5
URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz
URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
)
@ -50,7 +53,7 @@ if(DOWNLOAD_KOKKOS)
target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
add_dependencies(LAMMPS::KOKKOS kokkos_build)
elseif(EXTERNAL_KOKKOS)
find_package(Kokkos 3.2.01 REQUIRED CONFIG)
find_package(Kokkos 3.3.01 REQUIRED CONFIG)
target_link_libraries(lammps PRIVATE Kokkos::kokkos)
else()
set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)

4
doc/Makefile
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@ -94,7 +94,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
-e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
-e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@$(MAKE) $(MFLAGS) -C graphviz all
@(\
@ -118,7 +118,7 @@ html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
@rm -rf html/PDF/.[sg]*
@echo "Build finished. The HTML pages are in doc/html."
spelling: xmlgen $(VENV) $(SPHINXCONFIG)/false_positives.txt
spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
@(\
. $(VENV)/bin/activate ; env PYTHONWARNINGS= \

2
doc/doxygen/Doxyfile.in
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@ -424,6 +424,8 @@ INPUT = @LAMMPS_SOURCE_DIR@/utils.cpp \
@LAMMPS_SOURCE_DIR@/input.h \
@LAMMPS_SOURCE_DIR@/tokenizer.cpp \
@LAMMPS_SOURCE_DIR@/tokenizer.h \
@LAMMPS_SOURCE_DIR@/arg_info.cpp \
@LAMMPS_SOURCE_DIR@/arg_info.h \
@LAMMPS_SOURCE_DIR@/text_file_reader.cpp \
@LAMMPS_SOURCE_DIR@/text_file_reader.h \
@LAMMPS_SOURCE_DIR@/potential_file_reader.cpp \

5
doc/src/Build_extras.rst
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@ -521,11 +521,14 @@ They must be specified in uppercase.
* - VEGA906
- GPU
- AMD GPU MI50/MI60 GFX906
* - VEGA908
- GPU
- AMD GPU GFX908
* - INTEL_GEN
- GPU
- Intel GPUs Gen9+
This list was last updated for version 3.2 of the Kokkos library.
This list was last updated for version 3.3 of the Kokkos library.
.. tabs::

1
doc/src/Commands_pair.rst
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@ -263,6 +263,7 @@ OPT.
* :doc:`ufm (got) <pair_ufm>`
* :doc:`vashishta (gko) <pair_vashishta>`
* :doc:`vashishta/table (o) <pair_vashishta>`
* :doc:`wf/cut <pair_wf_cut>`
* :doc:`yukawa (gko) <pair_yukawa>`
* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
* :doc:`zbl (gko) <pair_zbl>`

23
doc/src/Commands_parse.rst
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@ -162,3 +162,26 @@ LAMMPS:
triple quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
.. admonition:: ASCII versus UTF-8
:class: note
LAMMPS expects and processes 7-bit ASCII format text internally.
Many modern environments use UTF-8 encoding, which is a superset
of the 7-bit ASCII character table and thus mostly compatible.
However, there are several non-ASCII characters that can look
very similar to their ASCII equivalents or are invisible (so they
look like a blank), but are encoded differently. Web browsers,
PDF viewers, document editors are known to sometimes replace one
with the other for a better looking output. However, that can
lead to problems, for instance, when using cut-n-paste of input
file examples from web pages, or when using a document editor
(not a dedicated plain text editor) for writing LAMMPS inputs.
LAMMPS will try to detect this and substitute the non-ASCII
characters with their ASCII equivalents where known. There also
is going to be a warning printed, if this occurs. It is
recommended to avoid such characters altogether in LAMMPS input,
data and potential files. The replacement tables are likely
incomplete and dependent on users reporting problems processing
correctly looking input containing UTF-8 encoded non-ASCII
characters.

187
doc/src/Developer_org.rst
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@ -1,68 +1,75 @@
Source files
------------
The source files of the LAMMPS code are found in two
directories of the distribution: ``src`` and ``lib``.
Most of the code is C++ but there are small numbers of files
in several other languages.
The source files of the LAMMPS code are found in two directories of the
distribution: ``src`` and ``lib``. Most of the code is written in C++
but there are small a number of files in several other languages like C,
Fortran, Shell script, or Python.
The core of the code is located in the
``src`` folder and its sub-directories.
A sizable number of these files are in the ``src`` directory
itself, but there are plenty of :doc:`packages <Packages>`, which can be
included or excluded when LAMMPS is built. See the :doc:`Include
packages in build <Build_package>` section of the manual for more
information about that part of the build process. LAMMPS currently
supports building with :doc:`conventional makefiles <Build_make>` and
through :doc:`CMake <Build_cmake>` which differ in how packages are
enabled or disabled for a LAMMPS binary. The source files for each
The core of the code is located in the ``src`` folder and its
sub-directories. A sizable number of these files are in the ``src``
directory itself, but there are plenty of :doc:`packages <Packages>`,
which can be included or excluded when LAMMPS is built. See the
:doc:`Include packages in build <Build_package>` section of the manual
for more information about that part of the build process. LAMMPS
currently supports building with :doc:`conventional makefiles
<Build_make>` and through :doc:`CMake <Build_cmake>`. Those procedures
differ in how packages are enabled or disabled for inclusion into a
LAMMPS binary so they cannot be mixed. The source files for each
package are in all-uppercase sub-directories of the ``src`` folder, for
example ``src/MOLECULE`` or ``src/USER-MISC``. The ``src/STUBS``
sub-directory is not a package but contains a dummy MPI library, that is
used when building a serial version of the code. The ``src/MAKE``
directory contains makefiles with settings and flags for a variety of
configuration and machines for the build process with traditional
makefiles.
directory and its sub-directories contain makefiles with settings and
flags for a variety of configuration and machines for the build process
with traditional makefiles.
The ``lib`` directory contains the source code for several supporting
libraries or files with configuration settings to use globally installed
libraries, that are required by some of the optional packages.
Each sub-directory, like ``lib/poems`` or ``lib/gpu``, contains the
source files, some of which are in different languages such as Fortran
or CUDA. These libraries are linked to during a LAMMPS build, if the
corresponding package is installed.
libraries, that are required by some of the optional packages. They may
include python scripts that can transparently download additional source
code on request. Each sub-directory, like ``lib/poems`` or ``lib/gpu``,
contains the source files, some of which are in different languages such
as Fortran or CUDA. These libraries included in the LAMMPS build,
if the corresponding package is installed.
LAMMPS C++ source files almost always come in pairs, such as
``src/run.cpp`` (implementation file) and ``src/run.h`` (header file).
Each pair of files defines a C++
class, for example the :cpp:class:`LAMMPS_NS::Run` class which contains
the code invoked by the :doc:`run <run>` command in a LAMMPS input script.
As this example illustrates, source file and class names often have a
one-to-one correspondence with a command used in a LAMMPS input script.
Some source files and classes do not have a corresponding input script
Each pair of files defines a C++ class, for example the
:cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the
:doc:`run <run>` command in a LAMMPS input script. As this example
illustrates, source file and class names often have a one-to-one
correspondence with a command used in a LAMMPS input script. Some
source files and classes do not have a corresponding input script
command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
class. They are discussed in the next section.
A small number of C++ classes and utility functions are implemented with
only a ``.h`` file. Examples are the Pointer class or the MathVec functions.
The names of all source files are in lower case and may use the
underscore character '_' to separate words. Outside of bundled libraries
which may have different conventions, all C and C++ header files have a
``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
``.c`` extension. A small number of C++ classes and utility functions
are implemented with only a ``.h`` file. Examples are the Pointer class
or the MathVec functions.
Class topology
--------------
Though LAMMPS has a lot of source files and classes, its class topology
is relative flat, as outlined in the :ref:`class-topology` figure. Each
name refers to a class and has a pair of associated source files in the
``src`` folder, for example the class :cpp:class:`LAMMPS_NS::Memory`
corresponds to the files ``memory.cpp`` and ``memory.h``, or the class
:cpp:class:`LAMMPS_NS::AtomVec` corresponds to the files
``atom_vec.cpp`` and ``atom_vec.h``. Full lines in the figure represent
compositing: that is the class to the left holds a pointer to an
instance of the class to the right. Dashed lines instead represent
inheritance: the class to the right is derived from the class on the
left. Classes with a red boundary are not instantiated directly, but
they represent the base classes for "styles". Those "styles" make up
the bulk of the LAMMPS code and only a few typical examples are included
in the figure for demonstration purposes.
is not very deep, which can be seen from the :ref:`class-topology`
figure. In that figure, each name refers to a class and has a pair of
associated source files in the ``src`` folder, for example the class
:cpp:class:`LAMMPS_NS::Memory` corresponds to the files ``memory.cpp``
and ``memory.h``, or the class :cpp:class:`LAMMPS_NS::AtomVec`
corresponds to the files ``atom_vec.cpp`` and ``atom_vec.h``. Full
lines in the figure represent compositing: that is the class at the base
of the arrow holds a pointer to an instance of the class at the tip.
Dashed lines instead represent inheritance: the class to the tip of the
arrow is derived from the class at the base. Classes with a red boundary
are not instantiated directly, but they represent the base classes for
"styles". Those "styles" make up the bulk of the LAMMPS code and only
a few representative examples are included in the figure so it remains
readable.
.. _class-topology:
.. figure:: JPG/lammps-classes.png
@ -82,8 +89,8 @@ in the figure for demonstration purposes.
derived classes, which may also hold instances of other classes.
The :cpp:class:`LAMMPS_NS::LAMMPS` class is the topmost class and
represents what is referred to an "instance" of LAMMPS. It is a
composite holding references to instances of other core classes
represents what is generally referred to an "instance" of LAMMPS. It is
a composite holding pointers to instances of other core classes
providing the core functionality of the MD engine in LAMMPS and through
them abstractions of the required operations. The constructor of the
LAMMPS class will instantiate those instances, process the command line
@ -91,60 +98,67 @@ flags, initialize MPI (if not already done) and set up file pointers for
input and output. The destructor will shut everything down and free all
associated memory. Thus code for the standalone LAMMPS executable in
``main.cpp`` simply initializes MPI, instantiates a single instance of
LAMMPS, and passes it the command line flags and input script. It
LAMMPS while passing it the command line flags and input script. It
deletes the LAMMPS instance after the method reading the input returns
and shuts down the MPI environment before it exits the executable.
The :cpp:class:`LAMMPS_NS::Pointers` is not shown in the
:ref:`class-topology` figure, it holds references to members of the
`LAMMPS_NS::LAMMPS`, so that all classes derived from
:cpp:class:`LAMMPS_NS::Pointers` have direct access to those reference.
From the class topology all classes with blue boundary are referenced in
this class and all classes in the second and third columns, that are not
listed as derived classes are instead derived from
:cpp:class:`LAMMPS_NS::Pointers`.
:ref:`class-topology` figure for clarity. It holds references to many
of the members of the `LAMMPS_NS::LAMMPS`, so that all classes derived
from :cpp:class:`LAMMPS_NS::Pointers` have direct access to those
reference. From the class topology all classes with blue boundary are
referenced in the Pointers class and all classes in the second and third
columns, that are not listed as derived classes are instead derived from
:cpp:class:`LAMMPS_NS::Pointers`. To initialize the pointer references
in Pointers, a pointer to the LAMMPS class instance needs to be passed
to the constructor and thus all constructors for classes derived from it
must do so and pass this pointer to the constructor for Pointers.
Since all storage is encapsulated, the LAMMPS class can also be
instantiated multiple times by a calling code, and that can be either
simultaneously or consecutively. When running in parallel with MPI,
care has to be taken, that suitable communicators are used to not
create conflicts between different instances.
Since all storage is supposed to be encapsulated (there are a few
exceptions), the LAMMPS class can also be instantiated multiple times by
a calling code. Outside of the aforementioned exceptions, those LAMMPS
instances can be used alternately. As of the time of this writing
(early 2021) LAMMPS is not yet sufficiently thread-safe for concurrent
execution. When running in parallel with MPI, care has to be taken,
that suitable copies of communicators are used to not create conflicts
between different instances.
The LAMMPS class currently holds instances of 19 classes representing
different core functionalities There are a handful of virtual parent
classes in LAMMPS that define what LAMMPS calls ``styles``. They are
shaded red in the :ref:`class-topology` figure. Each of these are
The LAMMPS class currently (early 2021) holds instances of 19 classes
representing the core functionality. There are a handful of virtual
parent classes in LAMMPS that define what LAMMPS calls ``styles``. They
are shaded red in the :ref:`class-topology` figure. Each of these are
parents of a number of child classes that implement the interface
defined by the parent class. There are two main categories of these
``styles``: some may only have one instance active at a time (e.g. atom,
pair, bond, angle, dihedral, improper, kspace, comm) and there is a
dedicated pointer variable in the composite class that manages them.
dedicated pointer variable for each of them in the composite class.
Setups that require a mix of different such styles have to use a
*hybrid* class that manages and forwards calls to the corresponding
sub-styles for the designated subset of atoms or data. or the composite
class may have lists of class instances, e.g. Modify handles lists of
compute and fix styles, while Output handles dumps class instances.
*hybrid* class that takes the place of the one allowed instance and then
manages and forwards calls to the corresponding sub-styles for the
designated subset of atoms or data. The composite class may also have
lists of class instances, e.g. Modify handles lists of compute and fix
styles, while Output handles a list of dump class instances.
The exception to this scheme are the ``command`` style classes. These
implement specific commands that can be invoked before, after, or between
runs or are commands which launch a simulation. For these an instance
of the class is created, its command() method called and then, after
completion, the class instance deleted. Examples for this are the
create_box, create_atoms, minimize, run, or velocity command styles.
implement specific commands that can be invoked before, after, or in
between runs. For these an instance of the class is created, its
command() method called and then, after completion, the class instance
deleted. Examples for this are the create_box, create_atoms, minimize,
run, or velocity command styles.
For all those ``styles`` certain naming conventions are employed: for
the fix nve command the class is called FixNVE and the files are
the fix nve command the class is called FixNVE and the source files are
``fix_nve.h`` and ``fix_nve.cpp``. Similarly for fix ave/time we have
FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``. Style names
are lower case and without spaces or special characters. A suffix or
multiple appended with a forward slash '/' denotes a variant of the
corresponding class without the suffix. To connect the style name and
the class name, LAMMPS uses macros like the following ATOM\_CLASS,
PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS, FIX\_CLASS, COMPUTE\_CLASS,
or DUMP\_CLASS in the corresponding header file. During compilation
files with the pattern ``style_name.h`` are created that contain include
statements including all headers of all styles of a given type that
are currently active (or "installed).
words are appended with a forward slash '/' which denotes a variant of
the corresponding class without the suffix. To connect the style name
and the class name, LAMMPS uses macros like: ``AtomStyle()``,
``PairStyle()``, ``BondStyle()``, ``RegionStyle()``, and so on in the
corresponding header file. During configuration or compilation files
with the pattern ``style_<name>.h`` are created that consist of a list
of include statements including all headers of all styles of a given
type that are currently active (or "installed).
More details on individual classes in the :ref:`class-topology` are as
@ -152,11 +166,11 @@ follows:
- The Memory class handles allocation of all large vectors and arrays.
- The Error class prints all error and warning messages.
- The Error class prints all (terminal) error and warning messages.
- The Universe class sets up partitions of processors so that multiple
simulations can be run, each on a subset of the processors allocated
for a run, e.g. by the mpirun command.
- The Universe class sets up one or more partitions of processors so
that one or multiple simulations can be run, on the processors
allocated for a run, e.g. by the mpirun command.
- The Input class reads and processes input input strings and files,
stores variables, and invokes :doc:`commands <Commands_all>`.
@ -241,7 +255,8 @@ follows:
.. TODO section on "Spatial decomposition and parallel operations"
.. diagram of 3d processor grid, brick vs. tiled. local vs. ghost
.. atoms, 6-way communication with pack/unpack functions,
.. PBC as part of the communication
.. PBC as part of the communication, forward and reverse communication
.. rendezvous communication, ring communication.
.. TODO section on "Fixes, Computes, and Variables"
.. how and when data is computed and provided and how it is

53
doc/src/Developer_utils.rst
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@ -71,12 +71,21 @@ and parsing files or arguments.
----------
.. doxygenfunction:: strdup
:project: progguide
.. doxygenfunction:: trim
:project: progguide
.. doxygenfunction:: trim_comment
:project: progguide
.. doxygenfunction:: has_utf8
:project: progguide
.. doxygenfunction:: utf8_subst
:project: progguide
.. doxygenfunction:: count_words(const char *text)
:project: progguide
@ -286,6 +295,50 @@ This code example should produce the following output:
----------
Argument parsing classes
---------------------------
The purpose of argument parsing classes it to simplify and unify how
arguments of commands in LAMMPS are parsed and to make abstractions of
repetitive tasks.
The :cpp:class:`LAMMPS_NS::ArgInfo` class provides an abstraction
for parsing references to compute or fix styles or variables. These
would start with a "c\_", "f\_", "v\_" followed by the ID or name of
than instance and may be postfixed with one or two array indices
"[<number>]" with numbers > 0.
A typical code segment would look like this:
.. code-block:: C++
:caption: Usage example for ArgInfo class
int nvalues = 0;
for (iarg = 0; iarg < nargnew; iarg++) {
ArgInfo argi(arg[iarg]);
which[nvalues] = argi.get_type();
argindex[nvalues] = argi.get_index1();
ids[nvalues] = argi.copy_name();
if ((which[nvalues] == ArgInfo::UNKNOWN)
|| (which[nvalues] == ArgInfo::NONE)
|| (argi.get_dim() > 1))
error->all(FLERR,"Illegal compute XXX command");
nvalues++;
}
----------
.. doxygenclass:: LAMMPS_NS::ArgInfo
:project: progguide
:members:
----------
File reader classes
-------------------

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doc/src/Python_install.rst
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@ -69,7 +69,7 @@ this.
cd build
# configure LAMMPS compilation
cmake -C cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
cmake -C ../cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
-D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
# compile LAMMPS
@ -97,10 +97,12 @@ this.
For a system-wide installation you need to set
``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
``/usr/local``). The installation step (**not** the
``/usr/local``); the default is ``${HOME}/.local``. The
installation step for a system folder installation (**not** the
configuration/compilation) needs to be done with superuser
privilege, e.g. by using ``sudo cmake --install .``. The
installation folders will then by changed to:
installation folders will then be changed to (assuming ``/usr`` as
prefix):
+------------------------+---------------------------------------------------------+-------------------------------------------------------------+
| File | Location | Notes |

9
doc/src/Speed_kokkos.rst
View File

@ -26,6 +26,15 @@ task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
produce an executable compatible with a specific hardware.
.. admonition:: C++14 support
:class: note
Kokkos requires using a compiler that supports the c++14 standard. For
some compilers, it may be necessary to add a flag to enable c++14 support.
For example, the GNU compiler uses the -std=c++14 flag. For a list of
compilers that have been tested with the Kokkos library, see the Kokkos
`README <https://github.com/kokkos/kokkos/blob/master/README.md>`_.
.. admonition:: NVIDIA CUDA support
:class: note

86
doc/src/fix_bond_react.rst
View File

@ -41,7 +41,7 @@ Syntax
* template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
* map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
* zero or more individual keyword/value pairs may be appended to each react argument
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges*
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create*
.. parsed-literal::
@ -59,6 +59,12 @@ Syntax
off = allow both inter- and intramolecular reactions (default)
inter = search for reactions between molecules with different IDs
intra = search for reactions within the same molecule
*modify_create* keyword values
*fit* value = *all* or *fragmentID*
all = use all eligible atoms for create-atoms fit (default)
fragmentID = ID of molecule fragment used for create-atoms fit
*overlap* value = R
R = only insert atom/molecule if further than R from existing particles (distance units)
Examples
""""""""
@ -89,7 +95,9 @@ documentation. Topology changes are defined in pre- and post-reaction
molecule templates and can include creation and deletion of bonds,
angles, dihedrals, impropers, bond types, angle types, dihedral types,
atom types, or atomic charges. In addition, reaction by-products or
other molecules can be identified and deleted.
other molecules can be identified and deleted. Finally, atoms can be
created and inserted at specific positions relative to the reaction
site.
Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
@ -262,14 +270,14 @@ command page.
The post-reacted molecule template contains a sample of the reaction
site and its surrounding topology after the reaction has occurred. It
must contain the same number of atoms as the pre-reacted template. A
one-to-one correspondence between the atom IDs in the pre- and
post-reacted templates is specified in the map file as described
below. Note that during a reaction, an atom, bond, etc. type may
change to one that was previously not present in the simulation. These
new types must also be defined during the setup of a given simulation.
A discussion of correctly handling this is also provided on the
:doc:`molecule <molecule>` command page.
must contain the same number of atoms as the pre-reacted template
(unless there are created atoms). A one-to-one correspondence between
the atom IDs in the pre- and post-reacted templates is specified in
the map file as described below. Note that during a reaction, an atom,
bond, etc. type may change to one that was previously not present in
the simulation. These new types must also be defined during the setup
of a given simulation. A discussion of correctly handling this is also
provided on the :doc:`molecule <molecule>` command page.
.. note::
@ -283,7 +291,7 @@ A discussion of correctly handling this is also provided on the
The map file is a text document with the following format:
A map file has a header and a body. The header of map file the
contains one mandatory keyword and four optional keywords. The
contains one mandatory keyword and five optional keywords. The
mandatory keyword is 'equivalences':
.. parsed-literal::
@ -296,11 +304,12 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
.. parsed-literal::
N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
N *deleteIDs* = # of atoms N that are specified for deletion
N *chiralIDs* = # of specified chiral centers N
N *constraints* = # of specified reaction constraints N
N *deleteIDs* = # of atoms N that are deleted
N *createIDs* = # of atoms N that are created
N *chiralIDs* = # of chiral centers N
N *constraints* = # of reaction constraints N
The body of the map file contains two mandatory sections and four
The body of the map file contains two mandatory sections and five
optional sections. The first mandatory section begins with the keyword
'InitiatorIDs' and lists the two atom IDs of the initiator atom pair
in the pre-reacted molecule template. The second mandatory section
@ -313,8 +322,10 @@ the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the
pre-reacted molecule template. The second optional section begins with
the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction
template atoms to delete. The third optional section begins with the
keyword 'CreateIDs' and lists the atom IDs of the post-reaction
template atoms to create. The fourth optional section begins with the
keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
handedness should be enforced. The fourth optional section begins with
handedness should be enforced. The fifth optional section begins with
the keyword 'Constraints' and lists additional criteria that must be
satisfied in order for the reaction to occur. Currently, there are
five types of constraints available, as discussed below: 'distance',
@ -353,6 +364,38 @@ A sample map file is given below:
----------
A user-specified set of atoms can be deleted by listing their
pre-reaction template IDs in the DeleteIDs section. A deleted atom
must still be included in the post-reaction molecule template, in
which it cannot be bonded to an atom that is not deleted. In addition
to deleting unwanted reaction by-products, this feature can be used to
remove specific topologies, such as small rings, that may be otherwise
indistinguishable.
Atoms can be created by listing their post-reaction template IDs in
the CreateIDs section. A created atom should not be included in the
pre-reaction template. The inserted positions of created atoms are
determined by the coordinates of the post-reaction template, after
optimal translation and rotation of the post-reaction template to the
reaction site (using a fit with atoms that are neither created nor
deleted). The *modify_create* keyword can be used to modify the
default behavior when creating atoms. The *modify_create* keyword has
two sub-keywords, *fit* and *overlap*. One or more of the sub-keywords
may be used after the *modify_create* keyword. The *fit* sub-keyword
can be used to specify which post-reaction atoms are used for the
optimal translation and rotation of the post-reaction template. The
*fragmentID* value of the *fit* sub-keyword must be the name of a
molecule fragment defined in the post-reaction :doc:`molecule
<molecule>` template, and only atoms in this fragment are used for the
fit. Atoms are created only if no current atom in the simulation is
within a distance R of any created atom, including the effect of
periodic boundary conditions if applicable. R is defined by the
*overlap* sub-keyword. Note that the default value for R is 0.0, which
will allow atoms to strongly overlap if you are inserting where other
atoms are present. The velocity of each created atom is initialized in
a random direction with a magnitude calculated from the instantaneous
temperature of the reaction site.
The handedness of atoms that are chiral centers can be enforced by
listing their IDs in the ChiralIDs section. A chiral atom must be
bonded to four atoms with mutually different atom types. This feature
@ -528,15 +571,6 @@ the same molecule ID are considered for the reaction.
A few other considerations:
Many reactions result in one or more atoms that are considered
unwanted by-products. Therefore, bond/react provides the option to
delete a user-specified set of atoms. These pre-reaction atoms are
identified in the map file. A deleted atom must still be included in
the post-reaction molecule template, in which it cannot be bonded to
an atom that is not deleted. In addition to deleting unwanted reaction
by-products, this feature can be used to remove specific topologies,
such as small rings, that may be otherwise indistinguishable.
Optionally, you can enforce additional behaviors on reacting atoms.
For example, it may be beneficial to force reacting atoms to remain at
a certain temperature. For this, you can use the internally-created
@ -610,7 +644,7 @@ Default
"""""""
The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
reset_mol_ids = yes, custom_charges = no, molecule = off
reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
----------

13
doc/src/fix_ti_spring.rst
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@ -139,11 +139,14 @@ output <thermo_style>`. The default setting for this fix is
This fix computes a global scalar and a global vector quantities which
can be accessed by various :doc:`output commands <Howto_output>`. The
scalar is the sum of the spring energy for each atom, where the
per-atom energy is 0.5 \* k \* r\^2. The vector has 2 positions, the
first one is the coupling parameter lambda and the second one is the
time derivative of lambda. The scalar and vector values calculated by
this fix are "extensive".
scalar is an energy which is the sum of the spring energy for each
atom, where the per-atom energy is 0.5 \* k \* r\^2. The vector stores
2 values. The first value is the coupling parameter lambda. The
second value is the derivative of lambda with respect to the integer
timestep *s*, i.e. d lambda / ds. In order to obtain d lambda / dt,
where t is simulation time, this 2nd value needs to be divided by the
timestep size (e.g. 0.5 fs). The scalar and vector values calculated
by this fix are "extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

1
doc/src/pair_style.rst
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@ -327,6 +327,7 @@ accelerated styles exist.
* :doc:`ufm <pair_ufm>` -
* :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential
* :doc:`vashishta/table <pair_vashishta>` -
* :doc:`wf/cut <pair_wf_cut>` - Wang-Frenkel Potential for short-ranged interactions
* :doc:`yukawa <pair_yukawa>` - Yukawa potential
* :doc:`yukawa/colloid <pair_yukawa_colloid>` - screened Yukawa potential for finite-size particles
* :doc:`zbl <pair_zbl>` - Ziegler-Biersack-Littmark potential

117
doc/src/pair_wf_cut.rst Normal file
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@ -0,0 +1,117 @@
.. index:: pair_style wf/cut
pair_style wf/cut command
===========================
Syntax
""""""
.. code-block:: LAMMPS
pair_style wf/cut cutoff
* cutoff = cutoff for wf interactions (distance units)
Examples
""""""""
.. code-block:: LAMMPS
pair_style wf/cut 2.0
pair_coeff 1 1 1.0 1.0 1 1 2.0
Description
"""""""""""
The *wf/cut* (Wang-Frenkel) style computes LJ-like potentials as
described in :ref:`Wang2020 <Wang2020>`. This potential is by
construction finite ranged and it vanishes quadratically at the cutoff
distance, avoiding truncation, shifting, interpolation and other typical
procedures with the LJ potential. The *wf/cut* can be used when a
typical short-ranged potential with attraction is required. The
potential is given by which is given by:
.. math::
\phi(r)= \epsilon \alpha \left(\left[{\sigma\over r}\right]^{2\mu} -1 \right)\left(\left[{r_c\over r}\right]^{2\mu}-1\right)^{2\nu}
with
.. math::
\alpha=2\nu\left(\frac{r_c}{\sigma}\right)^{2\mu}\left[\frac{1+2\nu}{2\nu\left[(r_c/\sigma)^{2\mu}-1\right]}\right]^{2\nu+1}
and
.. math::
r_{min}=r_c\left[\frac{1+2\nu}{1+2\nu(r_c/\sigma)^{2\nu}}\right]^{1/{2\nu}}
:math:`r_c` is the cutoff.
Comparison of the non-truncated Lennard-Jones 12-6 potential (red curve),
and the WF potentials with :math:`\mu=1` and :math:`\nu=1` are shown in
the figure below. The blue curve has :math:`r_c =2.0` and the green
curve has :math:`r_c =1.2` and can be used to describe colloidal
interactions.
.. image:: JPG/WF_LJ.jpg
:align: center
:scale: 33%
The following coefficients must be defined for each pair of atoms
types via the :doc:`pair_coeff <pair_coeff>` command as in the example
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`\epsilon` (energy units)
* :math:`\sigma` (distance units)
* :math:`\nu`
* :math:`\mu`
* :math:`r_c` (distance units)
The last coefficient is optional. If not specified, the global cutoff
given in the pair_style command is used. The exponents :math:`\nu` and
:math:`\mu` are positive integers, usually set to 1. There is usually
little to be gained by choosing other values of :math:`\nu` and
:math:`\mu` (See discussion in :ref:`Wang2020 <Wang2020>`)
----------
**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
This pair style does not support the :doc:`pair_modify <pair_modify>`
mixing and table options.
The :doc:`pair_modify <pair_modify>` tail option is not relevant
for this pair style as it goes to zero at the cut-off radius.
This pair style writes its information to :doc:`binary restart files
<restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file.
This pair style does not support the use of the *inner*\ , *middle*\ ,
and *outer* keywords of the :doc:`run_style respa <run_style>` command.
----------
Restrictions
""""""""""""
This pair style can only be used if LAMMPS was built with the
USER-MISC package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
**Default:** none
----------
.. _Wang2020:
**(Wang2020)** X. Wang, S. Ramirez-Hinestrosa, J. Dobnikar, and D. Frenkel, Phys. Chem. Chem. Phys. 22, 10624 (2020).

8
doc/src/thermo_modify.rst
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@ -96,9 +96,11 @@ always include a divide by the number of atoms in the variable formula
if this is not the case.
The *flush* keyword invokes a flush operation after thermodynamic info
is written to the log file. This insures the output in that file is
current (no buffering by the OS), even if LAMMPS halts before the
simulation completes.
is written to the screen and log file. This insures the output is
updated and not buffered (by the application) even if LAMMPS halts
before the simulation completes. Please note that this does not
affect buffering by the OS or devices, so you may still lose data
in case the simulation stops due to a hardware failure.
The *line* keyword determines whether thermodynamics will be output as
a series of numeric values on one line or in a multi-line format with

6
doc/utils/sphinx-config/false_positives.txt
View File

@ -692,6 +692,7 @@ dmi
dnf
DNi
Dobson
Dobnikar
Dodds
docenv
dodgerblue
@ -1232,6 +1233,7 @@ Hibbs
Higdon
Hijazi
Hilger
Hinestrosa
histo
histogrammed
histogramming
@ -2476,6 +2478,9 @@ Poresag
pos
Poschel
posix
postfix
postfixed
postfixes
Postma
Potapkin
potin
@ -3406,6 +3411,7 @@ WeinanE
Wennberg
Westmere
Westview
wf
wget
Whelan
whitesmoke

92
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@ -0,0 +1,92 @@
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
processors * * 1
units metal
boundary p p f
read_data adatom.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (17.121441 14.827603 39.319732)
1 by 1 by 1 MPI processor grid
reading atoms ...
181 atoms
read_data CPU = 0.002 seconds
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 500 12345
fix 1 all nvt temp 250 250 0.2
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 5 4 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.072 | 3.072 | 3.072 Mbytes
Step KinEng Temp
0 11.633413 500
100 4.6059941 197.96401
200 7.3700156 316.76068
300 6.0443915 259.78582
400 6.163119 264.88869
500 6.2647284 269.25582
600 5.2732533 226.64257
700 5.651448 242.89725
800 6.5572404 281.82788
900 6.0576743 260.35671
1000 6.5622234 282.04205
Loop time of 16.4158 on 1 procs for 1000 steps with 181 atoms
Performance: 2.632 ns/day, 9.120 hours/ns, 60.917 timesteps/s
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.395 | 16.395 | 16.395 | 0.0 | 99.88
Neigh | 0.013275 | 0.013275 | 0.013275 | 0.0 | 0.08
Comm | 0.0023484 | 0.0023484 | 0.0023484 | 0.0 | 0.01
Output | 0.00014842 | 0.00014842 | 0.00014842 | 0.0 | 0.00
Modify | 0.0035522 | 0.0035522 | 0.0035522 | 0.0 | 0.02
Other | | 0.001173 | | | 0.01
Nlocal: 181.000 ave 181 max 181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 563.000 ave 563 max 563 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 19484.0 ave 19484 max 19484 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19484
Ave neighs/atom = 107.64641
Neighbor list builds = 33
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:16

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@ -0,0 +1,92 @@
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
processors * * 1
units metal
boundary p p f
read_data adatom.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (17.121441 14.827603 39.319732)
2 by 2 by 1 MPI processor grid
reading atoms ...
181 atoms
read_data CPU = 0.001 seconds
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 500 12345
fix 1 all nvt temp 250 250 0.2
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 5 4 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.063 | 3.063 | 3.063 Mbytes
Step KinEng Temp
0 11.633413 500
100 4.6059939 197.964
200 7.3700154 316.76067
300 6.0443914 259.78582
400 6.1631193 264.8887
500 6.2647281 269.25581
600 5.273254 226.6426
700 5.6514484 242.89726
800 6.5572409 281.82791
900 6.0576737 260.35668
1000 6.5622233 282.04205
Loop time of 4.67437 on 4 procs for 1000 steps with 181 atoms
Performance: 9.242 ns/day, 2.597 hours/ns, 213.933 timesteps/s
98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0668 | 4.2058 | 4.4078 | 7.1 | 89.98
Neigh | 0.0033048 | 0.0033794 | 0.0034381 | 0.1 | 0.07
Comm | 0.2547 | 0.45656 | 0.59576 | 21.5 | 9.77
Output | 9.8817e-05 | 0.00035464 | 0.001121 | 0.0 | 0.01
Modify | 0.0059429 | 0.0060754 | 0.0061966 | 0.2 | 0.13
Other | | 0.002172 | | | 0.05
Nlocal: 45.2500 ave 52 max 40 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 376.500 ave 382 max 366 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4871.00 ave 5578 max 4374 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 19484
Ave neighs/atom = 107.64641
Neighbor list builds = 33
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

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@ -0,0 +1,92 @@
LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
units metal
boundary p p p
read_data vacancy.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (8.0711250 8.0711250 8.0711250)
1 by 1 by 1 MPI processor grid
reading atoms ...
31 atoms
read_data CPU = 0.002 seconds
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 1000 12345
fix 1 all nvt temp 900 900 200
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke etotal temp
dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.241 | 4.241 | 4.241 Mbytes
Step KinEng TotEng Temp
0 3.8778043 3.8778043 1000
100 2.9986261 2.9986261 773.27936
200 3.6860313 3.6860313 950.54598
300 3.8133153 3.8133153 983.3697
400 3.7330285 3.7330285 962.6655
500 3.5875467 3.5875467 925.14897
600 3.533152 3.533152 911.12178
700 2.6509457 2.6509457 683.62028
800 3.376349 3.376349 870.68576
900 3.9036736 3.9036736 1006.6711
1000 3.0884833 3.0884833 796.45156
Loop time of 2.92678 on 1 procs for 1000 steps with 31 atoms
Performance: 14.760 ns/day, 1.626 hours/ns, 341.673 timesteps/s
97.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9144 | 2.9144 | 2.9144 | 0.0 | 99.58
Neigh | 0.0068263 | 0.0068263 | 0.0068263 | 0.0 | 0.23
Comm | 0.0029868 | 0.0029868 | 0.0029868 | 0.0 | 0.10
Output | 0.00050202 | 0.00050202 | 0.00050202 | 0.0 | 0.02
Modify | 0.0013382 | 0.0013382 | 0.0013382 | 0.0 | 0.05
Other | | 0.0007672 | | | 0.03
Nlocal: 31.0000 ave 31 max 31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 869.000 ave 869 max 869 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4360.00 ave 4360 max 4360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4360
Ave neighs/atom = 140.64516
Neighbor list builds = 53
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

92
examples/USER/misc/agni/log.20Jan21.vacancy.g++.4 Normal file
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LAMMPS (24 Dec 2020)
using 1 OpenMP thread(s) per MPI task
units metal
boundary p p p
read_data vacancy.data
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (8.0711250 8.0711250 8.0711250)
1 by 2 by 2 MPI processor grid
reading atoms ...
31 atoms
read_data CPU = 0.001 seconds
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading agni potential file Al_jpc.agni with DATE: 2017-02-24
WARNING: Ignoring unknown tag 'Rs' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'neighbors' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
WARNING: Ignoring unknown tag 'lambda' in AGNI potential file. (src/USER-MISC/pair_agni.cpp:440)
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 1000 12345
fix 1 all nvt temp 900 900 200
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke etotal temp
dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.227 | 4.227 | 4.227 Mbytes
Step KinEng TotEng Temp
0 3.8778043 3.8778043 1000
100 2.9986264 2.9986264 773.27944
200 3.6860316 3.6860316 950.54606
300 3.8133152 3.8133152 983.36966
400 3.7330288 3.7330288 962.66559
500 3.5875468 3.5875468 925.149
600 3.5331519 3.5331519 911.12176
700 2.6509452 2.6509452 683.62015
800 3.3763492 3.3763492 870.68579
900 3.9036736 3.9036736 1006.6711
1000 3.0884821 3.0884821 796.45125
Loop time of 0.91769 on 4 procs for 1000 steps with 31 atoms
Performance: 47.075 ns/day, 0.510 hours/ns, 1089.693 timesteps/s
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.67405 | 0.76047 | 0.81748 | 6.1 | 82.87
Neigh | 0.0015411 | 0.001691 | 0.001774 | 0.2 | 0.18
Comm | 0.091364 | 0.14959 | 0.23513 | 13.8 | 16.30
Output | 0.00027996 | 0.00040391 | 0.00075917 | 0.0 | 0.04
Modify | 0.0028397 | 0.0039247 | 0.0050072 | 1.7 | 0.43
Other | | 0.001611 | | | 0.18
Nlocal: 7.75000 ave 8 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 617.250 ave 621 max 612 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0.00000 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1090.00 ave 1131 max 993 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 4360
Ave neighs/atom = 140.64516
Neighbor list builds = 53
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

87
examples/USER/misc/agni/log.21Feb17.adatom.g++.1
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LAMMPS (21 Feb 2017)
using 1 OpenMP thread(s) per MPI task
processors * * 1
units metal
boundary p p f
read_data adatom.data
orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
1 by 1 by 1 MPI processor grid
reading atoms ...
181 atoms
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading potential file Al_jpc.agni with DATE: 2017-02-24
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 500 12345
fix 1 all nvt temp 250 250 0.2
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 5 4 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 2.69795 Mbytes
Step KinEng Temp
0 11.633413 500
100 4.6059939 197.964
200 7.3700149 316.76065
300 6.0443913 259.78581
400 6.1631189 264.88868
500 6.2647272 269.25577
600 5.2732539 226.6426
700 5.6514471 242.89721
800 6.5572407 281.8279
900 6.0576738 260.35669
1000 6.5622233 282.04205
Loop time of 51.9308 on 1 procs for 1000 steps with 181 atoms
Performance: 0.832 ns/day, 28.850 hours/ns, 19.256 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 51.89 | 51.89 | 51.89 | 0.0 | 99.92
Neigh | 0.023158 | 0.023158 | 0.023158 | 0.0 | 0.04
Comm | 0.0049036 | 0.0049036 | 0.0049036 | 0.0 | 0.01
Output | 0.0002594 | 0.0002594 | 0.0002594 | 0.0 | 0.00
Modify | 0.010244 | 0.010244 | 0.010244 | 0.0 | 0.02
Other | | 0.002483 | | | 0.00
Nlocal: 181 ave 181 max 181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 563 ave 563 max 563 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 19484 ave 19484 max 19484 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19484
Ave neighs/atom = 107.646
Neighbor list builds = 33
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:52

87
examples/USER/misc/agni/log.21Feb17.adatom.g++.4
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LAMMPS (21 Feb 2017)
using 1 OpenMP thread(s) per MPI task
processors * * 1
units metal
boundary p p f
read_data adatom.data
orthogonal box = (0 0 0) to (17.1214 14.8276 39.3197)
2 by 2 by 1 MPI processor grid
reading atoms ...
181 atoms
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading potential file Al_jpc.agni with DATE: 2017-02-24
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 500 12345
fix 1 all nvt temp 250 250 0.2
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 5 4 10
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 3.06041 Mbytes
Step KinEng Temp
0 11.633413 500
100 4.6059941 197.96401
200 7.3700154 316.76067
300 6.0443913 259.78581
400 6.1631193 264.8887
500 6.2647281 269.25581
600 5.2732537 226.64259
700 5.651448 242.89725
800 6.5572405 281.82789
900 6.0576741 260.3567
1000 6.562224 282.04208
Loop time of 14.5263 on 4 procs for 1000 steps with 181 atoms
Performance: 2.974 ns/day, 8.070 hours/ns, 68.841 timesteps/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.858 | 13.227 | 13.574 | 8.0 | 91.06
Neigh | 0.0056965 | 0.0058173 | 0.0060787 | 0.2 | 0.04
Comm | 0.92934 | 1.276 | 1.6455 | 25.7 | 8.78
Output | 0.00013971 | 0.00017625 | 0.00025463 | 0.0 | 0.00
Modify | 0.012693 | 0.012756 | 0.012911 | 0.1 | 0.09
Other | | 0.004066 | | | 0.03
Nlocal: 45.25 ave 52 max 40 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 376.5 ave 382 max 366 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 4871 ave 5578 max 4374 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 19484
Ave neighs/atom = 107.646
Neighbor list builds = 33
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:14

87
examples/USER/misc/agni/log.21Feb17.vacancy.g++.1
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LAMMPS (21 Feb 2017)
using 1 OpenMP thread(s) per MPI task
units metal
boundary p p p
read_data vacancy.data
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
1 by 1 by 1 MPI processor grid
reading atoms ...
31 atoms
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading potential file Al_jpc.agni with DATE: 2017-02-24
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 1000 12345
fix 1 all nvt temp 900 900 200
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke etotal temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 2.73416 Mbytes
Step KinEng TotEng Temp
0 3.8778043 3.8778043 1000
100 2.9986261 2.9986261 773.27937
200 3.6860314 3.6860314 950.54599
300 3.813315 3.813315 983.36961
400 3.7330285 3.7330285 962.6655
500 3.5875467 3.5875467 925.14896
600 3.5331529 3.5331529 911.12202
700 2.6509449 2.6509449 683.62008
800 3.3763492 3.3763492 870.68582
900 3.903673 3.903673 1006.6709
1000 3.0884824 3.0884824 796.45133
Loop time of 9.02712 on 1 procs for 1000 steps with 31 atoms
Performance: 4.786 ns/day, 5.015 hours/ns, 110.777 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.0039 | 9.0039 | 9.0039 | 0.0 | 99.74
Neigh | 0.011892 | 0.011892 | 0.011892 | 0.0 | 0.13
Comm | 0.0061693 | 0.0061693 | 0.0061693 | 0.0 | 0.07
Output | 0.00014615 | 0.00014615 | 0.00014615 | 0.0 | 0.00
Modify | 0.0035009 | 0.0035009 | 0.0035009 | 0.0 | 0.04
Other | | 0.001521 | | | 0.02
Nlocal: 31 ave 31 max 31 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 869 ave 869 max 869 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4360 ave 4360 max 4360 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4360
Ave neighs/atom = 140.645
Neighbor list builds = 53
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:09

87
examples/USER/misc/agni/log.21Feb17.vacancy.g++.4
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LAMMPS (21 Feb 2017)
using 1 OpenMP thread(s) per MPI task
units metal
boundary p p p
read_data vacancy.data
orthogonal box = (0 0 0) to (8.07113 8.07113 8.07113)
1 by 2 by 2 MPI processor grid
reading atoms ...
31 atoms
pair_style agni
pair_coeff * * Al_jpc.agni Al
Reading potential file Al_jpc.agni with DATE: 2017-02-24
neighbor 0.3 bin
neigh_modify delay 2 check yes
timestep 0.0005
velocity all create 1000 12345
fix 1 all nvt temp 900 900 200
fix 5 all momentum 1 linear 1 1 1
thermo 100
thermo_style custom step ke etotal temp
# dump MyDump all custom 250 dump.atoms id type x y z vx vy vz fx fy fz
run 1000
Neighbor list info ...
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.3
ghost atom cutoff = 8.3
binsize = 4.15, bins = 2 2 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair agni, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Memory usage per processor = 2.72175 Mbytes
Step KinEng TotEng Temp
0 3.8778044 3.8778044 1000
100 2.9986263 2.9986263 773.27942
200 3.6860315 3.6860315 950.54602
300 3.8133145 3.8133145 983.3695
400 3.7330282 3.7330282 962.66543
500 3.5875466 3.5875466 925.14895
600 3.5331523 3.5331523 911.12186
700 2.6509448 2.6509448 683.62005
800 3.3763493 3.3763493 870.68584
900 3.9036733 3.9036733 1006.671
1000 3.0884818 3.0884818 796.45116
Loop time of 2.46785 on 4 procs for 1000 steps with 31 atoms
Performance: 17.505 ns/day, 1.371 hours/ns, 405.212 timesteps/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.0737 | 2.299 | 2.3902 | 8.7 | 93.16
Neigh | 0.0025222 | 0.0027327 | 0.0028174 | 0.2 | 0.11
Comm | 0.059817 | 0.15141 | 0.37684 | 33.8 | 6.14
Output | 0.0001502 | 0.00016767 | 0.00021219 | 0.0 | 0.01
Modify | 0.0098755 | 0.010248 | 0.010664 | 0.3 | 0.42
Other | | 0.004321 | | | 0.18
Nlocal: 7.75 ave 8 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 617.25 ave 621 max 612 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1090 ave 1131 max 993 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 4360
Ave neighs/atom = 140.645
Neighbor list builds = 53
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

66
examples/USER/reaction/create_atoms_polystyrene/grow_styrene.map Normal file
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map file: styrene growth
1 edgeIDs
30 equivalences
16 createIDs
InitiatorIDs
4
13
EdgeIDs
30
CreateIDs
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
Equivalences
1 45
2 46
3 44
4 43
5 42
6 41
7 40
8 39
9 38
10 37
11 36
12 35
13 34
14 33
15 32
16 31
17 17
18 18
19 19
20 20
21 21
22 22
23 23
24 24
25 25
26 26
27 27
28 28
29 29
30 30

456
examples/USER/reaction/create_atoms_polystyrene/grow_styrene_post.data_template Executable file
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molecule template: end of chain plus polymerized styrene
46 atoms
48 bonds
81 angles
121 dihedrals
35 impropers
1 fragments
Fragments
create_fit 34 44
Types
1 1
2 2
3 1
4 5
5 1
6 2
7 1
8 2
9 1
10 2
11 1
12 2
13 2
14 6
15 2
16 2
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
31 1
32 2
33 1
34 5
35 1
36 2
37 1
38 2
39 1
40 2
41 1
42 2
43 2
44 6
45 2
46 2
Charges
1 -0.129000
2 0.123700
3 0.026600
4 -0.018200
5 -0.129000
6 0.123700
7 -0.173400
8 0.140300
9 -0.113400
10 0.128800
11 -0.173400
12 0.140300
13 0.051600
14 -0.069600
15 0.035400
16 0.035400
17 -0.129000
18 0.123700
19 0.026600
20 -0.018200
21 -0.129000
22 0.123700
23 -0.173400
24 0.140300
25 -0.113400
26 0.128800
27 -0.173400
28 0.140300
29 0.051600
30 -0.069600
31 -0.129000
32 0.123700
33 0.026600
34 -0.018200
35 -0.129000
36 0.123700
37 -0.173400
38 0.140300
39 -0.113400
40 0.128800
41 -0.173400
42 0.140300
43 0.051600
44 -0.069600
45 0.035400
46 0.035400
Coords
1 24.130699 1.043900 -1.309300
2 25.062700 1.582900 -1.309300
3 22.900700 1.753900 -1.309300
4 22.900700 3.253900 -1.309300
5 21.670700 1.043900 -1.309300
6 20.738701 1.582900 -1.309300
7 21.670700 -0.376100 -1.309300
8 20.738701 -0.915100 -1.309300
9 22.900700 -1.086100 -1.309300
10 22.900700 -2.163100 -1.309300
11 24.130699 -0.376100 -1.309300
12 25.062700 -0.915100 -1.309300
13 23.766701 3.658900 -0.952300
14 21.622700 3.802900 -1.871300
15 21.672701 4.544900 -1.970300
16 20.979700 2.979900 -2.165300
17 13.465800 0.682500 -1.658900
18 14.397800 1.221500 -1.658900
19 12.235800 1.392500 -1.658900
20 12.235800 2.892500 -1.658900
21 11.005800 0.682500 -1.658900
22 10.073800 1.221500 -1.658900
23 11.005800 -0.737500 -1.658900
24 10.073800 -1.276500 -1.658900
25 12.235800 -1.447500 -1.658900
26 12.235800 -2.524500 -1.658900
27 13.465800 -0.737500 -1.658900
28 14.397800 -1.276500 -1.658900
29 13.101800 3.297500 -1.301900
30 10.957800 3.441500 -2.220900
31 18.663500 0.855500 -1.372100
32 19.595501 1.394500 -1.372100
33 17.433500 1.565500 -1.372100
34 17.433500 3.065500 -1.372100
35 16.203501 0.855500 -1.372100
36 15.271500 1.394500 -1.372100
37 16.203501 -0.564500 -1.372100
38 15.271500 -1.103500 -1.372100
39 17.433500 -1.274500 -1.372100
40 17.433500 -2.351500 -1.372100
41 18.663500 -0.564500 -1.372100
42 19.595501 -1.103500 -1.372100
43 18.299500 3.470500 -1.015100
44 16.155500 3.614500 -1.934100
45 16.205500 4.356500 -2.033100
46 15.512500 2.791500 -2.228100
Bonds
1 1 1 2
2 2 1 3
3 2 1 11
4 11 3 4
5 2 3 5
6 12 13 4
7 13 4 14
8 1 5 6
9 2 5 7
10 1 7 8
11 2 7 9
12 1 9 10
13 2 9 11
14 1 11 12
15 10 15 14
16 10 16 14
17 9 14 34
18 1 17 18
19 2 17 19
20 2 17 27
21 7 19 20
22 2 19 21
23 8 29 20
24 9 30 20
25 9 44 20
26 1 21 22
27 2 21 23
28 1 23 24
29 2 23 25
30 1 25 26
31 2 25 27
32 1 27 28
33 1 31 32
34 2 31 33
35 2 31 41
36 7 33 34
37 2 33 35
38 8 43 34
39 9 44 34
40 1 35 36
41 2 35 37
42 1 37 38
43 2 37 39
44 1 39 40
45 2 39 41
46 1 41 42
47 10 45 44
48 10 46 44
Angles
1 1 3 1 2
2 1 11 1 2
3 2 3 1 11
4 17 1 3 4
5 2 1 3 5
6 17 5 3 4
7 18 3 4 13
8 19 3 4 14
9 20 13 4 14
10 1 3 5 6
11 2 3 5 7
12 1 7 5 6
13 1 5 7 8
14 2 5 7 9
15 1 9 7 8
16 1 7 9 10
17 2 7 9 11
18 1 11 9 10
19 2 1 11 9
20 1 1 11 12
21 1 9 11 12
22 21 15 14 4
23 21 16 14 4
24 22 4 14 34
25 15 15 14 16
26 14 15 14 34
27 14 16 14 34
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 44
37 12 29 20 30
38 12 29 20 44
39 13 30 20 44
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
52 1 33 31 32
53 1 41 31 32
54 2 33 31 41
55 9 31 33 34
56 2 31 33 35
57 9 35 33 34
58 11 33 34 14
59 12 43 34 14
60 13 14 34 44
61 10 33 34 43
62 11 33 34 44
63 12 43 34 44
64 1 33 35 36
65 2 33 35 37
66 1 37 35 36
67 1 35 37 38
68 2 35 37 39
69 1 39 37 38
70 1 37 39 40
71 2 37 39 41
72 1 41 39 40
73 2 31 41 39
74 1 31 41 42
75 1 39 41 42
76 16 20 44 34
77 14 45 44 20
78 14 46 44 20
79 14 45 44 34
80 14 46 44 34
81 15 45 44 46
Dihedrals
1 20 2 1 3 4
2 2 5 3 1 2
3 21 11 1 3 4
4 4 11 1 3 5
5 2 9 11 1 2
6 5 2 1 11 12
7 4 3 1 11 9
8 2 3 1 11 12
9 22 1 3 4 13
10 23 1 3 4 14
11 22 5 3 4 13
12 23 5 3 4 14
13 2 1 3 5 6
14 4 1 3 5 7
15 20 6 5 3 4
16 21 7 5 3 4
17 24 3 4 14 15
18 24 3 4 14 16
19 25 3 4 14 34
20 26 13 4 14 15
21 26 13 4 14 16
22 27 13 4 14 34
23 2 3 5 7 8
24 4 3 5 7 9
25 5 6 5 7 8
26 2 9 7 5 6
27 2 5 7 9 10
28 4 5 7 9 11
29 5 8 7 9 10
30 2 11 9 7 8
31 4 7 9 11 1
32 2 7 9 11 12
33 2 1 11 9 10
34 5 10 9 11 12
35 28 4 14 34 33
36 29 4 14 34 43
37 30 4 14 34 44
38 31 15 14 34 33
39 32 15 14 34 43
40 33 15 14 34 44
41 31 16 14 34 33
42 32 16 14 34 43
43 33 16 14 34 44
44 10 18 17 19 20
45 2 21 19 17 18
46 11 27 17 19 20
47 4 27 17 19 21
48 2 25 27 17 18
49 5 18 17 27 28
50 4 19 17 27 25
51 2 19 17 27 28
52 12 17 19 20 29
53 13 17 19 20 30
54 13 17 19 20 44
55 12 21 19 20 29
56 13 21 19 20 30
57 13 21 19 20 44
58 2 17 19 21 22
59 4 17 19 21 23
60 10 22 21 19 20
61 11 23 21 19 20
62 34 34 44 20 19
63 31 45 44 20 19
64 31 46 44 20 19
65 35 34 44 20 29
66 32 45 44 20 29
67 32 46 44 20 29
68 36 34 44 20 30
69 33 45 44 20 30
70 33 46 44 20 30
71 2 19 21 23 24
72 4 19 21 23 25
73 5 22 21 23 24
74 2 25 23 21 22
75 2 21 23 25 26
76 4 21 23 25 27
77 5 24 23 25 26
78 2 27 25 23 24
79 4 23 25 27 17
80 2 23 25 27 28
81 2 17 27 25 26
82 5 26 25 27 28
83 10 32 31 33 34
84 2 35 33 31 32
85 11 41 31 33 34
86 4 41 31 33 35
87 2 39 41 31 32
88 5 32 31 41 42
89 4 33 31 41 39
90 2 33 31 41 42
91 13 31 33 34 14
92 12 31 33 34 43
93 13 31 33 34 44
94 13 35 33 34 14
95 12 35 33 34 43
96 13 35 33 34 44
97 2 31 33 35 36
98 4 31 33 35 37
99 10 36 35 33 34
100 11 37 35 33 34
101 36 20 44 34 14
102 33 45 44 34 14
103 33 46 44 34 14
104 34 20 44 34 33
105 31 45 44 34 33
106 31 46 44 34 33
107 35 20 44 34 43
108 32 45 44 34 43
109 32 46 44 34 43
110 2 33 35 37 38
111 4 33 35 37 39
112 5 36 35 37 38
113 2 39 37 35 36
114 2 35 37 39 40
115 4 35 37 39 41
116 5 38 37 39 40
117 2 41 39 37 38
118 4 37 39 41 31
119 2 37 39 41 42
120 2 31 41 39 40
121 5 40 39 41 42
Impropers
1 1 3 1 11 2
2 8 1 3 5 4
3 9 3 4 13 14
4 1 3 5 7 6
5 1 5 7 9 8
6 1 7 9 11 10
7 1 1 11 9 12
8 1 19 17 27 18
9 5 17 19 21 20
10 1 19 21 23 22
11 1 21 23 25 24
12 1 23 25 27 26
13 1 17 27 25 28
14 1 33 31 41 32
15 5 31 33 35 34
16 1 33 35 37 36
17 1 35 37 39 38
18 1 37 39 41 40
19 1 31 41 39 42
20 1 15 14 16 4
21 1 15 14 4 34
22 1 16 14 4 34
23 1 15 14 16 34
24 1 19 20 29 30
25 1 19 20 29 44
26 1 19 20 30 44
27 1 29 20 30 44
28 1 33 34 43 14
29 1 33 34 14 44
30 1 43 34 14 44
31 1 33 34 43 44
32 1 45 44 34 20
33 1 46 44 34 20
34 1 45 44 46 20
35 1 45 44 46 34

294
examples/USER/reaction/create_atoms_polystyrene/grow_styrene_pre.data_template Normal file
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@ -0,0 +1,294 @@
molecule template: end of styrene chain
30 atoms
31 bonds
51 angles
73 dihedrals
21 impropers
Types
1 2
2 2
3 6
4 2
5 2
6 1
7 2
8 1
9 2
10 1
11 2
12 1
13 5
14 1
15 2
16 1
17 1
18 2
19 1
20 5
21 1
22 2
23 1
24 2
25 1
26 2
27 1
28 2
29 2
30 6
Coords
1 59.89981112372972 62.733697275315585 59.09884284578856
2 61.41970248324232 63.42116581894993 59.52874545893742
3 60.864754970096406 62.91724243011892 59.559720865992695
4 62.139819000186826 61.41011937002877 60.81065044071466
5 60.036455711425084 57.160029629288026 60.31958663310848
6 59.734195751174056 58.18706337912225 60.20562410798949
7 57.64574781117771 57.712432799329 59.860109977091554
8 58.37408644866664 58.50134169314242 59.94422053768215
9 56.94300092269842 60.093170109004795 59.5955638127831
10 57.974275786582744 59.85577775892068 59.793714995577716
11 58.63231375134033 61.922969938852454 59.79065033121885
12 58.934573711591355 60.89593618901822 59.904612856337835
13 61.30908151524225 61.68041745837013 60.28316188676589
14 60.29468229868386 60.58165855333751 60.16601625920239
15 61.725768540066994 58.98982945913568 60.51467315154424
16 60.69449367618267 59.2272218092198 60.31652196874961
17 56.90935800040509 62.609851248143706 59.150831390216375
18 57.940632148874506 62.37245957639904 59.3489824055682
19 56.509546622906285 63.96428799226142 59.00032568066915
20 57.52394583946467 65.06304689729403 59.11747130823266
21 55.14943732039887 64.27856630628159 58.738922110361806
22 54.84717807556275 65.30559937777636 58.62495975268562
23 54.18913939539026 63.23840787618404 58.62802424960169
24 53.15786524692084 63.4757995479287 58.42987323424986
25 54.58895077288906 61.88397113206633 58.77852995914891
26 53.86061213540014 61.09506223825291 58.69441939855832
27 55.94906007539648 61.56969281804616 59.039933529456256
28 56.2513193202326 60.54265974655139 59.15389588713244
29 58.35468332440925 64.79274880895268 59.64495986218142
30 57.07961929431883 66.29987186904283 58.394030287459465
Charges
1 0.0354
2 0.0354
3 -0.0696
4 0.0516
5 0.1403
6 -0.1734
7 0.1288
8 -0.1134
9 0.1403
10 -0.1734
11 0.1237
12 -0.129
13 -0.0182
14 0.0266
15 0.1237
16 -0.129
17 -0.129
18 0.1237
19 0.0266
20 -0.0182
21 -0.129
22 0.1237
23 -0.1734
24 0.1403
25 -0.1134
26 0.1288
27 -0.1734
28 0.1403
29 0.0516
30 -0.0696
Bonds
1 10 1 3
2 10 2 3
3 8 4 13
4 1 6 5
5 1 8 7
6 2 8 6
7 1 10 9
8 2 10 8
9 1 12 11
10 2 12 10
11 9 13 3
12 7 14 13
13 2 14 12
14 1 16 15
15 2 16 14
16 2 16 6
17 1 17 18
18 2 17 19
19 2 17 27
20 7 19 20
21 2 19 21
22 9 20 30
23 9 20 3
24 1 21 22
25 2 21 23
26 1 23 24
27 2 23 25
28 1 25 26
29 2 25 27
30 1 27 28
31 8 29 20
Angles
1 16 20 3 13
2 14 2 3 20
3 14 1 3 20
4 14 2 3 13
5 14 1 3 13
6 15 2 3 1
7 2 16 6 8
8 1 16 6 5
9 1 8 6 5
10 1 10 8 7
11 2 10 8 6
12 1 6 8 7
13 1 12 10 9
14 2 12 10 8
15 1 8 10 9
16 1 14 12 11
17 2 14 12 10
18 1 10 12 11
19 10 14 13 4
20 11 14 13 3
21 12 4 13 3
22 9 16 14 13
23 2 16 14 12
24 9 12 14 13
25 1 14 16 15
26 1 6 16 15
27 2 14 16 6
28 1 19 17 18
29 1 27 17 18
30 2 19 17 27
31 9 17 19 20
32 2 17 19 21
33 9 21 19 20
34 10 19 20 29
35 11 19 20 30
36 11 19 20 3
37 12 29 20 30
38 12 29 20 3
39 13 30 20 3
40 1 19 21 22
41 2 19 21 23
42 1 23 21 22
43 1 21 23 24
44 2 21 23 25
45 1 25 23 24
46 1 23 25 26
47 2 23 25 27
48 1 27 25 26
49 2 17 27 25
50 1 17 27 28
51 1 25 27 28
Dihedrals
1 2 8 6 16 15
2 2 16 6 8 7
3 2 6 8 10 9
4 4 10 8 6 16
5 2 10 8 6 5
6 5 7 8 6 5
7 2 8 10 12 11
8 2 12 10 8 7
9 4 12 10 8 6
10 5 9 10 8 7
11 10 11 12 14 13
12 11 10 12 14 13
13 2 14 12 10 9
14 4 14 12 10 8
15 5 11 12 10 9
16 17 14 13 3 20
17 14 14 13 3 2
18 14 14 13 3 1
19 18 4 13 3 20
20 15 4 13 3 2
21 15 4 13 3 1
22 2 12 14 16 15
23 12 16 14 13 4
24 13 16 14 13 3
25 12 12 14 13 4
26 13 12 14 13 3
27 2 16 14 12 11
28 4 16 14 12 10
29 10 15 16 14 13
30 11 6 16 14 13
31 4 6 16 14 12
32 5 15 16 6 5
33 4 14 16 6 8
34 2 14 16 6 5
35 10 18 17 19 20
36 11 27 17 19 20
37 4 27 17 19 21
38 5 18 17 27 28
39 4 19 17 27 25
40 2 19 17 27 28
41 2 21 19 17 18
42 12 17 19 20 29
43 13 17 19 20 30
44 13 17 19 20 3
45 12 21 19 20 29
46 13 21 19 20 30
47 13 21 19 20 3
48 2 17 19 21 22
49 4 17 19 21 23
50 17 19 20 3 13
51 14 19 20 3 2
52 14 19 20 3 1
53 18 29 20 3 13
54 15 29 20 3 2
55 15 29 20 3 1
56 19 30 20 3 13
57 16 30 20 3 2
58 16 30 20 3 1
59 10 22 21 19 20
60 11 23 21 19 20
61 2 19 21 23 24
62 4 19 21 23 25
63 5 22 21 23 24
64 2 25 23 21 22
65 2 21 23 25 26
66 4 21 23 25 27
67 5 24 23 25 26
68 2 27 25 23 24
69 4 23 25 27 17
70 2 23 25 27 28
71 5 26 25 27 28
72 2 25 27 17 18
73 2 17 27 25 26
Impropers
1 1 2 3 13 20
2 1 1 3 13 20
3 1 2 3 1 20
4 1 2 3 1 13
5 1 16 6 8 5
6 1 10 8 6 7
7 1 12 10 8 9
8 1 14 12 10 11
9 7 14 13 4 3
10 5 16 14 12 13
11 1 14 16 6 15
12 1 19 17 27 18
13 5 17 19 21 20
14 1 19 20 29 30
15 1 19 20 29 3
16 1 19 20 30 3
17 1 29 20 30 3
18 1 19 21 23 22
19 1 21 23 25 24
20 1 23 25 27 26
21 1 17 27 25 28

48
examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene Executable file
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@ -0,0 +1,48 @@
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
variable T equal 530
read_data trimer.data &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
molecule mol1 grow_styrene_pre.data_template
molecule mol2 grow_styrene_post.data_template
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 30
fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo 100
run 8000
# write_data final.data nofix

196
examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 Normal file
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LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.077 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 125000 91125
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 39 39 39
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 48.02 | 48.02 | 48.02 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.9852 -52.954497 0.00034590142 13
4100 3021.3611 -65.03731 0.00036752025 14
4200 3002.7136 1.5750081 0.00036752025 14
4300 3218.6248 -120.74039 0.00038913909 15
4400 3345.1482 -0.96545269 0.00038913909 15
4500 3603.2429 1.2438833 0.00038913909 15
4600 3129.8814 -249.91806 0.00041075793 16
4700 3769.052 -289.24351 0.00043237677 17
4800 3560.4714 -3.1655406 0.00043237677 17
4900 3452.2717 -2.1270765 0.00043237677 17
5000 3594.3247 -523.48506 0.00045399561 18
5100 3578.4199 1.0009097 0.00045399561 18
5200 3822.1566 1.0526914 0.00047561445 19
5300 3901.8883 -0.14607602 0.00047561445 19
5400 4059.3644 -1.7789927 0.00049723329 20
5500 4163.6847 1.0240127 0.00049723329 20
5600 4109.1649 0.80199787 0.00049723329 20
5700 4391.2091 2.8730036 0.00049723329 20
5800 4279.6579 -0.36499822 0.00051885212 21
5900 4296.2695 -1.3064528 0.00051885212 21
6000 4065.3758 -2.0483224 0.00051885212 21
6100 4772.5362 -2.6814694 0.00054047096 22
6200 4627.029 2.999215 0.0005620898 23
6300 5120.7881 0.65372968 0.00058370864 24
6400 4588.9559 3.7570705 0.00058370864 24
6500 5008.7814 2.3595833 0.00060532748 25
6600 5195.0053 1.4641612 0.00060532748 25
6700 5622.293 -0.33396047 0.00062694632 26
6800 5515.1957 -4.234874 0.00062694632 26
6900 5156.7455 0.40171954 0.00064856516 27
7000 5120.1639 -1.6065245 0.00064856516 27
7100 5650.0327 0.94436323 0.00067018399 28
7200 5985.1115 -3.8940347 0.00069180283 29
7300 5983.197 0.5293568 0.00069180283 29
7400 6001.1559 -0.13712834 0.00071342167 30
7500 5889.2134 0.17230892 0.00071342167 30
7600 5797.31 2.0920058 0.00071342167 30
7700 5865.2783 -0.18556395 0.00071342167 30
7800 6207.0659 -5.6237083 0.00071342167 30
7900 5627.5108 -2.3718942 0.00071342167 30
8000 5823.9502 -0.85418578 0.00071342167 30
Loop time of 184.87 on 1 procs for 8000 steps with 528 atoms
Performance: 3.739 ns/day, 6.419 hours/ns, 43.274 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3043 | 3.3043 | 3.3043 | 0.0 | 1.79
Bond | 8.0003 | 8.0003 | 8.0003 | 0.0 | 4.33
Kspace | 168.33 | 168.33 | 168.33 | 0.0 | 91.05
Neigh | 4.6322 | 4.6322 | 4.6322 | 0.0 | 2.51
Comm | 0.077927 | 0.077927 | 0.077927 | 0.0 | 0.04
Output | 0.0020548 | 0.0020548 | 0.0020548 | 0.0 | 0.00
Modify | 0.5005 | 0.5005 | 0.5005 | 0.0 | 0.27
Other | | 0.02483 | | | 0.01
Nlocal: 528.000 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 341.000 ave 341 max 341 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35111.0 ave 35111 max 35111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35111
Ave neighs/atom = 66.498106
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:03:05

196
examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 Normal file
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LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 2 by 2 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 39200 24300
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 39 39 39
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
Per MPI rank memory allocation (min/avg/max) = 38.70 | 38.92 | 39.43 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.2204 -53.187892 0.00034590142 13
4100 3024.6375 -65.068146 0.00036752025 14
4200 3004.6784 1.4155214 0.00036752025 14
4300 3033.1895 1.8572273 0.00036752025 14
4400 3157.2542 -0.92462977 0.00036752025 14
4500 3557.7137 -194.46498 0.00038913909 15
4600 3096.485 -1.830492 0.00038913909 15
4700 3488.088 -286.81055 0.00041075793 16
4800 3390.5493 -372.77818 0.00043237677 17
4900 3773.7226 -446.58574 0.00045399561 18
5000 3703.0159 -0.81188551 0.00045399561 18
5100 4051.3067 1.2567439 0.00045399561 18
5200 3813.3682 0.92945737 0.00047561445 19
5300 4036.0078 -2.5336258 0.00049723329 20
5400 4219.803 -0.96928261 0.00049723329 20
5500 4433.7447 -0.026762463 0.00051885212 21
5600 4477.4505 -1.417316 0.00054047096 22
5700 4500.0306 -1.0551443 0.00054047096 22
5800 4600.3507 -4.9580056 0.00054047096 22
5900 4765.4978 -2.2546941 0.0005620898 23
6000 5442.6193 0.91161284 0.00058370864 24
6100 5086.8047 -0.9875332 0.00060532748 25
6200 5485.3437 -2.8296626 0.00062694632 26
6300 4988.0396 -0.15179023 0.00064856516 27
6400 5597.3703 4.2941885 0.00067018399 28
6500 5677.0263 -2.8611595 0.00069180283 29
6600 6058.0009 1.4111778 0.00071342167 30
6700 5859.0817 -2.5782466 0.00071342167 30
6800 5879.3941 -4.5681807 0.00071342167 30
6900 6398.288 2.5259412 0.00071342167 30
7000 6250.1096 -2.6049627 0.00071342167 30
7100 5849.651 -0.44062578 0.00071342167 30
7200 5778.6532 -0.27299118 0.00071342167 30
7300 5977.6661 4.2483639 0.00071342167 30
7400 5862.4231 1.0289519 0.00071342167 30
7500 6482.376 7.5412373 0.00071342167 30
7600 5810.4325 1.0343075 0.00071342167 30
7700 5916.7304 2.304302 0.00071342167 30
7800 5869.9504 -0.5946555 0.00071342167 30
7900 5804.0522 -4.1207689 0.00071342167 30
8000 6077.1704 0.52211243 0.00071342167 30
Loop time of 60.5603 on 4 procs for 8000 steps with 528 atoms
Performance: 11.413 ns/day, 2.103 hours/ns, 132.100 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0041695 | 0.90113 | 2.3423 | 102.8 | 1.49
Bond | 0.011606 | 2.1188 | 5.8107 | 163.9 | 3.50
Kspace | 47.987 | 52.817 | 55.679 | 43.7 | 87.21
Neigh | 3.5961 | 3.6262 | 3.6496 | 1.2 | 5.99
Comm | 0.11097 | 0.16569 | 0.26369 | 15.3 | 0.27
Output | 0.0020366 | 0.0023427 | 0.0032469 | 1.1 | 0.00
Modify | 0.62302 | 0.91659 | 1.1227 | 21.5 | 1.51
Other | | 0.0126 | | | 0.02
Nlocal: 132.000 ave 295 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 133.000 ave 349 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 8383.50 ave 20143 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 33534
Ave neighs/atom = 63.511364
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:00

796
examples/USER/reaction/create_atoms_polystyrene/trimer.data Normal file
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@ -0,0 +1,796 @@
polystyrene trimer
48 atoms
7 atom types
50 bonds
13 bond types
84 angles
22 angle types
127 dihedrals
36 dihedral types
36 impropers
9 improper types
50 250 xlo xhi
50 250 ylo yhi
50 250 zlo zhi
Masses
1 12.0112
2 1.00797
3 12.0112
4 12.0112
5 12.0112
6 12.0112
7 12.0112
Pair Coeffs # lj/class2/coul/long
1 0.064 4.01
2 0.02 2.7
3 0.064 4.01
4 0.064 3.9
5 0.054 4.01
6 0.054 4.01
7 0.054 4.01
Bond Coeffs # class2
1 1.0982 372.825 -803.453 894.317
2 1.417 470.836 -627.618 1327.63
3 1.501 321.902 -521.821 572.163
4 1.0883 365.768 -725.54 781.662
5 1.34 543.99 -1238.2 1644.03
6 1.0883 365.768 -725.54 781.662
7 1.501 321.902 -521.821 572.163
8 1.101 345 -691.89 844.6
9 1.53 299.67 -501.77 679.81
10 1.101 345 -691.89 844.6
11 1.501 321.902 -521.821 572.163
12 1.101 345 -691.89 844.6
13 1.53 299.67 -501.77 679.81
Angle Coeffs # class2
1 117.94 35.1558 -12.4682 0
2 118.9 61.0226 -34.9931 0
3 120.05 44.7148 -22.7352 0
4 111 44.3234 -9.4454 0
5 108.4 43.9594 -8.3924 -9.3379
6 124.88 35.2766 -17.774 -1.6215
7 124.88 35.2766 -17.774 -1.6215
8 115.49 29.6363 -12.4853 -6.2218
9 120.05 44.7148 -22.7352 0
10 111 44.3234 -9.4454 0
11 108.4 43.9594 -8.3924 -9.3379
12 110.77 41.453 -10.604 5.129
13 112.67 39.516 -7.443 -9.5583
14 110.77 41.453 -10.604 5.129
15 107.66 39.641 -12.921 -2.4318
16 112.67 39.516 -7.443 -9.5583
17 120.05 44.7148 -22.7352 0
18 111 44.3234 -9.4454 0
19 108.4 43.9594 -8.3924 -9.3379
20 110.77 41.453 -10.604 5.129
21 110.77 41.453 -10.604 5.129
22 112.67 39.516 -7.443 -9.5583
BondBond Coeffs
1 1.0795 1.417 1.0982
2 68.2856 1.417 1.417
3 12.0676 1.417 1.501
4 2.9168 1.501 1.0883
5 0 1.501 1.34
6 10.1047 1.0883 1.34
7 10.1047 1.0883 1.34
8 4.8506 1.0883 1.0883
9 12.0676 1.417 1.501
10 2.9168 1.501 1.101
11 0 1.501 1.53
12 3.3872 1.101 1.53
13 0 1.53 1.53
14 3.3872 1.101 1.53
15 5.3316 1.101 1.101
16 0 1.53 1.53
17 12.0676 1.417 1.501
18 2.9168 1.501 1.101
19 0 1.501 1.53
20 3.3872 1.101 1.53
21 3.3872 1.101 1.53
22 0 1.53 1.53
BondAngle Coeffs
1 20.0033 24.2183 1.417 1.0982
2 28.8708 28.8708 1.417 1.417
3 31.0771 47.0579 1.417 1.501
4 26.4608 11.7717 1.501 1.0883
5 0 0 1.501 1.34
6 19.0592 23.3588 1.0883 1.34
7 19.0592 23.3588 1.0883 1.34
8 17.9795 17.9795 1.0883 1.0883
9 31.0771 47.0579 1.417 1.501
10 26.4608 11.7717 1.501 1.101
11 0 0 1.501 1.53
12 11.421 20.754 1.101 1.53
13 8.016 8.016 1.53 1.53
14 11.421 20.754 1.101 1.53
15 18.103 18.103 1.101 1.101
16 8.016 8.016 1.53 1.53
17 31.0771 47.0579 1.417 1.501
18 26.4608 11.7717 1.501 1.101
19 0 0 1.501 1.53
20 11.421 20.754 1.101 1.53
21 11.421 20.754 1.101 1.53
22 8.016 8.016 1.53 1.53
Dihedral Coeffs # class2
1 0 0 1.559 0 0 0
2 0 0 3.9661 0 0 0
3 0 0 4.4072 0 0 0
4 8.3667 0 1.1932 0 0 0
5 0 0 1.8769 0 0 0
6 0 0 0 0 0 0
7 0 0 0 0 0 0
8 0 0 0 0 0 0
9 0 0 4.8974 0 0 0
10 0 0 1.559 0 0 0
11 0 0 4.4072 0 0 0
12 -0.2801 0 -0.0678 0 -0.0122 0
13 -0.2802 0 -0.0678 0 -0.0122 0
14 -0.0228 0 0.028 0 -0.1863 0
15 -0.1432 0 0.0617 0 -0.1083 0
16 0 0 0.0316 0 -0.1681 0
17 0 0 0 0 0 0
18 0 0 0.0316 0 -0.1681 0
19 0 0 0.0514 0 -0.143 0
20 0 0 1.559 0 0 0
21 0 0 4.4072 0 0 0
22 -0.2801 0 -0.0678 0 -0.0122 0
23 -0.2802 0 -0.0678 0 -0.0122 0
24 -0.0228 0 0.028 0 -0.1863 0
25 0 0 0 0 0 0
26 -0.1432 0 0.0617 0 -0.1083 0
27 0 0 0.0316 0 -0.1681 0
28 0 0 0 0 0 0
29 0 0 0.0316 0 -0.1681 0
30 0 0 0.0514 0 -0.143 0
31 -0.0228 0 0.028 0 -0.1863 0
32 -0.1432 0 0.0617 0 -0.1083 0
33 0 0 0.0316 0 -0.1681 0
34 0 0 0 0 0 0
35 0 0 0.0316 0 -0.1681 0
36 0 0 0.0514 0 -0.143 0
AngleAngleTorsion Coeffs
1 4.4444 117.94 120.05
2 -4.8141 118.9 117.94
3 -14.4097 118.9 120.05
4 0 118.9 118.9
5 0.3598 117.94 117.94
6 0 120.05 111
7 0 120.05 108.4
8 0 108.4 124.88
9 -7.0058 124.88 124.88
10 4.4444 117.94 120.05
11 -14.4097 118.9 120.05
12 -5.8888 120.05 111
13 0 120.05 108.4
14 0 108.4 110.77
15 -12.564 110.77 110.77
16 -16.164 112.67 110.77
17 0 108.4 112.67
18 -16.164 110.77 112.67
19 -22.045 112.67 112.67
20 4.4444 117.94 120.05
21 -14.4097 118.9 120.05
22 -5.8888 120.05 111
23 0 120.05 108.4
24 0 108.4 110.77
25 0 108.4 112.67
26 -12.564 110.77 110.77
27 -16.164 110.77 112.67
28 0 112.67 108.4
29 -16.164 112.67 110.77
30 -22.045 112.67 112.67
31 0 110.77 108.4
32 -12.564 110.77 110.77
33 -16.164 110.77 112.67
34 0 112.67 108.4
35 -16.164 112.67 110.77
36 -22.045 112.67 112.67
EndBondTorsion Coeffs
1 0 -0.4879 0 0 -1.797 0 1.0982 1.501
2 0 -6.8958 0 0 -0.4669 0 1.417 1.0982
3 0 -0.6918 0 0 0.2421 0 1.417 1.501
4 -0.1185 6.3204 0 -0.1185 6.3204 0 1.417 1.417
5 0 -0.689 0 0 -0.689 0 1.0982 1.0982
6 0 0 0 0 0 0 1.417 1.0883
7 0 0 0 0 0 0 1.417 1.34
8 0 0 0 0 0 0 1.501 1.0883
9 0.7129 0.5161 0 0.7129 0.5161 0 1.0883 1.0883
10 0 -0.4879 0 0 -1.797 0 1.0982 1.501
11 0 -0.6918 0 0 0.2421 0 1.417 1.501
12 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101
13 0 0 0 0 0 0 1.417 1.53
14 0 0 0 0 0 0 1.501 1.101
15 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
16 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
17 0 0 0 0 0 0 1.501 1.53
18 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
19 -0.0732 0 0 -0.0732 0 0 1.53 1.53
20 0 -0.4879 0 0 -1.797 0 1.0982 1.501
21 0 -0.6918 0 0 0.2421 0 1.417 1.501
22 -0.5835 1.122 0.3978 1.3997 0.7756 0 1.417 1.101
23 0 0 0 0 0 0 1.417 1.53
24 0 0 0 0 0 0 1.501 1.101
25 0 0 0 0 0 0 1.501 1.53
26 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
27 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
28 0 0 0 0 0 0 1.53 1.501
29 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
30 -0.0732 0 0 -0.0732 0 0 1.53 1.53
31 0 0 0 0 0 0 1.101 1.501
32 0.213 0.312 0.0777 0.213 0.312 0.0777 1.101 1.101
33 0.0814 0.0591 0.2219 0.2486 0.2422 -0.0925 1.101 1.53
34 0 0 0 0 0 0 1.53 1.501
35 0.2486 0.2422 -0.0925 0.0814 0.0591 0.2219 1.53 1.101
36 -0.0732 0 0 -0.0732 0 0 1.53 1.53
MiddleBondTorsion Coeffs
1 0 3.9421 0 1.417
2 0 -1.1521 0 1.417
3 0 9.1792 0 1.417
4 27.5989 -2.312 0 1.417
5 0 4.8228 0 1.417
6 0 0 0 1.501
7 0 0 0 1.501
8 0 0 0 1.34
9 0.8558 6.3911 0 1.34
10 0 3.9421 0 1.417
11 0 9.1792 0 1.417
12 -5.5679 1.4083 0.301 1.501
13 0 0 0 1.501
14 0 0 0 1.53
15 -14.261 -0.5322 -0.4864 1.53
16 -14.879 -3.6581 -0.3138 1.53
17 0 0 0 1.53
18 -14.879 -3.6581 -0.3138 1.53
19 -17.787 -7.1877 0 1.53
20 0 3.9421 0 1.417
21 0 9.1792 0 1.417
22 -5.5679 1.4083 0.301 1.501
23 0 0 0 1.501
24 0 0 0 1.53
25 0 0 0 1.53
26 -14.261 -0.5322 -0.4864 1.53
27 -14.879 -3.6581 -0.3138 1.53
28 0 0 0 1.53
29 -14.879 -3.6581 -0.3138 1.53
30 -17.787 -7.1877 0 1.53
31 0 0 0 1.53
32 -14.261 -0.5322 -0.4864 1.53
33 -14.879 -3.6581 -0.3138 1.53
34 0 0 0 1.53
35 -14.879 -3.6581 -0.3138 1.53
36 -17.787 -7.1877 0 1.53
BondBond13 Coeffs
1 0.8743 1.0982 1.501
2 -6.2741 1.417 1.0982
3 2.5085 1.417 1.501
4 53 1.417 1.417
5 -1.7077 1.0982 1.0982
6 0 1.417 1.0883
7 0 1.417 1.34
8 0 1.501 1.0883
9 0 1.0883 1.0883
10 0.8743 1.0982 1.501
11 2.5085 1.417 1.501
12 -3.4826 1.417 1.101
13 0 1.417 1.53
14 0 1.501 1.101
15 0 1.101 1.101
16 0 1.53 1.101
17 0 1.501 1.53
18 0 1.101 1.53
19 0 1.53 1.53
20 0.8743 1.0982 1.501
21 2.5085 1.417 1.501
22 -3.4826 1.417 1.101
23 0 1.417 1.53
24 0 1.501 1.101
25 0 1.501 1.53
26 0 1.101 1.101
27 0 1.101 1.53
28 0 1.53 1.501
29 0 1.53 1.101
30 0 1.53 1.53
31 0 1.101 1.501
32 0 1.101 1.101
33 0 1.101 1.53
34 0 1.53 1.501
35 0 1.53 1.101
36 0 1.53 1.53
AngleTorsion Coeffs
1 0 3.4601 0 0 -0.1242 0 117.94 120.05
2 0 2.5014 0 0 2.7147 0 118.9 117.94
3 0 3.8987 0 0 -4.4683 0 118.9 120.05
4 1.9767 1.0239 0 1.9767 1.0239 0 118.9 118.9
5 0 2.4501 0 0 2.4501 0 117.94 117.94
6 0 0 0 0 0 0 120.05 111
7 0 0 0 0 0 0 120.05 108.4
8 0 0 0 0 0 0 108.4 124.88
9 -1.8911 3.254 0 -1.8911 3.254 0 124.88 124.88
10 0 3.4601 0 0 -0.1242 0 117.94 120.05
11 0 3.8987 0 0 -4.4683 0 118.9 120.05
12 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111
13 0 0 0 0 0 0 120.05 108.4
14 0 0 0 0 0 0 108.4 110.77
15 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
16 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
17 0 0 0 0 0 0 108.4 112.67
18 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
19 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
20 0 3.4601 0 0 -0.1242 0 117.94 120.05
21 0 3.8987 0 0 -4.4683 0 118.9 120.05
22 0.2251 0.6548 0.1237 4.6266 0.1632 0.0461 120.05 111
23 0 0 0 0 0 0 120.05 108.4
24 0 0 0 0 0 0 108.4 110.77
25 0 0 0 0 0 0 108.4 112.67
26 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
27 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
28 0 0 0 0 0 0 112.67 108.4
29 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
30 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
31 0 0 0 0 0 0 110.77 108.4
32 -0.8085 0.5569 -0.2466 -0.8085 0.5569 -0.2466 110.77 110.77
33 0.3113 0.4516 -0.1988 -0.2454 0 -0.1136 110.77 112.67
34 0 0 0 0 0 0 112.67 108.4
35 -0.2454 0 -0.1136 0.3113 0.4516 -0.1988 112.67 110.77
36 0.3886 -0.3139 0.1389 0.3886 -0.3139 0.1389 112.67 112.67
Improper Coeffs # class2
1 4.8912 0
2 7.8153 0
3 0 0
4 2.8561 0
5 7.8153 0
6 0 0
7 0 0
8 7.8153 0
9 0 0
AngleAngle Coeffs
1 0 0 0 118.9 117.94 117.94
2 0 0 0 118.9 120.05 120.05
3 0 0 0 111 124.88 108.4
4 0 0 0 115.49 124.88 124.88
5 0 0 0 118.9 120.05 120.05
6 0 0 0 107.66 110.77 110.77
7 0 0 0 111 110.77 108.4
8 0 0 0 118.9 120.05 120.05
9 0 0 0 111 110.77 108.4
Atoms # full
44 1 2 3.5400000000000001e-02 6.1476397222913839e+01 8.2376490601205234e+01 6.0906939115836181e+01
45 1276 2 3.5400000000000001e-02 5.8398688202244472e+01 8.0172948526664996e+01 6.2115536813582672e+01
46 1276 6 -6.9599999999999995e-02 5.9489073989392523e+01 8.0264057167571636e+01 6.1984002598976552e+01
48 1276 2 3.5400000000000001e-02 5.9675170230342431e+01 8.0048052449390738e+01 6.0920159395372401e+01
47 1276 2 1.2370000000000000e-01 5.9297455513100488e+01 8.3187777608476154e+01 5.9645157256520122e+01
18 1 5 -1.8200000000000001e-02 6.2426251430535707e+01 8.2055473568260709e+01 6.2971661388612958e+01
19 1 6 -6.9599999999999995e-02 6.1399255844467369e+01 8.1794665295860213e+01 6.1821819828185660e+01
21 1 1 -1.2900000000000000e-01 6.4032918371445831e+01 8.0190179089286701e+01 6.3021564712316334e+01
22 1 1 2.6599999999999999e-02 6.3672975135915053e+01 8.1418558650051665e+01 6.2448012627881994e+01
23 1 2 3.5400000000000001e-02 6.1545198223694939e+01 8.0836309422842305e+01 6.1349823957467130e+01
27 1276 2 5.1600000000000000e-02 5.9809503696580933e+01 8.1831265916389881e+01 6.3253745193271065e+01
28 1276 5 -1.8200000000000001e-02 5.9900307947967441e+01 8.1677453781363639e+01 6.2190757403657820e+01
31 1276 2 1.2370000000000000e-01 5.8050043823867973e+01 8.2698312265456622e+01 6.3667111329534436e+01
38 1 2 1.2370000000000000e-01 6.3754126973935612e+01 7.9931147303963002e+01 6.4022259163067275e+01
20 1 2 1.2370000000000000e-01 6.4070158368422781e+01 8.2950071388392274e+01 6.1042631212883315e+01
24 1 1 -1.2900000000000000e-01 6.4337973861569580e+01 8.1916618276489871e+01 6.1387866780102470e+01
37 1 2 1.4030000000000001e-01 6.5360115866618415e+01 7.8586112104863830e+01 6.3004997314380716e+01
39 1 1 -1.7340000000000000e-01 6.5018338085325610e+01 7.9478260591306125e+01 6.2440745569712817e+01
40 1 1 -1.1340000000000000e-01 6.5628759887796605e+01 7.9941156332165264e+01 6.1248476296558067e+01
41 1 1 -1.7340000000000000e-01 6.5247995680260402e+01 8.1172439250598345e+01 6.0753045571239831e+01
42 1 2 1.2880000000000000e-01 6.6569600059599281e+01 7.9514748976494360e+01 6.0810611807135601e+01
43 1 2 1.4030000000000001e-01 6.5780165393063371e+01 8.1570974991007958e+01 5.9850915261812396e+01
9 1276 2 1.2880000000000000e-01 5.5651795605743445e+01 8.5074472139235127e+01 6.1094480497979262e+01
30 1276 2 1.4030000000000001e-01 5.6082982679196888e+01 8.3912863624076010e+01 6.3351889697403472e+01
33 1276 1 -1.7340000000000000e-01 5.6718133911388506e+01 8.3758479063002000e+01 6.2493293749545209e+01
34 1276 1 -1.1340000000000000e-01 5.6498352105218459e+01 8.4426576393179090e+01 6.1290147608586011e+01
6 3822 1 -1.7340000000000000e-01 6.3308103537340351e+01 8.7713509787622499e+01 6.4643082313868433e+01
7 3822 1 -1.2900000000000000e-01 6.3010291684764312e+01 8.6423650045069493e+01 6.4252844241495922e+01
8 3822 2 1.2370000000000000e-01 6.2089199187020355e+01 8.6309198636296912e+01 6.3711263099850854e+01
10 1276 2 1.4030000000000001e-01 5.7266131308654970e+01 8.4599328362003035e+01 5.9281511478144402e+01
11 3822 2 3.5400000000000001e-02 6.1694306618059791e+01 8.3823470438280594e+01 6.3778953909925114e+01
12 3822 5 -1.8200000000000001e-02 6.3814926998838651e+01 8.3900077798460728e+01 6.4108991789590448e+01
13 3822 6 -6.9599999999999995e-02 6.2604540882379787e+01 8.3491998603381077e+01 6.3249610918984622e+01
14 3822 2 1.2370000000000000e-01 6.5739253131027880e+01 8.4813736128157771e+01 6.5351692111169555e+01
15 3822 1 -1.2900000000000000e-01 6.5071144269009466e+01 8.5646783550482454e+01 6.5086813218945636e+01
16 3822 1 2.6599999999999999e-02 6.3957099792282079e+01 8.5375816595044753e+01 6.4385073943729708e+01
17 1 2 5.1600000000000000e-02 6.2256484483973310e+01 8.1576962161157596e+01 6.3963984654065122e+01
26 3822 2 5.1600000000000000e-02 6.4196825763126355e+01 8.3291442832977836e+01 6.4907094488854057e+01
29 1276 1 2.6599999999999999e-02 5.8784742332505303e+01 8.2766055380197670e+01 6.1667239692876961e+01
32 1276 1 -1.2900000000000000e-01 5.7836199787435064e+01 8.3005060229118428e+01 6.2669788306756018e+01
35 1276 1 -1.2900000000000000e-01 5.8572661840325132e+01 8.3404075689965083e+01 6.0443288532625175e+01
36 1276 1 -1.7340000000000000e-01 5.7380616699226330e+01 8.4134680429976896e+01 6.0248710539932475e+01
25 3822 2 3.5400000000000001e-02 6.2750675036816460e+01 8.3891633300878468e+01 6.2249429178485677e+01
5 3822 2 1.4030000000000001e-01 6.2626160082050376e+01 8.8416565740835182e+01 6.4093918967496805e+01
1 3822 2 1.2880000000000000e-01 6.4863557606529355e+01 8.9096029197548390e+01 6.5342927535537825e+01
2 3822 1 -1.1340000000000000e-01 6.4627442641031166e+01 8.8047381925321190e+01 6.5138073202291650e+01
3 3822 2 1.4030000000000001e-01 6.6470254992065406e+01 8.6991893750821745e+01 6.5857474890608984e+01
4 3822 1 -1.7340000000000000e-01 6.5416488888088338e+01 8.6963894801200169e+01 6.5357641085394278e+01
Velocities
44 -1.1274099342391698e-02 2.8614364731871914e-02 7.8116535486555949e-03
45 2.3164382404151666e-03 3.9815732957733160e-03 -2.9971878581527899e-02
46 -7.1653099619954563e-03 4.5491360587300133e-04 4.9898614093692017e-03
48 9.8069086061434527e-03 4.0008139512159270e-03 6.2934259772882122e-03
47 2.2646445306743783e-03 1.3029071608409702e-03 4.2232440120174040e-02
18 7.0040064100195757e-03 3.2877451206009701e-03 -3.5376010407568422e-04
19 -1.3998188760009689e-02 7.2238210565990146e-03 7.7956220633332383e-03
21 3.1954292320462373e-03 -2.9717583309420764e-03 -3.1753395094325522e-03
22 5.2997643939121201e-03 -2.9646963088534335e-03 -4.1351926198204894e-03
23 7.6443400078766528e-03 4.0358953976530103e-02 -2.6684706183248367e-02
27 1.9261652416455359e-03 -1.1632914130150688e-02 1.0061732021630769e-02
28 -8.2251676802878315e-03 -1.5111873066969876e-04 1.3808893565582731e-02
31 5.2475840572179860e-03 1.8266996572138715e-02 2.3453280610166885e-03
38 -2.0343905130199073e-02 3.2815536859276281e-02 3.6511922534330152e-03
20 2.2914549087537126e-02 1.4424503744223915e-02 2.1708279654645496e-03
24 -2.4717233344142471e-03 1.2966123098719246e-02 8.1261459853411936e-03
37 -2.4547379584186218e-02 -3.0213966592845171e-02 -3.1437442951939183e-02
39 2.5476117829076835e-03 1.2743160680987653e-03 1.8775880208113892e-03
40 -6.9216508143939990e-03 1.0986173624795060e-02 8.4543093049661480e-03
41 -6.9641432145561661e-03 3.4497795547843439e-03 -6.5914679936187716e-03
42 -1.6682931637687005e-02 -7.9952140358728052e-03 -5.4993265930488526e-02
43 -1.2747392921213267e-03 -8.9033092043203244e-03 -1.4285400545629027e-02
9 -4.6235166357676289e-03 -1.3071850427027999e-02 -1.4097407987100977e-02
30 -1.0949617396609294e-02 2.8255703113196974e-03 1.7171748232322353e-02
33 -6.1375812469323665e-03 -2.4748644899411924e-03 -9.4761978149296138e-03
34 1.3676079846441525e-03 5.6076140293943458e-03 4.3217204641336267e-03
6 -1.0264635053701928e-02 6.5278337056107680e-03 7.0056151148588212e-04
7 -8.7519451205145676e-03 -4.6476440106580945e-03 2.5970484253527112e-03
8 2.1377395557690311e-02 -3.3261274153819453e-03 -1.0112266596677577e-02
10 -3.5793767912309253e-02 -4.7139872292323019e-02 -1.6709528481405608e-02
11 8.5071485795589590e-03 9.9402848610678270e-03 -3.8088596341056854e-03
12 -7.1678159384257103e-04 -6.9164463557228907e-04 -6.4073519808107186e-03
13 -4.8443902657902991e-03 -1.1919190682985097e-03 6.3946846087726637e-03
14 1.4810157483257907e-02 1.9829623839419017e-03 -2.7393844990063056e-02
15 2.4171850935506777e-03 8.5003135180758520e-03 -1.4373227798951704e-03
16 2.7567342910947553e-03 4.7168484476890456e-03 -5.5131873288712992e-03
17 -3.8456662730386774e-02 2.0220106671151108e-02 -1.3822049134399602e-02
26 2.7415414728694614e-02 1.4392155257037418e-03 -6.7281635499082748e-03
29 2.8284983560440745e-03 2.8809942505517976e-03 -9.0489583066552114e-04
32 -3.8543634697614316e-03 4.6751647301899795e-03 4.2171867397204537e-03
35 -8.6957974827209118e-03 -4.4615282666186267e-04 -2.6571026120482824e-03
36 9.4881057996863086e-04 -7.5665878069688429e-03 2.0333670960646154e-03
25 1.8105924111310519e-02 -8.6933495274689535e-03 -1.9695291360338044e-04
5 -5.0447438383189585e-03 -4.5665146331657552e-02 1.0653751333175230e-02
1 -1.7372868398038824e-02 -2.3625357536259349e-03 1.2220266128368908e-02
2 3.7050246021929395e-03 -1.0236943515935205e-03 7.2206774682170580e-03
3 2.3669435799326944e-02 2.7891427939155597e-02 -6.7091036888174346e-03
4 3.4910623999263577e-03 2.6370880132825258e-03 -6.4694788112864129e-03
Bonds
1 10 44 19
2 10 45 46
3 10 48 46
4 9 19 18
5 1 21 38
6 2 21 22
7 2 21 39
8 7 22 18
9 2 22 24
10 10 23 19
11 8 27 28
12 9 28 46
13 9 28 19
14 1 24 20
15 2 24 41
16 1 39 37
17 1 40 42
18 2 40 39
19 1 41 43
20 2 41 40
21 1 33 30
22 1 34 9
23 2 34 33
24 1 6 5
25 2 6 2
26 1 7 8
27 2 7 6
28 10 11 13
29 13 12 13
30 9 13 18
31 1 15 14
32 2 15 16
33 2 15 4
34 11 16 12
35 2 16 7
36 8 17 18
37 12 26 12
38 7 29 28
39 2 29 35
40 1 32 31
41 2 32 29
42 2 32 33
43 1 35 47
44 2 35 36
45 1 36 10
46 2 36 34
47 10 25 13
48 1 2 1
49 2 2 4
50 1 4 3
Angles
1 14 45 46 28
2 14 48 46 28
3 15 45 46 48
4 11 22 18 13
5 12 17 18 13
6 13 13 18 19
7 10 22 18 17
8 11 22 18 19
9 12 17 18 19
10 16 28 19 18
11 14 44 19 28
12 14 23 19 28
13 14 44 19 18
14 14 23 19 18
15 15 44 19 23
16 1 22 21 38
17 1 39 21 38
18 2 22 21 39
19 9 21 22 18
20 2 21 22 24
21 9 24 22 18
22 10 29 28 27
23 11 29 28 46
24 11 29 28 19
25 12 27 28 46
26 12 27 28 19
27 13 46 28 19
28 1 22 24 20
29 2 22 24 41
30 1 41 24 20
31 2 21 39 40
32 1 21 39 37
33 1 40 39 37
34 1 41 40 42
35 2 41 40 39
36 1 39 40 42
37 1 24 41 43
38 2 24 41 40
39 1 40 41 43
40 2 32 33 34
41 1 32 33 30
42 1 34 33 30
43 1 36 34 9
44 2 36 34 33
45 1 33 34 9
46 1 7 6 5
47 2 7 6 2
48 1 2 6 5
49 1 16 7 8
50 2 16 7 6
51 1 6 7 8
52 18 16 12 26
53 19 16 12 13
54 20 26 12 13
55 21 25 13 12
56 21 11 13 12
57 22 12 13 18
58 15 25 13 11
59 14 25 13 18
60 14 11 13 18
61 1 16 15 14
62 1 4 15 14
63 2 16 15 4
64 17 15 16 12
65 2 15 16 7
66 17 7 16 12
67 9 32 29 28
68 2 32 29 35
69 9 35 29 28
70 1 29 32 31
71 1 33 32 31
72 2 29 32 33
73 1 29 35 47
74 2 29 35 36
75 1 36 35 47
76 1 35 36 10
77 2 35 36 34
78 1 34 36 10
79 1 6 2 1
80 2 6 2 4
81 1 4 2 1
82 2 15 4 2
83 1 15 4 3
84 1 2 4 3
Dihedrals
1 34 18 19 28 29
2 31 44 19 28 29
3 31 23 19 28 29
4 35 18 19 28 27
5 32 44 19 28 27
6 32 23 19 28 27
7 36 18 19 28 46
8 33 44 19 28 46
9 33 23 19 28 46
10 36 28 19 18 13
11 33 44 19 18 13
12 33 23 19 18 13
13 34 28 19 18 22
14 31 44 19 18 22
15 31 23 19 18 22
16 35 28 19 18 17
17 32 44 19 18 17
18 32 23 19 18 17
19 10 38 21 22 18
20 11 39 21 22 18
21 4 39 21 22 24
22 5 38 21 39 37
23 4 22 21 39 40
24 2 22 21 39 37
25 2 24 22 21 38
26 13 21 22 18 13
27 12 21 22 18 17
28 13 21 22 18 19
29 13 24 22 18 13
30 12 24 22 18 17
31 13 24 22 18 19
32 2 21 22 24 20
33 4 21 22 24 41
34 14 29 28 46 45
35 14 29 28 46 48
36 15 27 28 46 45
37 15 27 28 46 48
38 16 19 28 46 45
39 16 19 28 46 48
40 10 20 24 22 18
41 11 41 24 22 18
42 2 22 24 41 43
43 4 22 24 41 40
44 5 20 24 41 43
45 2 40 39 21 38
46 2 21 39 40 42
47 2 39 40 41 43
48 4 41 40 39 21
49 2 41 40 39 37
50 5 42 40 39 37
51 2 40 41 24 20
52 2 24 41 40 42
53 4 24 41 40 39
54 5 43 41 40 42
55 2 34 33 32 31
56 2 32 33 34 9
57 2 33 34 36 10
58 4 36 34 33 32
59 2 36 34 33 30
60 5 9 34 33 30
61 2 2 6 7 8
62 2 7 6 2 1
63 4 7 6 2 4
64 5 5 6 2 1
65 20 8 7 16 12
66 21 6 7 16 12
67 2 16 7 6 5
68 4 16 7 6 2
69 5 8 7 6 5
70 24 16 12 13 25
71 24 16 12 13 11
72 25 16 12 13 18
73 26 26 12 13 25
74 26 26 12 13 11
75 27 26 12 13 18
76 28 12 13 18 22
77 29 12 13 18 17
78 30 12 13 18 19
79 31 25 13 18 22
80 32 25 13 18 17
81 33 25 13 18 19
82 31 11 13 18 22
83 32 11 13 18 17
84 33 11 13 18 19
85 20 14 15 16 12
86 21 4 15 16 12
87 4 4 15 16 7
88 5 14 15 4 3
89 4 16 15 4 2
90 2 16 15 4 3
91 2 7 16 15 14
92 22 15 16 12 26
93 23 15 16 12 13
94 22 7 16 12 26
95 23 7 16 12 13
96 2 15 16 7 8
97 4 15 16 7 6
98 2 35 29 32 31
99 12 32 29 28 27
100 13 32 29 28 46
101 13 32 29 28 19
102 12 35 29 28 27
103 13 35 29 28 46
104 13 35 29 28 19
105 2 32 29 35 47
106 4 32 29 35 36
107 10 31 32 29 28
108 11 33 32 29 28
109 4 33 32 29 35
110 5 31 32 33 30
111 4 29 32 33 34
112 2 29 32 33 30
113 10 47 35 29 28
114 11 36 35 29 28
115 2 29 35 36 10
116 4 29 35 36 34
117 5 47 35 36 10
118 2 34 36 35 47
119 2 35 36 34 9
120 4 35 36 34 33
121 5 10 36 34 9
122 2 4 2 6 5
123 4 6 2 4 15
124 2 6 2 4 3
125 5 1 2 4 3
126 2 2 4 15 14
127 2 15 4 2 1
Impropers
1 6 45 46 48 28
2 1 22 18 17 13
3 1 22 18 13 19
4 1 17 18 13 19
5 1 22 18 17 19
6 1 44 19 18 28
7 1 23 19 18 28
8 1 44 19 23 28
9 1 44 19 23 18
10 1 22 21 39 38
11 5 21 22 24 18
12 1 29 28 27 46
13 1 29 28 27 19
14 1 29 28 46 19
15 1 27 28 46 19
16 1 22 24 41 20
17 1 21 39 40 37
18 1 41 40 39 42
19 1 24 41 40 43
20 1 32 33 34 30
21 1 36 34 33 9
22 1 7 6 2 5
23 1 16 7 6 8
24 9 16 12 26 13
25 1 25 13 11 12
26 1 25 13 12 18
27 1 11 13 12 18
28 1 25 13 11 18
29 1 16 15 4 14
30 8 15 16 7 12
31 5 32 29 35 28
32 1 29 32 33 31
33 1 29 35 36 47
34 1 35 36 34 10
35 1 6 2 4 1
36 1 15 4 2 3

13
lib/kokkos/BUILD.md
View File

@ -65,10 +65,15 @@ which activates the OpenMP backend. All of the options controlling device backen
## Spack
An alternative to manually building with the CMake is to use the Spack package manager.
To do so, download the `kokkos-spack` git repo and add to the package list:
Make sure you have downloaded [Spack](https://github.com/spack/spack).
The easiest way to configure the Spack environment is:
````bash
> spack repo add $path-to-kokkos-spack
> source spack/share/spack/setup-env.sh
````
with other scripts available for other shells.
You can display information about how to install packages with:
````bash
> spack info kokkos
A basic installation would be done as:
````bash
> spack install kokkos
@ -178,8 +183,8 @@ Options can be enabled by specifying `-DKokkos_ENABLE_X`.
## Other Options
* Kokkos_CXX_STANDARD
* The C++ standard for Kokkos to use: c++11, c++14, c++17, or c++20. This should be given in CMake style as 11, 14, 17, or 20.
* STRING Default: 11
* The C++ standard for Kokkos to use: c++14, c++17, or c++20. This should be given in CMake style as 14, 17, or 20.
* STRING Default: 14
## Third-party Libraries (TPLs)
The following options control enabling TPLs:

120
lib/kokkos/CHANGELOG.md
View File

@ -1,5 +1,111 @@
# Change Log
## [3.3.01](https://github.com/kokkos/kokkos/tree/3.3.01) (2021-01-06)
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.3.00...3.3.01)
**Bug Fixes:**
- Fix severe performance bug in DualView which added memcpys for sync and modify [\#3693](https://github.com/kokkos/kokkos/issues/#3693)
- Fix performance bug in CUDA backend, where the cuda Cache config was not set correct.
## [3.3.00](https://github.com/kokkos/kokkos/tree/3.3.00) (2020-12-16)
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.2.01...3.3.00)
**Features:**
- Require C++14 as minimum C++ standard. C++17 and C++20 are supported too.
- HIP backend is nearly feature complete. Kokkos Dynamic Task Graphs are missing.
- Major update for OpenMPTarget: many capabilities now work. For details contact us.
- Added DPC++/SYCL backend: primary capabilites are working.
- Added Kokkos Graph API analogous to CUDA Graphs.
- Added parallel_scan support with TeamThreadRange [\#3536](https://github.com/kokkos/kokkos/pull/#3536)
- Added Logical Memory Spaces [\#3546](https://github.com/kokkos/kokkos/pull/#3546)
- Added initial half precision support [\#3439](https://github.com/kokkos/kokkos/pull/#3439)
- Experimental feature: control cuda occupancy [\#3379](https://github.com/kokkos/kokkos/pull/#3379)
**Implemented enhancements Backends and Archs:**
- Add a64fx and fujitsu Compiler support [\#3614](https://github.com/kokkos/kokkos/pull/#3614)
- Adding support for AMD gfx908 archictecture [\#3375](https://github.com/kokkos/kokkos/pull/#3375)
- SYCL parallel\_for MDRangePolicy [\#3583](https://github.com/kokkos/kokkos/pull/#3583)
- SYCL add parallel\_scan [\#3577](https://github.com/kokkos/kokkos/pull/#3577)
- SYCL custom reductions [\#3544](https://github.com/kokkos/kokkos/pull/#3544)
- SYCL Enable container unit tests [\#3550](https://github.com/kokkos/kokkos/pull/#3550)
- SYCL feature level 5 [\#3480](https://github.com/kokkos/kokkos/pull/#3480)
- SYCL Feature level 4 (parallel\_for) [\#3474](https://github.com/kokkos/kokkos/pull/#3474)
- SYCL feature level 3 [\#3451](https://github.com/kokkos/kokkos/pull/#3451)
- SYCL feature level 2 [\#3447](https://github.com/kokkos/kokkos/pull/#3447)
- OpenMPTarget: Hierarchial reduction for + operator on scalars [\#3504](https://github.com/kokkos/kokkos/pull/#3504)
- OpenMPTarget hierarchical [\#3411](https://github.com/kokkos/kokkos/pull/#3411)
- HIP Add Impl::atomic\_[store,load] [\#3440](https://github.com/kokkos/kokkos/pull/#3440)
- HIP enable global lock arrays [\#3418](https://github.com/kokkos/kokkos/pull/#3418)
- HIP Implement multiple occupancy paths for various HIP kernel launchers [\#3366](https://github.com/kokkos/kokkos/pull/#3366)
**Implemented enhancements Policies:**
- MDRangePolicy: Let it be semiregular [\#3494](https://github.com/kokkos/kokkos/pull/#3494)
- MDRangePolicy: Check narrowing conversion in construction [\#3527](https://github.com/kokkos/kokkos/pull/#3527)
- MDRangePolicy: CombinedReducers support [\#3395](https://github.com/kokkos/kokkos/pull/#3395)
- Kokkos Graph: Interface and Default Implementation [\#3362](https://github.com/kokkos/kokkos/pull/#3362)
- Kokkos Graph: add Cuda Graph implementation [\#3369](https://github.com/kokkos/kokkos/pull/#3369)
- TeamPolicy: implemented autotuning of team sizes and vector lengths [\#3206](https://github.com/kokkos/kokkos/pull/#3206)
- RangePolicy: Initialize all data members in default constructor [\#3509](https://github.com/kokkos/kokkos/pull/#3509)
**Implemented enhancements BuildSystem:**
- Auto-generate core test files for all backends [\#3488](https://github.com/kokkos/kokkos/pull/#3488)
- Avoid rewriting test files when calling cmake [\#3548](https://github.com/kokkos/kokkos/pull/#3548)
- RULE\_LAUNCH\_COMPILE and RULE\_LAUNCH\_LINK system for nvcc\_wrapper [\#3136](https://github.com/kokkos/kokkos/pull/#3136)
- Adding -include as a known argument to nvcc\_wrapper [\#3434](https://github.com/kokkos/kokkos/pull/#3434)
- Install hpcbind script [\#3402](https://github.com/kokkos/kokkos/pull/#3402)
- cmake/kokkos\_tribits.cmake: add parsing for args [\#3457](https://github.com/kokkos/kokkos/pull/#3457)
**Implemented enhancements Tools:**
- Changed namespacing of Kokkos::Tools::Impl::Impl::tune\_policy [\#3455](https://github.com/kokkos/kokkos/pull/#3455)
- Delegate to an impl allocate/deallocate method to allow specifying a SpaceHandle for MemorySpaces [\#3530](https://github.com/kokkos/kokkos/pull/#3530)
- Use the Kokkos Profiling interface rather than the Impl interface [\#3518](https://github.com/kokkos/kokkos/pull/#3518)
- Runtime option for tuning [\#3459](https://github.com/kokkos/kokkos/pull/#3459)
- Dual View Tool Events [\#3326](https://github.com/kokkos/kokkos/pull/#3326)
**Implemented enhancements Other:**
- Abort on errors instead of just printing [\#3528](https://github.com/kokkos/kokkos/pull/#3528)
- Enable C++14 macros unconditionally [\#3449](https://github.com/kokkos/kokkos/pull/#3449)
- Make ViewMapping trivially copyable [\#3436](https://github.com/kokkos/kokkos/pull/#3436)
- Rename struct ViewMapping to class [\#3435](https://github.com/kokkos/kokkos/pull/#3435)
- Replace enums in Kokkos\_ViewMapping.hpp (removes -Wextra) [\#3422](https://github.com/kokkos/kokkos/pull/#3422)
- Use bool for enums representing bools [\#3416](https://github.com/kokkos/kokkos/pull/#3416)
- Fence active instead of default execution space instances [\#3388](https://github.com/kokkos/kokkos/pull/#3388)
- Refactor parallel\_reduce fence usage [\#3359](https://github.com/kokkos/kokkos/pull/#3359)
- Moved Space EBO helpers to Kokkos\_EBO [\#3357](https://github.com/kokkos/kokkos/pull/#3357)
- Add remove\_cvref type trait [\#3340](https://github.com/kokkos/kokkos/pull/#3340)
- Adding identity type traits and update definition of identity\_t alias [\#3339](https://github.com/kokkos/kokkos/pull/#3339)
- Add is\_specialization\_of type trait [\#3338](https://github.com/kokkos/kokkos/pull/#3338)
- Make ScratchMemorySpace semi-regular [\#3309](https://github.com/kokkos/kokkos/pull/#3309)
- Optimize min/max atomics with early exit on no-op case [\#3265](https://github.com/kokkos/kokkos/pull/#3265)
- Refactor Backend Development [\#2941](https://github.com/kokkos/kokkos/pull/#2941)
**Fixed bugs:**
- Fixup MDRangePolicy construction from Kokkos arrays [\#3591](https://github.com/kokkos/kokkos/pull/#3591)
- Add atomic functions for unsigned long long using gcc built-in [\#3588](https://github.com/kokkos/kokkos/pull/#3588)
- Fixup silent pointless comparison with zero in checked\_narrow\_cast (compiler workaround) [\#3566](https://github.com/kokkos/kokkos/pull/#3566)
- Fixes for ROCm 3.9 [\#3565](https://github.com/kokkos/kokkos/pull/#3565)
- Fix windows build issues which crept in for the CUDA build [\#3532](https://github.com/kokkos/kokkos/pull/#3532)
- HIP Fix atomics of large data types and clean up lock arrays [\#3529](https://github.com/kokkos/kokkos/pull/#3529)
- Pthreads fix exception resulting from 0 grain size [\#3510](https://github.com/kokkos/kokkos/pull/#3510)
- Fixup do not require atomic operation to be default constructible [\#3503](https://github.com/kokkos/kokkos/pull/#3503)
- Fix race condition in HIP backend [\#3467](https://github.com/kokkos/kokkos/pull/#3467)
- Replace KOKKOS\_DEBUG with KOKKOS\_ENABLE\_DEBUG [\#3458](https://github.com/kokkos/kokkos/pull/#3458)
- Fix multi-stream team scratch space definition for HIP [\#3398](https://github.com/kokkos/kokkos/pull/#3398)
- HIP fix template deduction [\#3393](https://github.com/kokkos/kokkos/pull/#3393)
- Fix compiling with HIP and C++17 [\#3390](https://github.com/kokkos/kokkos/pull/#3390)
- Fix sigFPE in HIP blocksize deduction [\#3378](https://github.com/kokkos/kokkos/pull/#3378)
- Type alias change: replace CS with CTS to avoid conflicts with NVSHMEM [\#3348](https://github.com/kokkos/kokkos/pull/#3348)
- Clang compilation of CUDA backend on Windows [\#3345](https://github.com/kokkos/kokkos/pull/#3345)
- Fix HBW support [\#3343](https://github.com/kokkos/kokkos/pull/#3343)
- Added missing fences to unique token [\#3260](https://github.com/kokkos/kokkos/pull/#3260)
**Incompatibilities:**
- Remove unused utilities (forward, move, and expand\_variadic) from Kokkos::Impl [\#3535](https://github.com/kokkos/kokkos/pull/#3535)
- Remove unused traits [\#3534](https://github.com/kokkos/kokkos/pull/#3534)
- HIP: Remove old HCC code [\#3301](https://github.com/kokkos/kokkos/pull/#3301)
- Prepare for deprecation of ViewAllocateWithoutInitializing [\#3264](https://github.com/kokkos/kokkos/pull/#3264)
- Remove ROCm backend [\#3148](https://github.com/kokkos/kokkos/pull/#3148)
## [3.2.01](https://github.com/kokkos/kokkos/tree/3.2.01) (2020-11-17)
[Full Changelog](https://github.com/kokkos/kokkos/compare/3.2.00...3.2.01)
@ -36,37 +142,31 @@
- Windows Cuda support [\#3018](https://github.com/kokkos/kokkos/issues/3018)
- Pass `-Wext-lambda-captures-this` to NVCC when support for `__host__ __device__` lambda is enabled from CUDA 11 [\#3241](https://github.com/kokkos/kokkos/issues/3241)
- Use explicit staging buffer for constant memory kernel launches and cleanup host/device synchronization [\#3234](https://github.com/kokkos/kokkos/issues/3234)
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 1: [\#3202](https://github.com/kokkos/kokkos/issues/3202)
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 2: [\#3203](https://github.com/kokkos/kokkos/issues/3203)
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable 3: [\#3196](https://github.com/kokkos/kokkos/issues/3196)
- Various fixup to policies including making TeamPolicy default constructible and making RangePolicy and TeamPolicy assignable: [\#3202](https://github.com/kokkos/kokkos/issues/3202) , [\#3203](https://github.com/kokkos/kokkos/issues/3203) , [\#3196](https://github.com/kokkos/kokkos/issues/3196)
- Annotations for `DefaultExectutionSpace` and `DefaultHostExectutionSpace` to use in static analysis [\#3189](https://github.com/kokkos/kokkos/issues/3189)
- Add documentation on using Spack to install Kokkos and developing packages that depend on Kokkos [\#3187](https://github.com/kokkos/kokkos/issues/3187)
- Improve support for nvcc\_wrapper with exotic host compiler [\#3186](https://github.com/kokkos/kokkos/issues/3186)
- Add OpenMPTarget backend flags for NVC++ compiler [\#3185](https://github.com/kokkos/kokkos/issues/3185)
- Move deep\_copy/create\_mirror\_view on Experimental::OffsetView into Kokkos:: namespace [\#3166](https://github.com/kokkos/kokkos/issues/3166)
- Allow for larger block size in HIP [\#3165](https://github.com/kokkos/kokkos/issues/3165)
- View: Added names of Views to the different View initialize/free kernels [\#3159](https://github.com/kokkos/kokkos/issues/3159)
- Cuda: Caching cudaFunctorAttributes and whether L1/Shmem prefer was set [\#3151](https://github.com/kokkos/kokkos/issues/3151)
- BuildSystem: Provide an explicit default CMAKE\_BUILD\_TYPE [\#3131](https://github.com/kokkos/kokkos/issues/3131)
- BuildSystem: Improved performance in default configuration by defaulting to Release build [\#3131](https://github.com/kokkos/kokkos/issues/3131)
- Cuda: Update CUDA occupancy calculation [\#3124](https://github.com/kokkos/kokkos/issues/3124)
- Vector: Adding data() to Vector [\#3123](https://github.com/kokkos/kokkos/issues/3123)
- BuildSystem: Add CUDA Ampere configuration support [\#3122](https://github.com/kokkos/kokkos/issues/3122)
- General: Apply [[noreturn]] to Kokkos::abort when applicable [\#3106](https://github.com/kokkos/kokkos/issues/3106)
- TeamPolicy: Validate storage level argument passed to TeamPolicy::set\_scratch\_size() [\#3098](https://github.com/kokkos/kokkos/issues/3098)
- nvcc\_wrapper: send --cudart to nvcc instead of host compiler [\#3092](https://github.com/kokkos/kokkos/issues/3092)
- BuildSystem: Make kokkos\_has\_string() function in Makefile.kokkos case insensitive [\#3091](https://github.com/kokkos/kokkos/issues/3091)
- Modify KOKKOS\_FUNCTION macro for clang-tidy analysis [\#3087](https://github.com/kokkos/kokkos/issues/3087)
- Move allocation profiling to allocate/deallocate calls [\#3084](https://github.com/kokkos/kokkos/issues/3084)
- BuildSystem: FATAL\_ERROR when attempting in-source build [\#3082](https://github.com/kokkos/kokkos/issues/3082)
- Change enums in ScatterView to types [\#3076](https://github.com/kokkos/kokkos/issues/3076)
- HIP: Changes for new compiler/runtime [\#3067](https://github.com/kokkos/kokkos/issues/3067)
- Extract and use get\_gpu [\#3061](https://github.com/kokkos/kokkos/issues/3061)
- Extract and use get\_gpu [\#3048](https://github.com/kokkos/kokkos/issues/3048)
- Extract and use get\_gpu [\#3061](https://github.com/kokkos/kokkos/issues/3061) , [\#3048](https://github.com/kokkos/kokkos/issues/3048)
- Add is\_allocated to View-like containers [\#3059](https://github.com/kokkos/kokkos/issues/3059)
- Combined reducers for scalar references [\#3052](https://github.com/kokkos/kokkos/issues/3052)
- Add configurable capacity for UniqueToken [\#3051](https://github.com/kokkos/kokkos/issues/3051)
- Add installation testing [\#3034](https://github.com/kokkos/kokkos/issues/3034)
- BuildSystem: Add -expt-relaxed-constexpr flag to nvcc\_wrapper [\#3021](https://github.com/kokkos/kokkos/issues/3021)
- HIP: Add UniqueToken [\#3020](https://github.com/kokkos/kokkos/issues/3020)
- Autodetect number of devices [\#3013](https://github.com/kokkos/kokkos/issues/3013)
@ -82,11 +182,13 @@
- ScatterView: fix for OpenmpTarget remove inheritance from reducers [\#3162](https://github.com/kokkos/kokkos/issues/3162)
- BuildSystem: Set OpenMP flags according to host compiler [\#3127](https://github.com/kokkos/kokkos/issues/3127)
- OpenMP: Fix logic for nested omp in partition\_master bug [\#3101](https://github.com/kokkos/kokkos/issues/3101)
- nvcc\_wrapper: send --cudart to nvcc instead of host compiler [\#3092](https://github.com/kokkos/kokkos/issues/3092)
- BuildSystem: Fixes for Cuda/11 and c++17 [\#3085](https://github.com/kokkos/kokkos/issues/3085)
- HIP: Fix print\_configuration [\#3080](https://github.com/kokkos/kokkos/issues/3080)
- Conditionally define get\_gpu [\#3072](https://github.com/kokkos/kokkos/issues/3072)
- Fix bounds for ranges in random number generator [\#3069](https://github.com/kokkos/kokkos/issues/3069)
- Fix Cuda minor arch check [\#3035](https://github.com/kokkos/kokkos/issues/3035)
- BuildSystem: Add -expt-relaxed-constexpr flag to nvcc\_wrapper [\#3021](https://github.com/kokkos/kokkos/issues/3021)
**Incompatibilities:**

17
lib/kokkos/CMakeLists.txt
View File

@ -111,7 +111,7 @@ ENDIF()
set(Kokkos_VERSION_MAJOR 3)
set(Kokkos_VERSION_MINOR 2)
set(Kokkos_VERSION_MINOR 3)
set(Kokkos_VERSION_PATCH 1)
set(Kokkos_VERSION "${Kokkos_VERSION_MAJOR}.${Kokkos_VERSION_MINOR}.${Kokkos_VERSION_PATCH}")
math(EXPR KOKKOS_VERSION "${Kokkos_VERSION_MAJOR} * 10000 + ${Kokkos_VERSION_MINOR} * 100 + ${Kokkos_VERSION_PATCH}")
@ -139,13 +139,15 @@ ENDIF()
# I really wish these were regular variables
# but scoping issues can make it difficult
GLOBAL_SET(KOKKOS_COMPILE_OPTIONS)
GLOBAL_SET(KOKKOS_LINK_OPTIONS)
GLOBAL_SET(KOKKOS_LINK_OPTIONS -DKOKKOS_DEPENDENCE)
GLOBAL_SET(KOKKOS_CUDA_OPTIONS)
GLOBAL_SET(KOKKOS_CUDAFE_OPTIONS)
GLOBAL_SET(KOKKOS_XCOMPILER_OPTIONS)
# We need to append text here for making sure TPLs
# we import are available for an installed Kokkos
GLOBAL_SET(KOKKOS_TPL_EXPORTS)
# this could probably be scoped to project
GLOBAL_SET(KOKKOS_COMPILE_DEFINITIONS KOKKOS_DEPENDENCE)
# Include a set of Kokkos-specific wrapper functions that
# will either call raw CMake or TriBITS
@ -191,8 +193,6 @@ ELSE()
SET(KOKKOS_IS_SUBDIRECTORY FALSE)
ENDIF()
#------------------------------------------------------------------------------
#
# A) Forward declare the package so that certain options are also defined for
@ -253,9 +253,7 @@ KOKKOS_PROCESS_SUBPACKAGES()
KOKKOS_PACKAGE_DEF()
KOKKOS_EXCLUDE_AUTOTOOLS_FILES()
KOKKOS_PACKAGE_POSTPROCESS()
#We are ready to configure the header
CONFIGURE_FILE(cmake/KokkosCore_config.h.in KokkosCore_config.h @ONLY)
KOKKOS_CONFIGURE_CORE()
IF (NOT KOKKOS_HAS_TRILINOS AND NOT Kokkos_INSTALL_TESTING)
ADD_LIBRARY(kokkos INTERFACE)
@ -272,7 +270,10 @@ INCLUDE(${KOKKOS_SRC_PATH}/cmake/kokkos_install.cmake)
# executables also need nvcc_wrapper. Thus, we need to install it.
# If the argument of DESTINATION is a relative path, CMake computes it
# as relative to ${CMAKE_INSTALL_PATH}.
INSTALL(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper DESTINATION ${CMAKE_INSTALL_BINDIR})
# KOKKOS_INSTALL_ADDITIONAL_FILES will install nvcc wrapper and other generated
# files
KOKKOS_INSTALL_ADDITIONAL_FILES()
# Finally - if we are a subproject - make sure the enabled devices are visible
IF (HAS_PARENT)

106
lib/kokkos/Makefile.kokkos
View File

@ -11,27 +11,27 @@ CXXFLAGS += $(SHFLAGS)
endif
KOKKOS_VERSION_MAJOR = 3
KOKKOS_VERSION_MINOR = 2
KOKKOS_VERSION_MINOR = 3
KOKKOS_VERSION_PATCH = 1
KOKKOS_VERSION = $(shell echo $(KOKKOS_VERSION_MAJOR)*10000+$(KOKKOS_VERSION_MINOR)*100+$(KOKKOS_VERSION_PATCH) | bc)
# Options: Cuda,HIP,ROCm,OpenMP,Pthread,Serial
# Options: Cuda,HIP,OpenMP,Pthread,Serial
KOKKOS_DEVICES ?= "OpenMP"
#KOKKOS_DEVICES ?= "Pthread"
# Options:
# Intel: KNC,KNL,SNB,HSW,BDW,SKX
# NVIDIA: Kepler,Kepler30,Kepler32,Kepler35,Kepler37,Maxwell,Maxwell50,Maxwell52,Maxwell53,Pascal60,Pascal61,Volta70,Volta72,Turing75,Ampere80
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2
# ARM: ARMv80,ARMv81,ARMv8-ThunderX,ARMv8-TX2,A64FX
# IBM: BGQ,Power7,Power8,Power9
# AMD-GPUS: Vega900,Vega906
# AMD-GPUS: Vega900,Vega906,Vega908
# AMD-CPUS: AMDAVX,Zen,Zen2
KOKKOS_ARCH ?= ""
# Options: yes,no
KOKKOS_DEBUG ?= "no"
# Options: hwloc,librt,experimental_memkind
KOKKOS_USE_TPLS ?= ""
# Options: c++11,c++14,c++1y,c++17,c++1z,c++2a
KOKKOS_CXX_STANDARD ?= "c++11"
# Options: c++14,c++1y,c++17,c++1z,c++2a
KOKKOS_CXX_STANDARD ?= "c++14"
# Options: aggressive_vectorization,disable_profiling,enable_large_mem_tests,disable_complex_align
KOKKOS_OPTIONS ?= ""
KOKKOS_CMAKE ?= "no"
@ -66,7 +66,6 @@ kokkos_path_exists=$(if $(wildcard $1),1,0)
# Check for general settings
KOKKOS_INTERNAL_ENABLE_DEBUG := $(call kokkos_has_string,$(KOKKOS_DEBUG),yes)
KOKKOS_INTERNAL_ENABLE_CXX11 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++11)
KOKKOS_INTERNAL_ENABLE_CXX14 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++14)
KOKKOS_INTERNAL_ENABLE_CXX1Y := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++1y)
KOKKOS_INTERNAL_ENABLE_CXX17 := $(call kokkos_has_string,$(KOKKOS_CXX_STANDARD),c++17)
@ -279,14 +278,12 @@ else
endif
endif
# Set C++11 flags.
# Set C++ version flags.
ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1)
KOKKOS_INTERNAL_CXX11_FLAG := --c++11
KOKKOS_INTERNAL_CXX14_FLAG := --c++14
KOKKOS_INTERNAL_CXX17_FLAG := --c++17
else
ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1)
KOKKOS_INTERNAL_CXX11_FLAG := -std=c++11
KOKKOS_INTERNAL_CXX14_FLAG := -std=c++14
KOKKOS_INTERNAL_CXX1Y_FLAG := -std=c++1y
#KOKKOS_INTERNAL_CXX17_FLAG := -std=c++17
@ -294,17 +291,12 @@ else
#KOKKOS_INTERNAL_CXX2A_FLAG := -std=c++2a
else
ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1)
KOKKOS_INTERNAL_CXX11_FLAG := -hstd=c++11
KOKKOS_INTERNAL_CXX14_FLAG := -hstd=c++14
#KOKKOS_INTERNAL_CXX1Y_FLAG := -hstd=c++1y
#KOKKOS_INTERNAL_CXX17_FLAG := -hstd=c++17
#KOKKOS_INTERNAL_CXX1Z_FLAG := -hstd=c++1z
#KOKKOS_INTERNAL_CXX2A_FLAG := -hstd=c++2a
else
ifeq ($(KOKKOS_INTERNAL_COMPILER_HCC), 1)
KOKKOS_INTERNAL_CXX11_FLAG :=
else
KOKKOS_INTERNAL_CXX11_FLAG := --std=c++11
KOKKOS_INTERNAL_CXX14_FLAG := --std=c++14
KOKKOS_INTERNAL_CXX1Y_FLAG := --std=c++1y
KOKKOS_INTERNAL_CXX17_FLAG := --std=c++17
@ -313,7 +305,6 @@ else
endif
endif
endif
endif
# Check for Kokkos Architecture settings.
@ -377,7 +368,8 @@ KOKKOS_INTERNAL_USE_ARCH_ARMV80 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8
KOKKOS_INTERNAL_USE_ARCH_ARMV81 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv81)
KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-ThunderX)
KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2 := $(call kokkos_has_string,$(KOKKOS_ARCH),ARMv8-TX2)
KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2) | bc))
KOKKOS_INTERNAL_USE_ARCH_A64FX := $(call kokkos_has_string,$(KOKKOS_ARCH),A64FX)
KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX2)+$(KOKKOS_INTERNAL_USE_ARCH_A64FX) | bc))
# IBM based.
KOKKOS_INTERNAL_USE_ARCH_BGQ := $(call kokkos_has_string,$(KOKKOS_ARCH),BGQ)
@ -392,6 +384,7 @@ KOKKOS_INTERNAL_USE_ARCH_ZEN2 := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen2)
KOKKOS_INTERNAL_USE_ARCH_ZEN := $(call kokkos_has_string,$(KOKKOS_ARCH),Zen)
KOKKOS_INTERNAL_USE_ARCH_VEGA900 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega900)
KOKKOS_INTERNAL_USE_ARCH_VEGA906 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega906)
KOKKOS_INTERNAL_USE_ARCH_VEGA908 := $(call kokkos_has_string,$(KOKKOS_ARCH),Vega908)
# Any AVX?
KOKKOS_INTERNAL_USE_ARCH_SSE42 := $(shell expr $(KOKKOS_INTERNAL_USE_ARCH_WSM))
@ -459,7 +452,6 @@ H := \#
# Do not append first line
tmp := $(shell echo "/* ---------------------------------------------" > KokkosCore_config.tmp)
tmp := $(call kokkos_append_header,"Makefile constructed configuration:")
tmp := $(call kokkos_append_header,"$(shell date)")
tmp := $(call kokkos_append_header,"----------------------------------------------*/")
tmp := $(call kokkos_append_header,'$H''if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H)')
@ -479,10 +471,6 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_COMPILER_CUDA_VERSION $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION)")
endif
ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_ROCM')
tmp := $(call kokkos_append_header,'$H''define KOKKOS_IMPL_ROCM_CLANG_WORKAROUND 1')
endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
tmp := $(call kokkos_append_header,'$H''define KOKKOS_ENABLE_HIP')
endif
@ -542,12 +530,6 @@ endif
#only add the c++ standard flags if this is not CMake
tmp := $(call kokkos_append_header,"/* General Settings */")
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX11), 1)
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX11_FLAG)
endif
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ENABLE_CXX11")
endif
ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX14), 1)
ifneq ($(KOKKOS_STANDALONE_CMAKE), yes)
KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CXX14_FLAG)
@ -765,6 +747,13 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV81), 1)
endif
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_A64FX), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_A64FX")
KOKKOS_CXXFLAGS += -march=armv8.2-a+sve
KOKKOS_LDFLAGS += -march=armv8.2-a+sve
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ZEN), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_ZEN")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_AMD_AVX2")
@ -1143,6 +1132,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA906")
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx906
endif
ifeq ($(KOKKOS_INTERNAL_USE_ARCH_VEGA908), 1)
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_HIP 908")
tmp := $(call kokkos_append_header,"$H""define KOKKOS_ARCH_VEGA908")
KOKKOS_INTERNAL_HIP_ARCH_FLAG := --amdgpu-target=gfx908
endif
KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.cpp)
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/HIP/*.hpp)
@ -1173,6 +1168,55 @@ ifneq ($(KOKKOS_INTERNAL_NEW_CONFIG), 0)
tmp := $(shell cp KokkosCore_config.tmp KokkosCore_config.h)
endif
# Functions for generating config header file
kokkos_start_config_header = $(shell sed 's~@INCLUDE_NEXT_FILE@~~g' $(KOKKOS_PATH)/cmake/KokkosCore_Config_HeaderSet.in > $1)
kokkos_update_config_header = $(shell sed 's~@HEADER_GUARD_TAG@~$1~g' $2 > $3)
kokkos_append_config_header = $(shell echo $1 >> $2))
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_FwdBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_SetupBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_DeclareBackend.tmp")
tmp := $(call kokkos_start_config_header, "KokkosCore_Config_PostInclude.tmp")
tmp := $(call kokkos_update_config_header, KOKKOS_FWD_HPP_, "KokkosCore_Config_FwdBackend.tmp", "KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_SETUP_HPP_, "KokkosCore_Config_SetupBackend.tmp", "KokkosCore_Config_SetupBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_DECLARE_HPP_, "KokkosCore_Config_DeclareBackend.tmp", "KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_update_config_header, KOKKOS_POST_INCLUDE_HPP_, "KokkosCore_Config_PostInclude.tmp", "KokkosCore_Config_PostInclude.hpp")
ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_CUDA.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_CUDA.hpp>","KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <setup/Kokkos_Setup_Cuda.hpp>","KokkosCore_Config_SetupBackend.hpp")
ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1)
else
endif
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1)
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_OPENMPTARGET.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_OPENMPTARGET.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_HIP.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_HIP.hpp>","KokkosCore_Config_DeclareBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <setup/Kokkos_Setup_HIP.hpp>","KokkosCore_Config_SetupBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1)
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_OPENMP.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_OPENMP.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_THREADS.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_THREADS.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_HPX), 1)
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_HPX.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_HPX.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_SERIAL.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_SERIAL.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1)
tmp := $(call kokkos_append_config_header,"\#include <fwd/Kokkos_Fwd_HBWSpace.hpp>","KokkosCore_Config_FwdBackend.hpp")
tmp := $(call kokkos_append_config_header,"\#include <decl/Kokkos_Declare_HBWSpace.hpp>","KokkosCore_Config_DeclareBackend.hpp")
endif
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/*.hpp)
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/impl/*.hpp)
KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/containers/src/*.hpp)
@ -1290,7 +1334,7 @@ ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1)
endif
# With Cygwin functions such as fdopen and fileno are not defined
# when strict ansi is enabled. strict ansi gets enabled with --std=c++11
# when strict ansi is enabled. strict ansi gets enabled with --std=c++14
# though. So we hard undefine it here. Not sure if that has any bad side effects
# This is needed for gtest actually, not for Kokkos itself!
ifeq ($(KOKKOS_INTERNAL_OS_CYGWIN), 1)
@ -1313,7 +1357,9 @@ KOKKOS_OBJ_LINK = $(notdir $(KOKKOS_OBJ))
include $(KOKKOS_PATH)/Makefile.targets
kokkos-clean:
rm -f $(KOKKOS_OBJ_LINK) KokkosCore_config.h KokkosCore_config.tmp libkokkos.a
rm -f $(KOKKOS_OBJ_LINK) KokkosCore_config.h KokkosCore_config.tmp libkokkos.a KokkosCore_Config_SetupBackend.hpp \
KokkosCore_Config_FwdBackend.hpp KokkosCore_Config_DeclareBackend.hpp KokkosCore_Config_DeclareBackend.tmp \
KokkosCore_Config_FwdBackend.tmp KokkosCore_Config_PostInclude.hpp KokkosCore_Config_PostInclude.tmp KokkosCore_Config_SetupBackend.tmp
libkokkos.a: $(KOKKOS_OBJ_LINK) $(KOKKOS_SRC) $(KOKKOS_HEADERS)
ar cr libkokkos.a $(KOKKOS_OBJ_LINK)

13
lib/kokkos/Makefile.targets
View File

@ -53,23 +53,10 @@ Kokkos_HIP_Space.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Space.cpp
Kokkos_HIP_Instance.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Instance.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Instance.cpp
Kokkos_HIP_KernelLaunch.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_KernelLaunch.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_KernelLaunch.cpp
Kokkos_HIP_Locks.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Locks.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/HIP/Kokkos_HIP_Locks.cpp
endif
ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
Kokkos_ROCm_Exec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Exec.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Exec.cpp
Kokkos_ROCm_Space.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Space.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Space.cpp
Kokkos_ROCm_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Task.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Task.cpp
Kokkos_ROCm_Impl.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/ROCm/Kokkos_ROCm_Impl.cpp
endif
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
Kokkos_ThreadsExec_base.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec_base.cpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/Threads/Kokkos_ThreadsExec_base.cpp

16
lib/kokkos/README.md
View File

@ -54,24 +54,16 @@ For specifics see the LICENSE file contained in the repository or distribution.
# Requirements
### Primary tested compilers on X86 are:
* GCC 4.8.4
* GCC 4.9.3
* GCC 5.1.0
* GCC 5.3.0
* GCC 5.4.0
* GCC 5.5.0
* GCC 6.1.0
* GCC 7.2.0
* GCC 7.3.0
* GCC 8.1.0
* Intel 15.0.2
* Intel 16.0.1
* Intel 17.0.1
* Intel 17.4.196
* Intel 18.2.128
* Clang 3.6.1
* Clang 3.7.1
* Clang 3.8.1
* Clang 3.9.0
* Clang 4.0.0
* Clang 6.0.0 for CUDA (CUDA Toolkit 9.0)
* Clang 7.0.0 for CUDA (CUDA Toolkit 9.1)
@ -81,6 +73,7 @@ For specifics see the LICENSE file contained in the repository or distribution.
* NVCC 9.2 for CUDA (with gcc 7.2.0)
* NVCC 10.0 for CUDA (with gcc 7.4.0)
* NVCC 10.1 for CUDA (with gcc 7.4.0)
* NVCC 11.0 for CUDA (with gcc 8.4.0)
### Primary tested compilers on Power 8 are:
* GCC 6.4.0 (OpenMP,Serial)
@ -89,9 +82,8 @@ For specifics see the LICENSE file contained in the repository or distribution.
* NVCC 9.2.88 for CUDA (with gcc 7.2.0 and XL 16.1.0)
### Primary tested compilers on Intel KNL are:
* Intel 16.4.258 (with gcc 4.7.2)
* Intel 17.2.174 (with gcc 4.9.3)
* Intel 18.2.199 (with gcc 4.9.3)
* Intel 17.2.174 (with gcc 6.2.0 and 6.4.0)
* Intel 18.2.199 (with gcc 6.2.0 and 6.4.0)
### Primary tested compilers on ARM (Cavium ThunderX2)
* GCC 7.2.0

4
lib/kokkos/algorithms/src/Kokkos_Random.hpp
View File

@ -806,7 +806,7 @@ class Random_XorShift64 {
const double V = 2.0 * drand() - 1.0;
S = U * U + V * V;
}
return U * std::sqrt(-2.0 * log(S) / S);
return U * std::sqrt(-2.0 * std::log(S) / S);
}
KOKKOS_INLINE_FUNCTION
@ -1042,7 +1042,7 @@ class Random_XorShift1024 {
const double V = 2.0 * drand() - 1.0;
S = U * U + V * V;
}
return U * std::sqrt(-2.0 * log(S) / S);
return U * std::sqrt(-2.0 * std::log(S) / S);
}
KOKKOS_INLINE_FUNCTION

6
lib/kokkos/algorithms/src/Kokkos_Sort.hpp
View File

@ -222,11 +222,11 @@ class BinSort {
"Kokkos::SortImpl::BinSortFunctor::bin_count", bin_op.max_bins());
bin_count_const = bin_count_atomic;
bin_offsets =
offset_type(ViewAllocateWithoutInitializing(
offset_type(view_alloc(WithoutInitializing,
"Kokkos::SortImpl::BinSortFunctor::bin_offsets"),
bin_op.max_bins());
sort_order =
offset_type(ViewAllocateWithoutInitializing(
offset_type(view_alloc(WithoutInitializing,
"Kokkos::SortImpl::BinSortFunctor::sort_order"),
range_end - range_begin);
}
@ -279,7 +279,7 @@ class BinSort {
}
scratch_view_type sorted_values(
ViewAllocateWithoutInitializing(
view_alloc(WithoutInitializing,
"Kokkos::SortImpl::BinSortFunctor::sorted_values"),
values.rank_dynamic > 0 ? len : KOKKOS_IMPL_CTOR_DEFAULT_ARG,
values.rank_dynamic > 1 ? values.extent(1)

2
lib/kokkos/algorithms/unit_tests/CMakeLists.txt
View File

@ -24,7 +24,7 @@ KOKKOS_ADD_TEST_LIBRARY(
# avoid deprecation warnings from MSVC
TARGET_COMPILE_DEFINITIONS(kokkosalgorithms_gtest PUBLIC GTEST_HAS_TR1_TUPLE=0 GTEST_HAS_PTHREAD=0)
IF(NOT (Kokkos_ENABLE_CUDA AND WIN32))
IF((NOT (Kokkos_ENABLE_CUDA AND WIN32)) AND (NOT ("${KOKKOS_CXX_COMPILER_ID}" STREQUAL "Fujitsu")))
TARGET_COMPILE_FEATURES(kokkosalgorithms_gtest PUBLIC cxx_std_11)
ENDIF()

16
lib/kokkos/algorithms/unit_tests/Makefile
View File

@ -31,10 +31,10 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1)
TEST_TARGETS += test-cuda
endif
ifeq ($(KOKKOS_INTERNAL_USE_ROCM), 1)
OBJ_ROCM = TestROCm.o UnitTestMain.o gtest-all.o
TARGETS += KokkosAlgorithms_UnitTest_ROCm
TEST_TARGETS += test-rocm
ifeq ($(KOKKOS_INTERNAL_USE_HIP), 1)
OBJ_HIP = TestHIP.o UnitTestMain.o gtest-all.o
TARGETS += KokkosAlgorithms_UnitTest_HIP
TEST_TARGETS += test-hip
endif
ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 1)
@ -64,8 +64,8 @@ endif
KokkosAlgorithms_UnitTest_Cuda: $(OBJ_CUDA) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(EXTRA_PATH) $(OBJ_CUDA) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Cuda
KokkosAlgorithms_UnitTest_ROCm: $(OBJ_ROCM) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(EXTRA_PATH) $(OBJ_ROCM) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_ROCm
KokkosAlgorithms_UnitTest_HIP: $(OBJ_HIP) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(EXTRA_PATH) $(OBJ_HIP) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_HIP
KokkosAlgorithms_UnitTest_Threads: $(OBJ_THREADS) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(EXTRA_PATH) $(OBJ_THREADS) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Threads
@ -82,8 +82,8 @@ KokkosAlgorithms_UnitTest_Serial: $(OBJ_SERIAL) $(KOKKOS_LINK_DEPENDS)
test-cuda: KokkosAlgorithms_UnitTest_Cuda
./KokkosAlgorithms_UnitTest_Cuda
test-rocm: KokkosAlgorithms_UnitTest_ROCm
./KokkosAlgorithms_UnitTest_ROCm
test-hip: KokkosAlgorithms_UnitTest_HIP
./KokkosAlgorithms_UnitTest_HIP
test-threads: KokkosAlgorithms_UnitTest_Threads
./KokkosAlgorithms_UnitTest_Threads

41
lib/kokkos/benchmarks/atomic/Makefile
View File

@ -1,31 +1,38 @@
KOKKOS_PATH = ${HOME}/kokkos
KOKKOS_DEVICES = "OpenMP"
KOKKOS_ARCH = "SNB"
EXE_NAME = "test"
KOKKOS_DEVICES=Cuda
KOKKOS_CUDA_OPTIONS=enable_lambda
KOKKOS_ARCH = "SNB,Volta70"
SRC = $(wildcard *.cpp)
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
ifndef KOKKOS_PATH
KOKKOS_PATH = $(MAKEFILE_PATH)../..
endif
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
vpath %.cpp $(sort $(dir $(SRC)))
default: build
echo "Start Build"
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
EXE = ${EXE_NAME}.cuda
KOKKOS_CUDA_OPTIONS = "enable_lambda"
EXE = atomic_perf.cuda
else
CXX = g++
EXE = ${EXE_NAME}.host
EXE = atomic_perf.exe
endif
CXXFLAGS = -O3
LINK = ${CXX}
LINKFLAGS = -O3
CXXFLAGS ?= -O3 -g
override CXXFLAGS += -I$(MAKEFILE_PATH)
DEPFLAGS = -M
LINK = ${CXX}
LINKFLAGS =
OBJ = $(SRC:.cpp=.o)
OBJ = $(notdir $(SRC:.cpp=.o))
LIB =
include $(KOKKOS_PATH)/Makefile.kokkos
@ -36,9 +43,9 @@ $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
clean: kokkos-clean
rm -f *.o *.cuda *.host
rm -f *.o atomic_perf.cuda atomic_perf.exe
# Compilation rules
%.o:%.cpp $(KOKKOS_CPP_DEPENDS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)

2
lib/kokkos/benchmarks/benchmark_suite/scripts/run_tests.bash
View File

@ -9,7 +9,7 @@ if [[ ${USE_CUDA} > 0 ]]; then
BAF_EXE=bytes_and_flops.cuda
TEAM_SIZE=256
else
BAF_EXE=bytes_and_flops.host
BAF_EXE=bytes_and_flops.exe
TEAM_SIZE=1
fi

4
lib/kokkos/benchmarks/bytes_and_flops/Makefile
View File

@ -1,6 +1,6 @@
KOKKOS_DEVICES=Cuda
KOKKOS_CUDA_OPTIONS=enable_lambda
KOKKOS_ARCH = "SNB,Kepler35"
KOKKOS_ARCH = "SNB,Volta70"
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
@ -22,7 +22,7 @@ CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
EXE = bytes_and_flops.cuda
else
CXX = g++
EXE = bytes_and_flops.host
EXE = bytes_and_flops.exe
endif
CXXFLAGS ?= -O3 -g

33
lib/kokkos/benchmarks/gather/Makefile
View File

@ -1,7 +1,18 @@
KOKKOS_PATH = ${HOME}/kokkos
SRC = $(wildcard *.cpp)
KOKKOS_DEVICES=Cuda
KOKKOS_CUDA_OPTIONS=enable_lambda
KOKKOS_ARCH = "SNB,Volta70"
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
ifndef KOKKOS_PATH
KOKKOS_PATH = $(MAKEFILE_PATH)../..
endif
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
vpath %.cpp $(sort $(dir $(SRC)))
default: build
echo "Start Build"
@ -9,36 +20,32 @@ default: build
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
EXE = gather.cuda
KOKKOS_DEVICES = "Cuda,OpenMP"
KOKKOS_ARCH = "SNB,Kepler35"
else
CXX = g++
EXE = gather.host
KOKKOS_DEVICES = "OpenMP"
KOKKOS_ARCH = "SNB"
EXE = gather.exe
endif
CXXFLAGS = -O3 -g
CXXFLAGS ?= -O3 -g
override CXXFLAGS += -I$(MAKEFILE_PATH)
DEPFLAGS = -M
LINK = ${CXX}
LINKFLAGS =
OBJ = $(SRC:.cpp=.o)
OBJ = $(notdir $(SRC:.cpp=.o))
LIB =
include $(KOKKOS_PATH)/Makefile.kokkos
$(warning ${KOKKOS_CPPFLAGS})
build: $(EXE)
$(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
clean: kokkos-clean
rm -f *.o *.cuda *.host
rm -f *.o gather.cuda gather.exe
# Compilation rules
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) gather_unroll.hpp gather.hpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)

46
lib/kokkos/benchmarks/gups/Makefile
View File

@ -1,28 +1,38 @@
#Set your Kokkos path to something appropriate
KOKKOS_PATH = ${HOME}/git/kokkos-github-repo
KOKKOS_DEVICES = "Cuda"
KOKKOS_ARCH = "Pascal60"
KOKKOS_DEVICES=Cuda
KOKKOS_CUDA_OPTIONS=enable_lambda
#KOKKOS_DEVICES = "OpenMP"
#KOKKOS_ARCH = "Power8"
KOKKOS_ARCH = "SNB,Volta70"
SRC = gups-kokkos.cc
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
ifndef KOKKOS_PATH
KOKKOS_PATH = $(MAKEFILE_PATH)../..
endif
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
vpath %.cpp $(sort $(dir $(SRC)))
default: build
echo "Start Build"
CXXFLAGS = -O3
CXX = ${HOME}/git/kokkos-github-repo/bin/nvcc_wrapper
#CXX = g++
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
EXE = gups.cuda
else
CXX = g++
EXE = gups.exe
endif
LINK = ${CXX}
LINKFLAGS =
EXE = gups-kokkos
CXXFLAGS ?= -O3 -g
override CXXFLAGS += -I$(MAKEFILE_PATH)
DEPFLAGS = -M
LINK = ${CXX}
LINKFLAGS =
OBJ = $(SRC:.cc=.o)
OBJ = $(notdir $(SRC:.cpp=.o))
LIB =
include $(KOKKOS_PATH)/Makefile.kokkos
@ -33,9 +43,9 @@ $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
clean: kokkos-clean
rm -f *.o $(EXE)
rm -f *.o gups.cuda gups.exe
# Compilation rules
%.o:%.cc $(KOKKOS_CPP_DEPENDS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)

0
lib/kokkos/benchmarks/gups/gups-kokkos.cc → lib/kokkos/benchmarks/gups/gups-kokkos.cpp
View File

47
lib/kokkos/benchmarks/policy_performance/Makefile
View File

@ -1,31 +1,38 @@
KOKKOS_PATH = ../..
SRC = $(wildcard *.cpp)
KOKKOS_DEVICES=Cuda
KOKKOS_CUDA_OPTIONS=enable_lambda
KOKKOS_ARCH = "SNB,Volta70"
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
ifndef KOKKOS_PATH
KOKKOS_PATH = $(MAKEFILE_PATH)../..
endif
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
vpath %.cpp $(sort $(dir $(SRC)))
default: build
echo "Start Build"
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
CXXFLAGS = -O3 -g
LINK = ${CXX}
LINKFLAGS =
EXE = policy_performance.cuda
KOKKOS_DEVICES = "Cuda,OpenMP"
KOKKOS_ARCH = "SNB,Kepler35"
KOKKOS_CUDA_OPTIONS+=enable_lambda
EXE = policy_perf.cuda
else
CXX = g++
CXXFLAGS = -O3 -g -Wall -Werror
LINK = ${CXX}
LINKFLAGS =
EXE = policy_performance.host
KOKKOS_DEVICES = "OpenMP"
KOKKOS_ARCH = "SNB"
EXE = policy_perf.exe
endif
DEPFLAGS = -M
CXXFLAGS ?= -O3 -g
override CXXFLAGS += -I$(MAKEFILE_PATH)
OBJ = $(SRC:.cpp=.o)
DEPFLAGS = -M
LINK = ${CXX}
LINKFLAGS =
OBJ = $(notdir $(SRC:.cpp=.o))
LIB =
include $(KOKKOS_PATH)/Makefile.kokkos
@ -36,9 +43,9 @@ $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
clean: kokkos-clean
rm -f *.o *.cuda *.host
rm -f *.o policy_perf.cuda policy_perf.exe
# Compilation rules
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) main.cpp policy_perf_test.hpp
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)

6
lib/kokkos/benchmarks/policy_performance/main.cpp
View File

@ -146,11 +146,11 @@ int main(int argc, char* argv[]) {
// Call a 'warmup' test with 1 repeat - this will initialize the corresponding
// view appropriately for test and should obey first-touch etc Second call to
// test is the one we actually care about and time
view_type_1d v_1(Kokkos::ViewAllocateWithoutInitializing("v_1"),
view_type_1d v_1(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_1"),
team_range * team_size);
view_type_2d v_2(Kokkos::ViewAllocateWithoutInitializing("v_2"),
view_type_2d v_2(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_2"),
team_range * team_size, thread_range);
view_type_3d v_3(Kokkos::ViewAllocateWithoutInitializing("v_3"),
view_type_3d v_3(Kokkos::view_alloc(Kokkos::WithoutInitializing, "v_3"),
team_range * team_size, thread_range, vector_range);
double result_computed = 0.0;

46
lib/kokkos/benchmarks/stream/Makefile
View File

@ -1,28 +1,38 @@
#Set your Kokkos path to something appropriate
KOKKOS_PATH = ${HOME}/git/kokkos-github-repo
#KOKKOS_DEVICES = "Cuda"
#KOKKOS_ARCH = "Pascal60"
#KOKKOS_CUDA_OPTIONS = enable_lambda
KOKKOS_DEVICES = "OpenMP"
KOKKOS_ARCH = "Power8"
KOKKOS_DEVICES=Cuda
KOKKOS_CUDA_OPTIONS=enable_lambda
KOKKOS_ARCH = "SNB,Volta70"
SRC = stream-kokkos.cc
MAKEFILE_PATH := $(subst Makefile,,$(abspath $(lastword $(MAKEFILE_LIST))))
ifndef KOKKOS_PATH
KOKKOS_PATH = $(MAKEFILE_PATH)../..
endif
SRC = $(wildcard $(MAKEFILE_PATH)*.cpp)
HEADERS = $(wildcard $(MAKEFILE_PATH)*.hpp)
vpath %.cpp $(sort $(dir $(SRC)))
default: build
echo "Start Build"
CXXFLAGS = -O3
#CXX = ${HOME}/git/kokkos-github-repo/bin/nvcc_wrapper
ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES)))
CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper
EXE = stream.cuda
else
CXX = g++
EXE = stream.exe
endif
LINK = ${CXX}
LINKFLAGS =
EXE = stream-kokkos
CXXFLAGS ?= -O3 -g
override CXXFLAGS += -I$(MAKEFILE_PATH)
DEPFLAGS = -M
LINK = ${CXX}
LINKFLAGS =
OBJ = $(SRC:.cc=.o)
OBJ = $(notdir $(SRC:.cpp=.o))
LIB =
include $(KOKKOS_PATH)/Makefile.kokkos
@ -33,9 +43,9 @@ $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE)
clean: kokkos-clean
rm -f *.o $(EXE)
rm -f *.o stream.cuda stream.exe
# Compilation rules
%.o:%.cc $(KOKKOS_CPP_DEPENDS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $<
%.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(HEADERS)
$(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -o $(notdir $@)

0
lib/kokkos/benchmarks/stream/stream-kokkos.cc → lib/kokkos/benchmarks/stream/stream-kokkos.cpp
View File

87
lib/kokkos/bin/kokkos_launch_compiler Executable file
View File

@ -0,0 +1,87 @@
#!/bin/bash -e
#
# This script allows CMAKE_CXX_COMPILER to be a standard
# C++ compiler and Kokkos sets RULE_LAUNCH_COMPILE and
# RULE_LAUNCH_LINK in CMake so that all compiler and link
# commands are prefixed with this script followed by the
# C++ compiler. Thus if $1 == $2 then we know the command
# was intended for the C++ compiler and we discard both
# $1 and $2 and redirect the command to NVCC_WRAPPER.
# If $1 != $2 then we know that the command was not intended
# for the C++ compiler and we just discard $1 and launch
# the original command. Examples of when $2 will not equal
# $1 are 'ar', 'cmake', etc. during the linking phase
#
# check the arguments for the KOKKOS_DEPENDENCE compiler definition
KOKKOS_DEPENDENCE=0
for i in ${@}
do
if [ -n "$(echo ${i} | grep 'KOKKOS_DEPENDENCE$')" ]; then
KOKKOS_DEPENDENCE=1
break
fi
done
# if C++ is not passed, someone is probably trying to invoke it directly
if [ -z "${1}" ]; then
echo -e "\n${BASH_SOURCE[0]} was invoked without the C++ compiler as the first argument."
echo "This script is not indended to be directly invoked by any mechanism other"
echo -e "than through a RULE_LAUNCH_COMPILE or RULE_LAUNCH_LINK property set in CMake\n"
exit 1
fi
# if there aren't two args, this isn't necessarily invalid, just a bit strange
if [ -z "${2}" ]; then exit 0; fi
# store the expected C++ compiler
CXX_COMPILER=${1}
# remove the expected C++ compiler from the arguments
shift
# after the above shift, $1 is now the exe for the compile or link command, e.g.
# kokkos_launch_compiler g++ gcc -c file.c -o file.o
# becomes:
# kokkos_launch_compiler gcc -c file.c -o file.o
# Check to see if the executable is the C++ compiler and if it is not, then
# just execute the command.
#
# Summary:
# kokkos_launch_compiler g++ gcc -c file.c -o file.o
# results in this command being executed:
# gcc -c file.c -o file.o
# and
# kokkos_launch_compiler g++ g++ -c file.cpp -o file.o
# results in this command being executed:
# nvcc_wrapper -c file.cpp -o file.o
if [[ "${KOKKOS_DEPENDENCE}" -eq "0" || "${CXX_COMPILER}" != "${1}" ]]; then
# the command does not depend on Kokkos so just execute the command w/o re-directing to nvcc_wrapper
eval $@
else
# the executable is the C++ compiler, so we need to re-direct to nvcc_wrapper
# find the nvcc_wrapper from the same build/install
NVCC_WRAPPER="$(dirname ${BASH_SOURCE[0]})/nvcc_wrapper"
if [ -z "${NVCC_WRAPPER}" ]; then
echo -e "\nError: nvcc_wrapper not found in $(dirname ${BASH_SOURCE[0]}).\n"
exit 1
fi
# set default nvcc wrapper compiler if not specified
: ${NVCC_WRAPPER_DEFAULT_COMPILER:=${CXX_COMPILER}}
export NVCC_WRAPPER_DEFAULT_COMPILER
# calling itself will cause an infinitely long build
if [ "${NVCC_WRAPPER}" = "${NVCC_WRAPPER_DEFAULT_COMPILER}" ]; then
echo -e "\nError: NVCC_WRAPPER == NVCC_WRAPPER_DEFAULT_COMPILER. Terminating to avoid infinite loop!\n"
exit 1
fi
# discard the compiler from the command
shift
# execute nvcc_wrapper
${NVCC_WRAPPER} $@
fi

7
lib/kokkos/bin/nvcc_wrapper
View File

@ -90,7 +90,12 @@ replace_pragma_ident=0
# Mark first host compiler argument
first_xcompiler_arg=1
# Allow for setting temp dir without setting TMPDIR in parent (see https://docs.olcf.ornl.gov/systems/summit_user_guide.html#setting-tmpdir-causes-jsm-jsrun-errors-job-state-flip-flop)
if [[ ! -z ${NVCC_WRAPPER_TMPDIR+x} ]]; then
temp_dir=${TMPDIR:-/tmp}
else
temp_dir=${NVCC_WRAPPER_TMPDIR+x}
fi
# optimization flag added as a command-line argument
optimization_flag=""
@ -194,7 +199,7 @@ do
cuda_args="$cuda_args $1"
;;
#Handle known nvcc args that have an argument
-rdc|-maxrregcount|--default-stream|-Xnvlink|--fmad|-cudart|--cudart)
-rdc|-maxrregcount|--default-stream|-Xnvlink|--fmad|-cudart|--cudart|-include)
cuda_args="$cuda_args $1 $2"
shift
;;

21
lib/kokkos/cmake/KokkosConfig.cmake.in
View File

@ -1,3 +1,9 @@
# No need for policy push/pop. CMake also manages a new entry for scripts
# loaded by include() and find_package() commands except when invoked with
# the NO_POLICY_SCOPE option
# CMP0057 + NEW -> IN_LIST operator in IF(...)
CMAKE_POLICY(SET CMP0057 NEW)
# Compute paths
@PACKAGE_INIT@
@ -12,3 +18,18 @@ GET_FILENAME_COMPONENT(Kokkos_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
INCLUDE("${Kokkos_CMAKE_DIR}/KokkosTargets.cmake")
INCLUDE("${Kokkos_CMAKE_DIR}/KokkosConfigCommon.cmake")
UNSET(Kokkos_CMAKE_DIR)
# if CUDA was enabled and separable compilation was specified, e.g.
# find_package(Kokkos COMPONENTS separable_compilation)
# then we set the RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK
IF(@Kokkos_ENABLE_CUDA@ AND NOT "separable_compilation" IN_LIST Kokkos_FIND_COMPONENTS)
# run test to see if CMAKE_CXX_COMPILER=nvcc_wrapper
kokkos_compiler_is_nvcc(IS_NVCC ${CMAKE_CXX_COMPILER})
# if not nvcc_wrapper, use RULE_LAUNCH_COMPILE and RULE_LAUNCH_LINK
IF(NOT IS_NVCC AND NOT CMAKE_CXX_COMPILER_ID STREQUAL Clang AND
(NOT DEFINED Kokkos_LAUNCH_COMPILER OR Kokkos_LAUNCH_COMPILER))
MESSAGE(STATUS "kokkos_launch_compiler is enabled globally. C++ compiler commands with -DKOKKOS_DEPENDENCE will be redirected to nvcc_wrapper")
kokkos_compilation(GLOBAL)
ENDIF()
UNSET(IS_NVCC) # be mindful of the environment, pollution is bad
ENDIF()

70
lib/kokkos/cmake/KokkosConfigCommon.cmake.in
View File

@ -89,3 +89,73 @@ function(kokkos_check)
set(${KOKKOS_CHECK_RETURN_VALUE} ${KOKKOS_CHECK_SUCCESS} PARENT_SCOPE)
endif()
endfunction()
# this function is provided to easily select which files use nvcc_wrapper:
#
# GLOBAL --> all files
# TARGET --> all files in a target
# SOURCE --> specific source files
# DIRECTORY --> all files in directory
# PROJECT --> all files/targets in a project/subproject
#
FUNCTION(kokkos_compilation)
CMAKE_PARSE_ARGUMENTS(COMP "GLOBAL;PROJECT" "" "DIRECTORY;TARGET;SOURCE" ${ARGN})
# search relative first and then absolute
SET(_HINTS "${CMAKE_CURRENT_LIST_DIR}/../.." "@CMAKE_INSTALL_PREFIX@")
# find kokkos_launch_compiler
FIND_PROGRAM(Kokkos_COMPILE_LAUNCHER
NAMES kokkos_launch_compiler
HINTS ${_HINTS}
PATHS ${_HINTS}
PATH_SUFFIXES bin)
IF(NOT Kokkos_COMPILE_LAUNCHER)
MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'")
ENDIF()
IF(COMP_GLOBAL)
# if global, don't bother setting others
SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
ELSE()
FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE)
# make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...)
IF("${_TYPE}" STREQUAL "PROJECT" AND COMP_${_TYPE})
LIST(APPEND COMP_DIRECTORY ${PROJECT_SOURCE_DIR})
UNSET(COMP_${_TYPE})
ENDIF()
# set the properties if defined
IF(COMP_${_TYPE})
# MESSAGE(STATUS "Using nvcc_wrapper :: ${_TYPE} :: ${COMP_${_TYPE}}")
SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
ENDIF()
ENDFOREACH()
ENDIF()
ENDFUNCTION()
# A test to check whether a downstream project set the C++ compiler to NVCC or not
# this is called only when Kokkos was installed with Kokkos_ENABLE_CUDA=ON
FUNCTION(kokkos_compiler_is_nvcc VAR COMPILER)
# Check if the compiler is nvcc (which really means nvcc_wrapper).
EXECUTE_PROCESS(COMMAND ${COMPILER} ${ARGN} --version
OUTPUT_VARIABLE INTERNAL_COMPILER_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE
RESULT_VARIABLE RET)
# something went wrong
IF(RET GREATER 0)
SET(${VAR} false PARENT_SCOPE)
ELSE()
STRING(REPLACE "\n" " - " INTERNAL_COMPILER_VERSION_ONE_LINE ${INTERNAL_COMPILER_VERSION} )
STRING(FIND ${INTERNAL_COMPILER_VERSION_ONE_LINE} "nvcc" INTERNAL_COMPILER_VERSION_CONTAINS_NVCC)
STRING(REGEX REPLACE "^ +" "" INTERNAL_HAVE_COMPILER_NVCC "${INTERNAL_HAVE_COMPILER_NVCC}")
IF(${INTERNAL_COMPILER_VERSION_CONTAINS_NVCC} GREATER -1)
SET(${VAR} true PARENT_SCOPE)
ELSE()
SET(${VAR} false PARENT_SCOPE)
ENDIF()
ENDIF()
ENDFUNCTION()

8
lib/kokkos/core/unit_test/cuda/TestCuda_Complex.cpp → lib/kokkos/cmake/KokkosCore_Config_HeaderSet.in
View File

@ -1,4 +1,3 @@
/*
//@HEADER
// ************************************************************************
@ -42,6 +41,9 @@
// ************************************************************************
//@HEADER
*/
#ifndef @HEADER_GUARD_TAG@
#define @HEADER_GUARD_TAG@
#include <cuda/TestCuda_Category.hpp>
#include <TestComplex.hpp>
@INCLUDE_NEXT_FILE@
#endif

4
lib/kokkos/cmake/KokkosCore_config.h.in
View File

@ -21,6 +21,7 @@
#cmakedefine KOKKOS_ENABLE_HPX
#cmakedefine KOKKOS_ENABLE_MEMKIND
#cmakedefine KOKKOS_ENABLE_LIBRT
#cmakedefine KOKKOS_ENABLE_SYCL
#ifndef __CUDA_ARCH__
#cmakedefine KOKKOS_ENABLE_TM
@ -31,7 +32,6 @@
#endif
/* General Settings */
#cmakedefine KOKKOS_ENABLE_CXX11
#cmakedefine KOKKOS_ENABLE_CXX14
#cmakedefine KOKKOS_ENABLE_CXX17
#cmakedefine KOKKOS_ENABLE_CXX20
@ -58,7 +58,7 @@
/* TPL Settings */
#cmakedefine KOKKOS_ENABLE_HWLOC
#cmakedefine KOKKOS_USE_LIBRT
#cmakedefine KOKKOS_ENABLE_HWBSPACE
#cmakedefine KOKKOS_ENABLE_HBWSPACE
#cmakedefine KOKKOS_ENABLE_LIBDL
#cmakedefine KOKKOS_IMPL_CUDA_CLANG_WORKAROUND

10
lib/kokkos/cmake/README.md
View File

@ -73,20 +73,20 @@ Compiler features are more fine-grained and require conflicting requests to be r
Suppose I have
````
add_library(A a.cpp)
target_compile_features(A PUBLIC cxx_std_11)
target_compile_features(A PUBLIC cxx_std_14)
````
then another target
````
add_library(B b.cpp)
target_compile_features(B PUBLIC cxx_std_14)
target_compile_features(B PUBLIC cxx_std_17)
target_link_libraries(A B)
````
I have requested two different features.
CMake understands the requests and knows that `cxx_std_11` is a subset of `cxx_std_14`.
CMake then picks C++14 for library `B`.
CMake understands the requests and knows that `cxx_std_14` is a subset of `cxx_std_17`.
CMake then picks C++17 for library `B`.
CMake would not have been able to do feature resolution if we had directly done:
````
target_compile_options(A PUBLIC -std=c++11)
target_compile_options(A PUBLIC -std=c++14)
````
### Adding Kokkos Options

35
lib/kokkos/cmake/deps/CUDA.cmake
View File

@ -1,14 +1,16 @@
# @HEADER
# ************************************************************************
#
# Trilinos: An Object-Oriented Solver Framework
# Copyright (2001) Sandia Corporation
# Kokkos v. 3.0
# Copyright (2020) National Technology & Engineering
# Solutions of Sandia, LLC (NTESS).
#
# Under the terms of Contract DE-NA0003525 with NTESS,
# the U.S. Government retains certain rights in this software.
#
# Copyright (2001) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
# work by or on behalf of the U.S. Government. Export of this program
# may require a license from the United States Government.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
@ -21,10 +23,10 @@
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
@ -33,22 +35,7 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# NOTICE: The United States Government is granted for itself and others
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
# license in this data to reproduce, prepare derivative works, and
# perform publicly and display publicly. Beginning five (5) years from
# July 25, 2001, the United States Government is granted for itself and
# others acting on its behalf a paid-up, nonexclusive, irrevocable
# worldwide license in this data to reproduce, prepare derivative works,
# distribute copies to the public, perform publicly and display
# publicly, and to permit others to do so.
#
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
#
# ************************************************************************
# @HEADER

35
lib/kokkos/cmake/deps/CUSPARSE.cmake
View File

@ -1,14 +1,16 @@
# @HEADER
# ************************************************************************
#
# Trilinos: An Object-Oriented Solver Framework
# Copyright (2001) Sandia Corporation
# Kokkos v. 3.0
# Copyright (2020) National Technology & Engineering
# Solutions of Sandia, LLC (NTESS).
#
# Under the terms of Contract DE-NA0003525 with NTESS,
# the U.S. Government retains certain rights in this software.
#
# Copyright (2001) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
# work by or on behalf of the U.S. Government. Export of this program
# may require a license from the United States Government.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
@ -21,10 +23,10 @@
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
@ -33,22 +35,7 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# NOTICE: The United States Government is granted for itself and others
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
# license in this data to reproduce, prepare derivative works, and
# perform publicly and display publicly. Beginning five (5) years from
# July 25, 2001, the United States Government is granted for itself and
# others acting on its behalf a paid-up, nonexclusive, irrevocable
# worldwide license in this data to reproduce, prepare derivative works,
# distribute copies to the public, perform publicly and display
# publicly, and to permit others to do so.
#
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
#
# ************************************************************************
# @HEADER

35
lib/kokkos/cmake/deps/HWLOC.cmake
View File

@ -1,14 +1,16 @@
# @HEADER
# ************************************************************************
#
# Trilinos: An Object-Oriented Solver Framework
# Copyright (2001) Sandia Corporation
# Kokkos v. 3.0
# Copyright (2020) National Technology & Engineering
# Solutions of Sandia, LLC (NTESS).
#
# Under the terms of Contract DE-NA0003525 with NTESS,
# the U.S. Government retains certain rights in this software.
#
# Copyright (2001) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
# work by or on behalf of the U.S. Government. Export of this program
# may require a license from the United States Government.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
@ -21,10 +23,10 @@
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
@ -33,22 +35,7 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# NOTICE: The United States Government is granted for itself and others
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
# license in this data to reproduce, prepare derivative works, and
# perform publicly and display publicly. Beginning five (5) years from
# July 25, 2001, the United States Government is granted for itself and
# others acting on its behalf a paid-up, nonexclusive, irrevocable
# worldwide license in this data to reproduce, prepare derivative works,
# distribute copies to the public, perform publicly and display
# publicly, and to permit others to do so.
#
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
#
# ************************************************************************
# @HEADER

35
lib/kokkos/cmake/deps/Pthread.cmake
View File

@ -1,14 +1,16 @@
# @HEADER
# ************************************************************************
#
# Trilinos: An Object-Oriented Solver Framework
# Copyright (2001) Sandia Corporation
# Kokkos v. 3.0
# Copyright (2020) National Technology & Engineering
# Solutions of Sandia, LLC (NTESS).
#
# Under the terms of Contract DE-NA0003525 with NTESS,
# the U.S. Government retains certain rights in this software.
#
# Copyright (2001) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
# work by or on behalf of the U.S. Government. Export of this program
# may require a license from the United States Government.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
@ -21,10 +23,10 @@
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
@ -33,22 +35,7 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# NOTICE: The United States Government is granted for itself and others
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
# license in this data to reproduce, prepare derivative works, and
# perform publicly and display publicly. Beginning five (5) years from
# July 25, 2001, the United States Government is granted for itself and
# others acting on its behalf a paid-up, nonexclusive, irrevocable
# worldwide license in this data to reproduce, prepare derivative works,
# distribute copies to the public, perform publicly and display
# publicly, and to permit others to do so.
#
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
#
# ************************************************************************
# @HEADER

44
lib/kokkos/cmake/fake_tribits.cmake
View File

@ -38,12 +38,6 @@ MACRO(GLOBAL_SET VARNAME)
SET(${VARNAME} ${ARGN} CACHE INTERNAL "" FORCE)
ENDMACRO()
FUNCTION(VERIFY_EMPTY CONTEXT)
if(${ARGN})
MESSAGE(FATAL_ERROR "Kokkos does not support all of Tribits. Unhandled arguments in ${CONTEXT}:\n${ARGN}")
endif()
ENDFUNCTION()
MACRO(PREPEND_GLOBAL_SET VARNAME)
ASSERT_DEFINED(${VARNAME})
GLOBAL_SET(${VARNAME} ${ARGN} ${${VARNAME}})
@ -89,7 +83,7 @@ FUNCTION(KOKKOS_ADD_TEST)
CMAKE_PARSE_ARGUMENTS(TEST
""
"EXE;NAME;TOOL"
""
"ARGS"
${ARGN})
IF(TEST_EXE)
SET(EXE_ROOT ${TEST_EXE})
@ -102,6 +96,7 @@ FUNCTION(KOKKOS_ADD_TEST)
NAME ${TEST_NAME}
COMM serial mpi
NUM_MPI_PROCS 1
ARGS ${TEST_ARGS}
${TEST_UNPARSED_ARGUMENTS}
ADDED_TESTS_NAMES_OUT ALL_TESTS_ADDED
)
@ -110,18 +105,25 @@ FUNCTION(KOKKOS_ADD_TEST)
SET(TEST_NAME ${PACKAGE_NAME}_${TEST_NAME})
SET(EXE ${PACKAGE_NAME}_${EXE_ROOT})
# The function TRIBITS_ADD_TEST() has a CATEGORIES argument that defaults
# to BASIC. If a project elects to only enable tests marked as PERFORMANCE,
# the test won't actually be added and attempting to set a property on it below
# will yield an error.
if(TARGET ${EXE})
if(TEST_TOOL)
add_dependencies(${EXE} ${TEST_TOOL}) #make sure the exe has to build the tool
foreach(TEST_ADDED ${ALL_TESTS_ADDED})
set_property(TEST ${TEST_ADDED} APPEND PROPERTY ENVIRONMENT "KOKKOS_PROFILE_LIBRARY=$<TARGET_FILE:${TEST_TOOL}>")
endforeach()
endif()
endif()
else()
CMAKE_PARSE_ARGUMENTS(TEST
"WILL_FAIL"
"FAIL_REGULAR_EXPRESSION;PASS_REGULAR_EXPRESSION;EXE;NAME;TOOL"
"CATEGORIES;CMD_ARGS"
"CATEGORIES;ARGS"
${ARGN})
SET(TESTS_ADDED)
# To match Tribits, we should always be receiving
# the root names of exes/libs
IF(TEST_EXE)
@ -133,11 +135,32 @@ FUNCTION(KOKKOS_ADD_TEST)
# These should be the full target name
SET(TEST_NAME ${PACKAGE_NAME}_${TEST_NAME})
SET(EXE ${PACKAGE_NAME}_${EXE_ROOT})
IF (TEST_ARGS)
SET(TEST_NUMBER 0)
FOREACH (ARG_STR ${TEST_ARGS})
# This is passed as a single string blob to match TriBITS behavior
# We need this to be turned into a list
STRING(REPLACE " " ";" ARG_STR_LIST ${ARG_STR})
IF(WIN32)
ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH} COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX} ${TEST_CMD_ARGS})
ADD_TEST(NAME ${TEST_NAME}${TEST_NUMBER} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH}
COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX} ${ARG_STR_LIST})
ELSE()
ADD_TEST(NAME ${TEST_NAME} COMMAND ${EXE} ${TEST_CMD_ARGS})
ADD_TEST(NAME ${TEST_NAME}${TEST_NUMBER} COMMAND ${EXE} ${ARG_STR_LIST})
ENDIF()
LIST(APPEND TESTS_ADDED "${TEST_NAME}${TEST_NUMBER}")
MATH(EXPR TEST_NUMBER "${TEST_NUMBER} + 1")
ENDFOREACH()
ELSE()
IF(WIN32)
ADD_TEST(NAME ${TEST_NAME} WORKING_DIRECTORY ${LIBRARY_OUTPUT_PATH}
COMMAND ${EXE}${CMAKE_EXECUTABLE_SUFFIX})
ELSE()
ADD_TEST(NAME ${TEST_NAME} COMMAND ${EXE})
ENDIF()
LIST(APPEND TESTS_ADDED "${TEST_NAME}")
ENDIF()
FOREACH(TEST_NAME ${TESTS_ADDED})
IF(TEST_WILL_FAIL)
SET_TESTS_PROPERTIES(${TEST_NAME} PROPERTIES WILL_FAIL ${TEST_WILL_FAIL})
ENDIF()
@ -151,6 +174,7 @@ FUNCTION(KOKKOS_ADD_TEST)
add_dependencies(${EXE} ${TEST_TOOL}) #make sure the exe has to build the tool
set_property(TEST ${TEST_NAME} APPEND_STRING PROPERTY ENVIRONMENT "KOKKOS_PROFILE_LIBRARY=$<TARGET_FILE:${TEST_TOOL}>")
endif()
ENDFOREACH()
VERIFY_EMPTY(KOKKOS_ADD_TEST ${TEST_UNPARSED_ARGUMENTS})
endif()
ENDFUNCTION()

18
lib/kokkos/cmake/intel.cmake
View File

@ -3,7 +3,7 @@ FUNCTION(kokkos_set_intel_flags full_standard int_standard)
STRING(TOLOWER ${full_standard} FULL_LC_STANDARD)
STRING(TOLOWER ${int_standard} INT_LC_STANDARD)
# The following three blocks of code were copied from
# /Modules/Compiler/Intel-CXX.cmake from CMake 3.7.2 and then modified.
# /Modules/Compiler/Intel-CXX.cmake from CMake 3.18.1 and then modified.
IF(CMAKE_CXX_SIMULATE_ID STREQUAL MSVC)
SET(_std -Qstd)
SET(_ext c++)
@ -11,20 +11,8 @@ FUNCTION(kokkos_set_intel_flags full_standard int_standard)
SET(_std -std)
SET(_ext gnu++)
ENDIF()
IF(NOT KOKKOS_CXX_STANDARD STREQUAL 11 AND NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.0.2)
#There is no gnu++14 value supported; figure out what to do.
SET(KOKKOS_CXX_STANDARD_FLAG "${_std}=c++${FULL_LC_STANDARD}" PARENT_SCOPE)
SET(KOKKOS_CXX_INTERMEDIATE_STANDARD_FLAG "${_std}=c++${INT_LC_STANDARD}" PARENT_SCOPE)
ELSEIF(KOKKOS_CXX_STANDARD STREQUAL 11 AND NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 13.0)
IF (CMAKE_CXX_EXTENSIONS)
SET(KOKKOS_CXX_STANDARD_FLAG "${_std}=${_ext}c++11" PARENT_SCOPE)
ELSE()
SET(KOKKOS_CXX_STANDARD_FLAG "${_std}=c++11" PARENT_SCOPE)
ENDIF()
ELSE()
MESSAGE(FATAL_ERROR "Intel compiler version too low - need 13.0 for C++11 and 15.0 for C++14")
ENDIF()
SET(KOKKOS_CXX_INTERMDIATE_STANDARD_FLAG "${_std}=${_ext}${INT_LC_STANDARD}" PARENT_SCOPE)
ENDFUNCTION()

79
lib/kokkos/cmake/kokkos_arch.cmake
View File

@ -35,6 +35,7 @@ KOKKOS_ARCH_OPTION(ARMV80 HOST "ARMv8.0 Compatible CPU")
KOKKOS_ARCH_OPTION(ARMV81 HOST "ARMv8.1 Compatible CPU")
KOKKOS_ARCH_OPTION(ARMV8_THUNDERX HOST "ARMv8 Cavium ThunderX CPU")
KOKKOS_ARCH_OPTION(ARMV8_THUNDERX2 HOST "ARMv8 Cavium ThunderX2 CPU")
KOKKOS_ARCH_OPTION(A64FX HOST "ARMv8.2 with SVE Suport")
KOKKOS_ARCH_OPTION(WSM HOST "Intel Westmere CPU")
KOKKOS_ARCH_OPTION(SNB HOST "Intel Sandy/Ivy Bridge CPUs")
KOKKOS_ARCH_OPTION(HSW HOST "Intel Haswell CPUs")
@ -63,6 +64,7 @@ KOKKOS_ARCH_OPTION(ZEN HOST "AMD Zen architecture")
KOKKOS_ARCH_OPTION(ZEN2 HOST "AMD Zen2 architecture")
KOKKOS_ARCH_OPTION(VEGA900 GPU "AMD GPU MI25 GFX900")
KOKKOS_ARCH_OPTION(VEGA906 GPU "AMD GPU MI50/MI60 GFX906")
KOKKOS_ARCH_OPTION(VEGA908 GPU "AMD GPU")
KOKKOS_ARCH_OPTION(INTEL_GEN GPU "Intel GPUs Gen9+")
@ -72,6 +74,11 @@ IF(KOKKOS_ENABLE_COMPILER_WARNINGS)
"-Wall" "-Wunused-parameter" "-Wshadow" "-pedantic"
"-Wsign-compare" "-Wtype-limits" "-Wuninitialized")
# OpenMPTarget compilers give erroneous warnings about sign comparison in loops
IF(KOKKOS_ENABLE_OPENMPTARGET)
LIST(REMOVE_ITEM COMMON_WARNINGS "-Wsign-compare")
ENDIF()
SET(GNU_WARNINGS "-Wempty-body" "-Wclobbered" "-Wignored-qualifiers"
${COMMON_WARNINGS})
@ -106,6 +113,12 @@ ENDIF()
IF (KOKKOS_CXX_COMPILER_ID STREQUAL Clang)
SET(CUDA_ARCH_FLAG "--cuda-gpu-arch")
GLOBAL_APPEND(KOKKOS_CUDA_OPTIONS -x cuda)
# Kokkos_CUDA_DIR has priority over CUDAToolkit_BIN_DIR
IF (Kokkos_CUDA_DIR)
GLOBAL_APPEND(KOKKOS_CUDA_OPTIONS --cuda-path=${Kokkos_CUDA_DIR})
ELSEIF(CUDAToolkit_BIN_DIR)
GLOBAL_APPEND(KOKKOS_CUDA_OPTIONS --cuda-path=${CUDAToolkit_BIN_DIR}/..)
ENDIF()
IF (KOKKOS_ENABLE_CUDA)
SET(KOKKOS_IMPL_CUDA_CLANG_WORKAROUND ON CACHE BOOL "enable CUDA Clang workarounds" FORCE)
ENDIF()
@ -167,6 +180,12 @@ IF (KOKKOS_ARCH_ARMV8_THUNDERX2)
)
ENDIF()
IF (KOKKOS_ARCH_A64FX)
COMPILER_SPECIFIC_FLAGS(
DEFAULT -march=armv8.2-a+sve
)
ENDIF()
IF (KOKKOS_ARCH_ZEN)
COMPILER_SPECIFIC_FLAGS(
Intel -mavx2
@ -327,6 +346,16 @@ IF (Kokkos_ENABLE_HIP)
ENDIF()
IF (Kokkos_ENABLE_SYCL)
COMPILER_SPECIFIC_FLAGS(
DEFAULT -fsycl
)
COMPILER_SPECIFIC_OPTIONS(
DEFAULT -fsycl-unnamed-lambda
)
ENDIF()
SET(CUDA_ARCH_ALREADY_SPECIFIED "")
FUNCTION(CHECK_CUDA_ARCH ARCH FLAG)
IF(KOKKOS_ARCH_${ARCH})
@ -392,6 +421,7 @@ ENDFUNCTION()
#to the corresponding flag name if ON
CHECK_AMDGPU_ARCH(VEGA900 gfx900) # Radeon Instinct MI25
CHECK_AMDGPU_ARCH(VEGA906 gfx906) # Radeon Instinct MI50 and MI60
CHECK_AMDGPU_ARCH(VEGA908 gfx908)
IF(KOKKOS_ENABLE_HIP AND NOT AMDGPU_ARCH_ALREADY_SPECIFIED)
MESSAGE(SEND_ERROR "HIP enabled but no AMD GPU architecture currently enabled. "
@ -477,35 +507,53 @@ ENDIF()
#CMake verbose is kind of pointless
#Let's just always print things
MESSAGE(STATUS "Execution Spaces:")
MESSAGE(STATUS "Built-in Execution Spaces:")
FOREACH (_BACKEND CUDA OPENMPTARGET HIP)
IF(KOKKOS_ENABLE_${_BACKEND})
FOREACH (_BACKEND Cuda OpenMPTarget HIP SYCL)
STRING(TOUPPER ${_BACKEND} UC_BACKEND)
IF(KOKKOS_ENABLE_${UC_BACKEND})
IF(_DEVICE_PARALLEL)
MESSAGE(FATAL_ERROR "Multiple device parallel execution spaces are not allowed! "
"Trying to enable execution space ${_BACKEND}, "
"but execution space ${_DEVICE_PARALLEL} is already enabled. "
"Remove the CMakeCache.txt file and re-configure.")
ENDIF()
SET(_DEVICE_PARALLEL ${_BACKEND})
IF (${_BACKEND} STREQUAL "Cuda")
IF(KOKKOS_ENABLE_CUDA_UVM)
SET(_DEFAULT_DEVICE_MEMSPACE "Kokkos::${_BACKEND}UVMSpace")
ELSE()
SET(_DEFAULT_DEVICE_MEMSPACE "Kokkos::${_BACKEND}Space")
ENDIF()
SET(_DEVICE_PARALLEL "Kokkos::${_BACKEND}")
ELSE()
SET(_DEFAULT_DEVICE_MEMSPACE "Kokkos::Experimental::${_BACKEND}Space")
SET(_DEVICE_PARALLEL "Kokkos::Experimental::${_BACKEND}")
ENDIF()
ENDIF()
ENDFOREACH()
IF(NOT _DEVICE_PARALLEL)
SET(_DEVICE_PARALLEL "NONE")
SET(_DEVICE_PARALLEL "NoTypeDefined")
SET(_DEFAULT_DEVICE_MEMSPACE "NoTypeDefined")
ENDIF()
MESSAGE(STATUS " Device Parallel: ${_DEVICE_PARALLEL}")
UNSET(_DEVICE_PARALLEL)
IF(KOKKOS_ENABLE_PTHREAD)
SET(KOKKOS_ENABLE_THREADS ON)
ENDIF()
FOREACH (_BACKEND OPENMP PTHREAD HPX)
IF(KOKKOS_ENABLE_${_BACKEND})
FOREACH (_BACKEND OpenMP Threads HPX)
STRING(TOUPPER ${_BACKEND} UC_BACKEND)
IF(KOKKOS_ENABLE_${UC_BACKEND})
IF(_HOST_PARALLEL)
MESSAGE(FATAL_ERROR "Multiple host parallel execution spaces are not allowed! "
"Trying to enable execution space ${_BACKEND}, "
"but execution space ${_HOST_PARALLEL} is already enabled. "
"Remove the CMakeCache.txt file and re-configure.")
ENDIF()
SET(_HOST_PARALLEL ${_BACKEND})
IF (${_BACKEND} STREQUAL "HPX")
SET(_HOST_PARALLEL "Kokkos::Experimental::${_BACKEND}")
ELSE()
SET(_HOST_PARALLEL "Kokkos::${_BACKEND}")
ENDIF()
ENDIF()
ENDFOREACH()
@ -515,14 +563,11 @@ IF(NOT _HOST_PARALLEL AND NOT KOKKOS_ENABLE_SERIAL)
"and Kokkos_ENABLE_SERIAL=OFF.")
ENDIF()
IF(NOT _HOST_PARALLEL)
SET(_HOST_PARALLEL "NONE")
ENDIF()
IF(_HOST_PARALLEL)
MESSAGE(STATUS " Host Parallel: ${_HOST_PARALLEL}")
UNSET(_HOST_PARALLEL)
IF(KOKKOS_ENABLE_PTHREAD)
SET(KOKKOS_ENABLE_THREADS ON)
ELSE()
SET(_HOST_PARALLEL "NoTypeDefined")
MESSAGE(STATUS " Host Parallel: NoTypeDefined")
ENDIF()
IF(KOKKOS_ENABLE_SERIAL)

98
lib/kokkos/cmake/kokkos_compiler_id.cmake
View File

@ -4,24 +4,42 @@ SET(KOKKOS_CXX_COMPILER ${CMAKE_CXX_COMPILER})
SET(KOKKOS_CXX_COMPILER_ID ${CMAKE_CXX_COMPILER_ID})
SET(KOKKOS_CXX_COMPILER_VERSION ${CMAKE_CXX_COMPILER_VERSION})
IF(Kokkos_ENABLE_CUDA)
MACRO(kokkos_internal_have_compiler_nvcc)
# Check if the compiler is nvcc (which really means nvcc_wrapper).
EXECUTE_PROCESS(COMMAND ${CMAKE_CXX_COMPILER} --version
EXECUTE_PROCESS(COMMAND ${ARGN} --version
OUTPUT_VARIABLE INTERNAL_COMPILER_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE)
STRING(REPLACE "\n" " - " INTERNAL_COMPILER_VERSION_ONE_LINE ${INTERNAL_COMPILER_VERSION} )
STRING(FIND ${INTERNAL_COMPILER_VERSION_ONE_LINE} "nvcc" INTERNAL_COMPILER_VERSION_CONTAINS_NVCC)
STRING(REGEX REPLACE "^ +" ""
INTERNAL_HAVE_COMPILER_NVCC "${INTERNAL_HAVE_COMPILER_NVCC}")
STRING(REGEX REPLACE "^ +" "" INTERNAL_HAVE_COMPILER_NVCC "${INTERNAL_HAVE_COMPILER_NVCC}")
IF(${INTERNAL_COMPILER_VERSION_CONTAINS_NVCC} GREATER -1)
SET(INTERNAL_HAVE_COMPILER_NVCC true)
ELSE()
SET(INTERNAL_HAVE_COMPILER_NVCC false)
ENDIF()
ENDMACRO()
IF(Kokkos_ENABLE_CUDA)
# find kokkos_launch_compiler
FIND_PROGRAM(Kokkos_COMPILE_LAUNCHER
NAMES kokkos_launch_compiler
HINTS ${PROJECT_SOURCE_DIR}
PATHS ${PROJECT_SOURCE_DIR}
PATH_SUFFIXES bin)
# check if compiler was set to nvcc_wrapper
kokkos_internal_have_compiler_nvcc(${CMAKE_CXX_COMPILER})
# if launcher was found and nvcc_wrapper was not specified as
# compiler, set to use launcher. Will ensure CMAKE_CXX_COMPILER
# is replaced by nvcc_wrapper
IF(Kokkos_COMPILE_LAUNCHER AND NOT INTERNAL_HAVE_COMPILER_NVCC AND NOT KOKKOS_CXX_COMPILER_ID STREQUAL Clang)
# the first argument to launcher is always the C++ compiler defined by cmake
# if the second argument matches the C++ compiler, it forwards the rest of the
# args to nvcc_wrapper
kokkos_internal_have_compiler_nvcc(
${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER} -DKOKKOS_DEPENDENCE)
SET(INTERNAL_USE_COMPILER_LAUNCHER true)
ENDIF()
ENDIF()
IF(INTERNAL_HAVE_COMPILER_NVCC)
@ -36,6 +54,35 @@ IF(INTERNAL_HAVE_COMPILER_NVCC)
STRING(SUBSTRING ${TEMP_CXX_COMPILER_VERSION} 1 -1 TEMP_CXX_COMPILER_VERSION)
SET(KOKKOS_CXX_COMPILER_VERSION ${TEMP_CXX_COMPILER_VERSION} CACHE STRING INTERNAL FORCE)
MESSAGE(STATUS "Compiler Version: ${KOKKOS_CXX_COMPILER_VERSION}")
IF(INTERNAL_USE_COMPILER_LAUNCHER)
IF(Kokkos_LAUNCH_COMPILER_INFO)
GET_FILENAME_COMPONENT(BASE_COMPILER_NAME ${CMAKE_CXX_COMPILER} NAME)
# does not have STATUS intentionally
MESSAGE("")
MESSAGE("Kokkos_LAUNCH_COMPILER_INFO (${Kokkos_COMPILE_LAUNCHER}):")
MESSAGE(" - Kokkos + CUDA backend requires the C++ files to be compiled as CUDA code.")
MESSAGE(" - kokkos_launch_compiler permits CMAKE_CXX_COMPILER to be set to a traditional C++ compiler when Kokkos_ENABLE_CUDA=ON")
MESSAGE(" by prefixing all the compile and link commands with the path to the script + CMAKE_CXX_COMPILER (${CMAKE_CXX_COMPILER}).")
MESSAGE(" - If any of the compile or link commands have CMAKE_CXX_COMPILER as the first argument, it replaces CMAKE_CXX_COMPILER with nvcc_wrapper.")
MESSAGE(" - If the compile or link command is not CMAKE_CXX_COMPILER, it just executes the command.")
MESSAGE(" - If using ccache, set CMAKE_CXX_COMPILER to nvcc_wrapper explicitly.")
MESSAGE(" - kokkos_compiler_launcher is available to downstream projects as well.")
MESSAGE(" - If CMAKE_CXX_COMPILER=nvcc_wrapper, all legacy behavior will be preserved during 'find_package(Kokkos)'")
MESSAGE(" - If CMAKE_CXX_COMPILER is not nvcc_wrapper, 'find_package(Kokkos)' will apply 'kokkos_compilation(GLOBAL)' unless separable compilation is enabled")
MESSAGE(" - This can be disabled via '-DKokkos_LAUNCH_COMPILER=OFF'")
MESSAGE(" - Use 'find_package(Kokkos COMPONENTS separable_compilation)' to enable separable compilation")
MESSAGE(" - Separable compilation allows you to control the scope of where the compiler transformation behavior (${BASE_COMPILER_NAME} -> nvcc_wrapper) is applied")
MESSAGE(" - The compiler transformation can be applied on a per-project, per-directory, per-target, and/or per-source-file basis")
MESSAGE(" - 'kokkos_compilation(PROJECT)' will apply the compiler transformation to all targets in a project/subproject")
MESSAGE(" - 'kokkos_compilation(TARGET <TARGET> [<TARGETS>...])' will apply the compiler transformation to the specified target(s)")
MESSAGE(" - 'kokkos_compilation(SOURCE <SOURCE> [<SOURCES>...])' will apply the compiler transformation to the specified source file(s)")
MESSAGE(" - 'kokkos_compilation(DIRECTORY <DIR> [<DIRS>...])' will apply the compiler transformation to the specified directories")
MESSAGE("")
ELSE()
MESSAGE(STATUS "kokkos_launch_compiler (${Kokkos_COMPILE_LAUNCHER}) is enabled... Set Kokkos_LAUNCH_COMPILER_INFO=ON for more info.")
ENDIF()
kokkos_compilation(GLOBAL)
ENDIF()
ENDIF()
IF(Kokkos_ENABLE_HIP)
@ -90,38 +137,49 @@ IF(KOKKOS_CXX_COMPILER_ID STREQUAL Cray OR KOKKOS_CLANG_IS_CRAY)
ENDIF()
ENDIF()
IF(KOKKOS_CXX_COMPILER_ID STREQUAL Fujitsu)
# SET Fujitsus compiler version which is not detected by CMake
EXECUTE_PROCESS(COMMAND ${CMAKE_CXX_COMPILER} --version
OUTPUT_VARIABLE INTERNAL_CXX_COMPILER_VERSION
OUTPUT_STRIP_TRAILING_WHITESPACE)
STRING(REGEX MATCH "[0-9]+\\.[0-9]+\\.[0-9]+"
TEMP_CXX_COMPILER_VERSION ${INTERNAL_CXX_COMPILER_VERSION})
SET(KOKKOS_CXX_COMPILER_VERSION ${TEMP_CXX_COMPILER_VERSION} CACHE STRING INTERNAL FORCE)
ENDIF()
# Enforce the minimum compilers supported by Kokkos.
SET(KOKKOS_MESSAGE_TEXT "Compiler not supported by Kokkos. Required compiler versions:")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Clang 3.5.2 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n GCC 4.8.4 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Intel 15.0.2 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n NVCC 9.0.69 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n HIPCC 3.5.0 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n PGI 17.1 or higher\n")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Clang 4.0.0 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n GCC 5.3.0 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Intel 17.0.0 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n NVCC 9.2.88 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n HIPCC 3.8.0 or higher")
SET(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n PGI 17.4 or higher\n")
IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 3.5.2)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 4.0.0)
MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}")
ENDIF()
ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL GNU)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 4.8.4)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 5.3.0)
MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}")
ENDIF()
ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL Intel)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 15.0.2)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 17.0.0)
MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}")
ENDIF()
ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 9.0.69)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 9.2.88)
MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}")
ENDIF()
SET(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Kokkos turns off CXX extensions" FORCE)
ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL HIP)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 3.5.0)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 3.8.0)
MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}")
ENDIF()
ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL PGI)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 17.1)
IF(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 17.4)
MESSAGE(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}")
ENDIF()
ENDIF()

2
lib/kokkos/cmake/kokkos_corner_cases.cmake
View File

@ -1,4 +1,4 @@
IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang AND KOKKOS_ENABLE_OPENMP AND NOT KOKKOS_CLANG_IS_CRAY AND NOT "x${CMAKE_CXX_SIMULATE_ID}" STREQUAL "xMSVC")
IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang AND KOKKOS_ENABLE_OPENMP AND NOT KOKKOS_CLANG_IS_CRAY AND NOT KOKKOS_COMPILER_CLANG_MSVC)
# The clang "version" doesn't actually tell you what runtimes and tools
# were built into Clang. We should therefore make sure that libomp
# was actually built into Clang. Otherwise the user will get nonsensical

36
lib/kokkos/cmake/kokkos_enable_devices.cmake
View File

@ -25,6 +25,18 @@ IF (KOKKOS_ENABLE_PTHREAD)
SET(KOKKOS_ENABLE_THREADS ON)
ENDIF()
# detect clang++ / cl / clang-cl clashes
IF (CMAKE_CXX_COMPILER_ID STREQUAL Clang AND "x${CMAKE_CXX_SIMULATE_ID}" STREQUAL "xMSVC")
# this specific test requires CMake >= 3.15
IF ("x${CMAKE_CXX_COMPILER_FRONTEND_VARIANT}" STREQUAL "xGNU")
# use pure clang++ instead of clang-cl
SET(KOKKOS_COMPILER_CLANG_MSVC OFF)
ELSE()
# it defaults to clang-cl
SET(KOKKOS_COMPILER_CLANG_MSVC ON)
ENDIF()
ENDIF()
IF(Trilinos_ENABLE_Kokkos AND Trilinos_ENABLE_OpenMP)
SET(OMP_DEFAULT ON)
ELSE()
@ -39,13 +51,16 @@ IF(KOKKOS_ENABLE_OPENMP)
IF(KOKKOS_CLANG_IS_INTEL)
SET(ClangOpenMPFlag -fiopenmp)
ENDIF()
IF(KOKKOS_CXX_COMPILER_ID STREQUAL Clang AND "x${CMAKE_CXX_SIMULATE_ID}" STREQUAL "xMSVC")
#expression /openmp yields error, so add a specific Clang flag
COMPILER_SPECIFIC_OPTIONS(Clang /clang:-fopenmp)
#link omp library from LLVM lib dir
IF(KOKKOS_COMPILER_CLANG_MSVC)
#for clang-cl expression /openmp yields an error, so directly add the specific Clang flag
SET(ClangOpenMPFlag /clang:-fopenmp=libomp)
ENDIF()
IF(WIN32 AND CMAKE_CXX_COMPILER_ID STREQUAL Clang)
#link omp library from LLVM lib dir, no matter if it is clang-cl or clang++
get_filename_component(LLVM_BIN_DIR ${CMAKE_CXX_COMPILER_AR} DIRECTORY)
COMPILER_SPECIFIC_LIBS(Clang "${LLVM_BIN_DIR}/../lib/libomp.lib")
ELSEIF(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA)
ENDIF()
IF(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA)
COMPILER_SPECIFIC_FLAGS(
COMPILER_ID KOKKOS_CXX_HOST_COMPILER_ID
Clang -Xcompiler ${ClangOpenMPFlag}
@ -105,9 +120,11 @@ KOKKOS_DEVICE_OPTION(CUDA ${CUDA_DEFAULT} DEVICE "Whether to build CUDA backend"
IF (KOKKOS_ENABLE_CUDA)
GLOBAL_SET(KOKKOS_DONT_ALLOW_EXTENSIONS "CUDA enabled")
IF(WIN32)
IF(WIN32 AND NOT KOKKOS_CXX_COMPILER_ID STREQUAL Clang)
GLOBAL_APPEND(KOKKOS_COMPILE_OPTIONS -x cu)
ENDIF()
## Cuda has extra setup requirements, turn on Kokkos_Setup_Cuda.hpp in macros
LIST(APPEND DEVICE_SETUP_LIST Cuda)
ENDIF()
# We want this to default to OFF for cache reasons, but if no
@ -128,3 +145,10 @@ KOKKOS_DEVICE_OPTION(SERIAL ${SERIAL_DEFAULT} HOST "Whether to build serial back
KOKKOS_DEVICE_OPTION(HPX OFF HOST "Whether to build HPX backend (experimental)")
KOKKOS_DEVICE_OPTION(HIP OFF DEVICE "Whether to build HIP backend")
## HIP has extra setup requirements, turn on Kokkos_Setup_HIP.hpp in macros
IF (KOKKOS_ENABLE_HIP)
LIST(APPEND DEVICE_SETUP_LIST HIP)
ENDIF()
KOKKOS_DEVICE_OPTION(SYCL OFF DEVICE "Whether to build SYCL backend")

120
lib/kokkos/cmake/kokkos_functions.cmake
View File

@ -154,13 +154,13 @@ MACRO(kokkos_export_imported_tpl NAME)
KOKKOS_APPEND_CONFIG_LINE("SET_TARGET_PROPERTIES(${NAME} PROPERTIES")
GET_TARGET_PROPERTY(TPL_LIBRARY ${NAME} IMPORTED_LOCATION)
IF(TPL_LIBRARY)
KOKKOS_APPEND_CONFIG_LINE("IMPORTED_LOCATION ${TPL_LIBRARY}")
KOKKOS_APPEND_CONFIG_LINE("IMPORTED_LOCATION \"${TPL_LIBRARY}\"")
ENDIF()
ENDIF()
GET_TARGET_PROPERTY(TPL_INCLUDES ${NAME} INTERFACE_INCLUDE_DIRECTORIES)
IF(TPL_INCLUDES)
KOKKOS_APPEND_CONFIG_LINE("INTERFACE_INCLUDE_DIRECTORIES ${TPL_INCLUDES}")
KOKKOS_APPEND_CONFIG_LINE("INTERFACE_INCLUDE_DIRECTORIES \"${TPL_INCLUDES}\"")
ENDIF()
GET_TARGET_PROPERTY(TPL_COMPILE_OPTIONS ${NAME} INTERFACE_COMPILE_OPTIONS)
@ -178,7 +178,7 @@ MACRO(kokkos_export_imported_tpl NAME)
GET_TARGET_PROPERTY(TPL_LINK_LIBRARIES ${NAME} INTERFACE_LINK_LIBRARIES)
IF(TPL_LINK_LIBRARIES)
KOKKOS_APPEND_CONFIG_LINE("INTERFACE_LINK_LIBRARIES ${TPL_LINK_LIBRARIES}")
KOKKOS_APPEND_CONFIG_LINE("INTERFACE_LINK_LIBRARIES \"${TPL_LINK_LIBRARIES}\"")
ENDIF()
KOKKOS_APPEND_CONFIG_LINE(")")
KOKKOS_APPEND_CONFIG_LINE("ENDIF()")
@ -770,7 +770,7 @@ FUNCTION(kokkos_link_tpl TARGET)
ENDFUNCTION()
FUNCTION(COMPILER_SPECIFIC_OPTIONS_HELPER)
SET(COMPILERS NVIDIA PGI XL DEFAULT Cray Intel Clang AppleClang IntelClang GNU HIP)
SET(COMPILERS NVIDIA PGI XL DEFAULT Cray Intel Clang AppleClang IntelClang GNU HIP Fujitsu)
CMAKE_PARSE_ARGUMENTS(
PARSE
"LINK_OPTIONS;COMPILE_OPTIONS;COMPILE_DEFINITIONS;LINK_LIBRARIES"
@ -844,7 +844,6 @@ ENDFUNCTION(COMPILER_SPECIFIC_DEFS)
FUNCTION(COMPILER_SPECIFIC_LIBS)
COMPILER_SPECIFIC_OPTIONS_HELPER(${ARGN} LINK_LIBRARIES)
ENDFUNCTION(COMPILER_SPECIFIC_LIBS)
# Given a list of the form
# key1;value1;key2;value2,...
# Create a list of all keys in a variable named ${KEY_LIST_NAME}
@ -877,3 +876,114 @@ FUNCTION(KOKKOS_CHECK_DEPRECATED_OPTIONS)
ENDIF()
ENDFOREACH()
ENDFUNCTION()
# this function checks whether the current CXX compiler supports building CUDA
FUNCTION(kokkos_cxx_compiler_cuda_test _VAR)
# don't run this test every time
IF(DEFINED ${_VAR})
RETURN()
ENDIF()
FILE(WRITE ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cpp
"
#include <cuda.h>
#include <cstdlib>
__global__
void kernel(int sz, double* data)
{
auto _beg = blockIdx.x * blockDim.x + threadIdx.x;
for(int i = _beg; i < sz; ++i)
data[i] += static_cast<double>(i);
}
int main()
{
double* data = nullptr;
int blocks = 64;
int grids = 64;
auto ret = cudaMalloc(&data, blocks * grids * sizeof(double));
if(ret != cudaSuccess)
return EXIT_FAILURE;
kernel<<<grids, blocks>>>(blocks * grids, data);
cudaDeviceSynchronize();
return EXIT_SUCCESS;
}
")
TRY_COMPILE(_RET
${PROJECT_BINARY_DIR}/compile_tests
SOURCES ${PROJECT_BINARY_DIR}/compile_tests/compiles_cuda.cpp)
SET(${_VAR} ${_RET} CACHE STRING "CXX compiler supports building CUDA")
ENDFUNCTION()
# this function is provided to easily select which files use nvcc_wrapper:
#
# GLOBAL --> all files
# TARGET --> all files in a target
# SOURCE --> specific source files
# DIRECTORY --> all files in directory
# PROJECT --> all files/targets in a project/subproject
#
FUNCTION(kokkos_compilation)
# check whether the compiler already supports building CUDA
KOKKOS_CXX_COMPILER_CUDA_TEST(Kokkos_CXX_COMPILER_COMPILES_CUDA)
# if CUDA compile test has already been performed, just return
IF(Kokkos_CXX_COMPILER_COMPILES_CUDA)
RETURN()
ENDIF()
CMAKE_PARSE_ARGUMENTS(COMP "GLOBAL;PROJECT" "" "DIRECTORY;TARGET;SOURCE" ${ARGN})
# find kokkos_launch_compiler
FIND_PROGRAM(Kokkos_COMPILE_LAUNCHER
NAMES kokkos_launch_compiler
HINTS ${PROJECT_SOURCE_DIR}
PATHS ${PROJECT_SOURCE_DIR}
PATH_SUFFIXES bin)
IF(NOT Kokkos_COMPILE_LAUNCHER)
MESSAGE(FATAL_ERROR "Kokkos could not find 'kokkos_launch_compiler'. Please set '-DKokkos_COMPILE_LAUNCHER=/path/to/launcher'")
ENDIF()
IF(COMP_GLOBAL)
# if global, don't bother setting others
SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
SET_PROPERTY(GLOBAL PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
ELSE()
FOREACH(_TYPE PROJECT DIRECTORY TARGET SOURCE)
# make project/subproject scoping easy, e.g. KokkosCompilation(PROJECT) after project(...)
IF("${_TYPE}" STREQUAL "PROJECT" AND COMP_${_TYPE})
LIST(APPEND COMP_DIRECTORY ${PROJECT_SOURCE_DIR})
UNSET(COMP_${_TYPE})
ENDIF()
# set the properties if defined
IF(COMP_${_TYPE})
# MESSAGE(STATUS "Using nvcc_wrapper :: ${_TYPE} :: ${COMP_${_TYPE}}")
SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_COMPILE "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
SET_PROPERTY(${_TYPE} ${COMP_${_TYPE}} PROPERTY RULE_LAUNCH_LINK "${Kokkos_COMPILE_LAUNCHER} ${CMAKE_CXX_COMPILER}")
ENDIF()
ENDFOREACH()
ENDIF()
ENDFUNCTION()
## KOKKOS_CONFIG_HEADER - parse the data list which is a list of backend names
## and create output config header file...used for
## creating dynamic include files based on enabled backends
##
## SRC_FILE is input file
## TARGET_FILE output file
## HEADER_GUARD TEXT used with include header guard
## HEADER_PREFIX prefix used with include (i.e. fwd, decl, setup)
## DATA_LIST list of backends to include in generated file
FUNCTION(KOKKOS_CONFIG_HEADER SRC_FILE TARGET_FILE HEADER_GUARD HEADER_PREFIX DATA_LIST)
SET(HEADER_GUARD_TAG "${HEADER_GUARD}_HPP_")
CONFIGURE_FILE(cmake/${SRC_FILE} ${PROJECT_BINARY_DIR}/temp/${TARGET_FILE}.work COPYONLY)
FOREACH( BACKEND_NAME ${DATA_LIST} )
SET(INCLUDE_NEXT_FILE "#include <${HEADER_PREFIX}_${BACKEND_NAME}.hpp>
\@INCLUDE_NEXT_FILE\@")
CONFIGURE_FILE(${PROJECT_BINARY_DIR}/temp/${TARGET_FILE}.work ${PROJECT_BINARY_DIR}/temp/${TARGET_FILE}.work @ONLY)
ENDFOREACH()
SET(INCLUDE_NEXT_FILE "" )
CONFIGURE_FILE(${PROJECT_BINARY_DIR}/temp/${TARGET_FILE}.work ${TARGET_FILE} @ONLY)
ENDFUNCTION()

12
lib/kokkos/cmake/kokkos_pick_cxx_std.cmake
View File

@ -1,19 +1,17 @@
# From CMake 3.10 documentation
#This can run at any time
KOKKOS_OPTION(CXX_STANDARD "" STRING "The C++ standard for Kokkos to use: 11, 14, 17, or 20. If empty, this will default to CMAKE_CXX_STANDARD. If both CMAKE_CXX_STANDARD and Kokkos_CXX_STANDARD are empty, this will default to 11")
KOKKOS_OPTION(CXX_STANDARD "" STRING "The C++ standard for Kokkos to use: 14, 17, or 20. If empty, this will default to CMAKE_CXX_STANDARD. If both CMAKE_CXX_STANDARD and Kokkos_CXX_STANDARD are empty, this will default to 14")
# Set CXX standard flags
SET(KOKKOS_ENABLE_CXX11 OFF)
SET(KOKKOS_ENABLE_CXX14 OFF)
SET(KOKKOS_ENABLE_CXX17 OFF)
SET(KOKKOS_ENABLE_CXX20 OFF)
IF (KOKKOS_CXX_STANDARD)
IF (${KOKKOS_CXX_STANDARD} STREQUAL "c++98")
MESSAGE(FATAL_ERROR "Kokkos no longer supports C++98 - minimum C++11")
MESSAGE(FATAL_ERROR "Kokkos no longer supports C++98 - minimum C++14")
ELSEIF (${KOKKOS_CXX_STANDARD} STREQUAL "c++11")
MESSAGE(WARNING "Deprecated Kokkos C++ standard set as 'c++11'. Use '11' instead.")
SET(KOKKOS_CXX_STANDARD "11")
MESSAGE(FATAL_ERROR "Kokkos no longer supports C++11 - minimum C++14")
ELSEIF(${KOKKOS_CXX_STANDARD} STREQUAL "c++14")
MESSAGE(WARNING "Deprecated Kokkos C++ standard set as 'c++14'. Use '14' instead.")
SET(KOKKOS_CXX_STANDARD "14")
@ -33,8 +31,8 @@ IF (KOKKOS_CXX_STANDARD)
ENDIF()
IF (NOT KOKKOS_CXX_STANDARD AND NOT CMAKE_CXX_STANDARD)
MESSAGE(STATUS "Setting default Kokkos CXX standard to 11")
SET(KOKKOS_CXX_STANDARD "11")
MESSAGE(STATUS "Setting default Kokkos CXX standard to 14")
SET(KOKKOS_CXX_STANDARD "14")
ELSEIF(NOT KOKKOS_CXX_STANDARD)
MESSAGE(STATUS "Setting default Kokkos CXX standard to ${CMAKE_CXX_STANDARD}")
SET(KOKKOS_CXX_STANDARD ${CMAKE_CXX_STANDARD})

29
lib/kokkos/cmake/kokkos_test_cxx_std.cmake
View File

@ -29,7 +29,7 @@ FUNCTION(kokkos_set_cxx_standard_feature standard)
ELSEIF(NOT KOKKOS_USE_CXX_EXTENSIONS AND ${STANDARD_NAME})
MESSAGE(STATUS "Using ${${STANDARD_NAME}} for C++${standard} standard as feature")
IF (KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA AND (KOKKOS_CXX_HOST_COMPILER_ID STREQUAL GNU OR KOKKOS_CXX_HOST_COMPILER_ID STREQUAL Clang))
SET(SUPPORTED_NVCC_FLAGS "-std=c++11;-std=c++14;-std=c++17")
SET(SUPPORTED_NVCC_FLAGS "-std=c++14;-std=c++17")
IF (NOT ${${STANDARD_NAME}} IN_LIST SUPPORTED_NVCC_FLAGS)
MESSAGE(FATAL_ERROR "CMake wants to use ${${STANDARD_NAME}} which is not supported by NVCC. Using a more recent host compiler or a more recent CMake version might help.")
ENDIF()
@ -42,13 +42,16 @@ FUNCTION(kokkos_set_cxx_standard_feature standard)
ELSEIF((KOKKOS_CXX_COMPILER_ID STREQUAL "NVIDIA") AND WIN32)
MESSAGE(STATUS "Using no flag for C++${standard} standard as feature")
GLOBAL_SET(KOKKOS_CXX_STANDARD_FEATURE "")
ELSEIF((KOKKOS_CXX_COMPILER_ID STREQUAL "Fujitsu"))
MESSAGE(STATUS "Using no flag for C++${standard} standard as feature")
GLOBAL_SET(KOKKOS_CXX_STANDARD_FEATURE "")
ELSE()
#nope, we can't do anything here
MESSAGE(WARNING "C++${standard} is not supported as a compiler feature. We will choose custom flags for now, but this behavior has been deprecated. Please open an issue at https://github.com/kokkos/kokkos/issues reporting that ${KOKKOS_CXX_COMPILER_ID} ${KOKKOS_CXX_COMPILER_VERSION} failed for ${KOKKOS_CXX_STANDARD}, preferrably including your CMake command.")
MESSAGE(WARNING "C++${standard} is not supported as a compiler feature. We will choose custom flags for now, but this behavior has been deprecated. Please open an issue at https://github.com/kokkos/kokkos/issues reporting that ${KOKKOS_CXX_COMPILER_ID} ${KOKKOS_CXX_COMPILER_VERSION} failed for ${KOKKOS_CXX_STANDARD}, preferably including your CMake command.")
GLOBAL_SET(KOKKOS_CXX_STANDARD_FEATURE "")
ENDIF()
IF(NOT WIN32)
IF((NOT WIN32) AND (NOT ("${KOKKOS_CXX_COMPILER_ID}" STREQUAL "Fujitsu")))
IF(NOT ${FEATURE_NAME} IN_LIST CMAKE_CXX_COMPILE_FEATURES)
MESSAGE(FATAL_ERROR "Compiler ${KOKKOS_CXX_COMPILER_ID} should support ${FEATURE_NAME}, but CMake reports feature not supported")
ENDIF()
@ -65,11 +68,7 @@ IF (KOKKOS_CXX_STANDARD AND CMAKE_CXX_STANDARD)
ENDIF()
IF (KOKKOS_CXX_STANDARD STREQUAL "11" )
kokkos_set_cxx_standard_feature(11)
SET(KOKKOS_ENABLE_CXX11 ON)
SET(KOKKOS_CXX_INTERMEDIATE_STANDARD "11")
ELSEIF(KOKKOS_CXX_STANDARD STREQUAL "14")
IF(KOKKOS_CXX_STANDARD STREQUAL "14")
kokkos_set_cxx_standard_feature(14)
SET(KOKKOS_CXX_INTERMEDIATE_STANDARD "1Y")
SET(KOKKOS_ENABLE_CXX14 ON)
@ -81,21 +80,21 @@ ELSEIF(KOKKOS_CXX_STANDARD STREQUAL "20")
kokkos_set_cxx_standard_feature(20)
SET(KOKKOS_CXX_INTERMEDIATE_STANDARD "2A")
SET(KOKKOS_ENABLE_CXX20 ON)
ELSEIF(KOKKOS_CXX_STANDARD STREQUAL "98")
MESSAGE(FATAL_ERROR "Kokkos requires C++11 or newer!")
ELSEIF(KOKKOS_CXX_STANDARD STREQUAL "98" OR KOKKOS_CXX_STANDARD STREQUAL "11")
MESSAGE(FATAL_ERROR "Kokkos requires C++14 or newer!")
ELSE()
MESSAGE(FATAL_ERROR "Unknown C++ standard ${KOKKOS_CXX_STANDARD} - must be 11, 14, 17, or 20")
MESSAGE(FATAL_ERROR "Unknown C++ standard ${KOKKOS_CXX_STANDARD} - must be 14, 17, or 20")
ENDIF()
# Enforce that extensions are turned off for nvcc_wrapper.
# For compiling CUDA code using nvcc_wrapper, we will use the host compiler's
# flags for turning on C++11. Since for compiler ID and versioning purposes
# flags for turning on C++14. Since for compiler ID and versioning purposes
# CMake recognizes the host compiler when calling nvcc_wrapper, this just
# works. Both NVCC and nvcc_wrapper only recognize '-std=c++11' which means
# works. Both NVCC and nvcc_wrapper only recognize '-std=c++14' which means
# that we can only use host compilers for CUDA builds that use those flags.
# It also means that extensions (gnu++11) can't be turned on for CUDA builds.
# It also means that extensions (gnu++14) can't be turned on for CUDA builds.
IF(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA)
IF(NOT DEFINED CMAKE_CXX_EXTENSIONS)
@ -117,7 +116,7 @@ IF(KOKKOS_ENABLE_CUDA)
MESSAGE(FATAL_ERROR "Compiling CUDA code with clang doesn't support C++ extensions. Set -DCMAKE_CXX_EXTENSIONS=OFF")
ENDIF()
ELSEIF(NOT KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA)
MESSAGE(FATAL_ERROR "Invalid compiler for CUDA. The compiler must be nvcc_wrapper or Clang, but compiler ID was ${KOKKOS_CXX_COMPILER_ID}")
MESSAGE(FATAL_ERROR "Invalid compiler for CUDA. The compiler must be nvcc_wrapper or Clang or use kokkos_launch_compiler, but compiler ID was ${KOKKOS_CXX_COMPILER_ID}")
ENDIF()
ENDIF()

4
lib/kokkos/cmake/kokkos_tpls.cmake
View File

@ -76,3 +76,7 @@ STRING(REPLACE ";" "\n" KOKKOS_TPL_EXPORT_TEMP "${KOKKOS_TPL_EXPORTS}")
#Convert to a regular variable
UNSET(KOKKOS_TPL_EXPORTS CACHE)
SET(KOKKOS_TPL_EXPORTS ${KOKKOS_TPL_EXPORT_TEMP})
IF (KOKKOS_ENABLE_MEMKIND)
SET(KOKKOS_ENABLE_HBWSPACE)
LIST(APPEND KOKKOS_MEMSPACE_LIST HBWSpace)
ENDIF()

111
lib/kokkos/cmake/kokkos_tribits.cmake
View File

@ -6,6 +6,12 @@ INCLUDE(GNUInstallDirs)
MESSAGE(STATUS "The project name is: ${PROJECT_NAME}")
FUNCTION(VERIFY_EMPTY CONTEXT)
if(${ARGN})
MESSAGE(FATAL_ERROR "Kokkos does not support all of Tribits. Unhandled arguments in ${CONTEXT}:\n${ARGN}")
endif()
ENDFUNCTION()
#Leave this here for now - but only do for tribits
#This breaks the standalone CMake
IF (KOKKOS_HAS_TRILINOS)
@ -135,28 +141,37 @@ FUNCTION(KOKKOS_ADD_EXECUTABLE ROOT_NAME)
ENDFUNCTION()
FUNCTION(KOKKOS_ADD_EXECUTABLE_AND_TEST ROOT_NAME)
IF (KOKKOS_HAS_TRILINOS)
TRIBITS_ADD_EXECUTABLE_AND_TEST(
${ROOT_NAME}
TESTONLYLIBS kokkos_gtest
${ARGN}
NUM_MPI_PROCS 1
COMM serial mpi
FAIL_REGULAR_EXPRESSION " FAILED "
)
ELSE()
CMAKE_PARSE_ARGUMENTS(PARSE
""
""
"SOURCES;CATEGORIES"
"SOURCES;CATEGORIES;ARGS"
${ARGN})
VERIFY_EMPTY(KOKKOS_ADD_EXECUTABLE_AND_TEST ${PARSE_UNPARSED_ARGUMENTS})
IF (KOKKOS_HAS_TRILINOS)
IF(DEFINED PARSE_ARGS)
STRING(REPLACE ";" " " PARSE_ARGS "${PARSE_ARGS}")
ENDIF()
TRIBITS_ADD_EXECUTABLE_AND_TEST(
${ROOT_NAME}
SOURCES ${PARSE_SOURCES}
TESTONLYLIBS kokkos_gtest
NUM_MPI_PROCS 1
COMM serial mpi
ARGS ${PARSE_ARGS}
CATEGORIES ${PARSE_CATEGORIES}
SOURCES ${PARSE_SOURCES}
FAIL_REGULAR_EXPRESSION " FAILED "
ARGS ${PARSE_ARGS}
)
ELSE()
KOKKOS_ADD_TEST_EXECUTABLE(${ROOT_NAME}
SOURCES ${PARSE_SOURCES}
)
KOKKOS_ADD_TEST(NAME ${ROOT_NAME}
EXE ${ROOT_NAME}
FAIL_REGULAR_EXPRESSION " FAILED "
ARGS ${PARSE_ARGS}
)
ENDIF()
ENDFUNCTION()
@ -219,6 +234,7 @@ MACRO(KOKKOS_ADD_TEST_EXECUTABLE ROOT_NAME)
${PARSE_UNPARSED_ARGUMENTS}
TESTONLYLIBS kokkos_gtest
)
SET(EXE_NAME ${PACKAGE_NAME}_${ROOT_NAME})
ENDMACRO()
MACRO(KOKKOS_PACKAGE_POSTPROCESS)
@ -227,6 +243,79 @@ MACRO(KOKKOS_PACKAGE_POSTPROCESS)
endif()
ENDMACRO()
## KOKKOS_CONFIGURE_CORE Configure/Generate header files for core content based
## on enabled backends.
## KOKKOS_FWD is the forward declare set
## KOKKOS_SETUP is included in Kokkos_Macros.hpp and include prefix includes/defines
## KOKKOS_DECLARE is the declaration set
## KOKKOS_POST_INCLUDE is included at the end of Kokkos_Core.hpp
MACRO(KOKKOS_CONFIGURE_CORE)
SET(FWD_BACKEND_LIST)
FOREACH(MEMSPACE ${KOKKOS_MEMSPACE_LIST})
LIST(APPEND FWD_BACKEND_LIST ${MEMSPACE})
ENDFOREACH()
FOREACH(BACKEND_ ${KOKKOS_ENABLED_DEVICES})
IF( ${BACKEND_} STREQUAL "PTHREAD")
LIST(APPEND FWD_BACKEND_LIST THREADS)
ELSE()
LIST(APPEND FWD_BACKEND_LIST ${BACKEND_})
ENDIF()
ENDFOREACH()
MESSAGE(STATUS "Kokkos Devices: ${KOKKOS_ENABLED_DEVICES}, Kokkos Backends: ${FWD_BACKEND_LIST}")
KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_FwdBackend.hpp "KOKKOS_FWD" "fwd/Kokkos_Fwd" "${FWD_BACKEND_LIST}")
KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_SetupBackend.hpp "KOKKOS_SETUP" "setup/Kokkos_Setup" "${DEVICE_SETUP_LIST}")
KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_DeclareBackend.hpp "KOKKOS_DECLARE" "decl/Kokkos_Declare" "${FWD_BACKEND_LIST}")
KOKKOS_CONFIG_HEADER( KokkosCore_Config_HeaderSet.in KokkosCore_Config_PostInclude.hpp "KOKKOS_POST_INCLUDE" "Kokkos_Post_Include" "${KOKKOS_BACKEND_POST_INCLUDE_LIST}")
SET(_DEFAULT_HOST_MEMSPACE "::Kokkos::HostSpace")
KOKKOS_OPTION(DEFAULT_DEVICE_MEMORY_SPACE "" STRING "Override default device memory space")
KOKKOS_OPTION(DEFAULT_HOST_MEMORY_SPACE "" STRING "Override default host memory space")
KOKKOS_OPTION(DEFAULT_DEVICE_EXECUTION_SPACE "" STRING "Override default device execution space")
KOKKOS_OPTION(DEFAULT_HOST_PARALLEL_EXECUTION_SPACE "" STRING "Override default host parallel execution space")
IF (NOT Kokkos_DEFAULT_DEVICE_EXECUTION_SPACE STREQUAL "")
SET(_DEVICE_PARALLEL ${Kokkos_DEFAULT_DEVICE_EXECUTION_SPACE})
MESSAGE(STATUS "Override default device execution space: ${_DEVICE_PARALLEL}")
SET(KOKKOS_DEVICE_SPACE_ACTIVE ON)
ELSE()
IF (_DEVICE_PARALLEL STREQUAL "NoTypeDefined")
SET(KOKKOS_DEVICE_SPACE_ACTIVE OFF)
ELSE()
SET(KOKKOS_DEVICE_SPACE_ACTIVE ON)
ENDIF()
ENDIF()
IF (NOT Kokkos_DEFAULT_HOST_PARALLEL_EXECUTION_SPACE STREQUAL "")
SET(_HOST_PARALLEL ${Kokkos_DEFAULT_HOST_PARALLEL_EXECUTION_SPACE})
MESSAGE(STATUS "Override default host parallel execution space: ${_HOST_PARALLEL}")
SET(KOKKOS_HOSTPARALLEL_SPACE_ACTIVE ON)
ELSE()
IF (_HOST_PARALLEL STREQUAL "NoTypeDefined")
SET(KOKKOS_HOSTPARALLEL_SPACE_ACTIVE OFF)
ELSE()
SET(KOKKOS_HOSTPARALLEL_SPACE_ACTIVE ON)
ENDIF()
ENDIF()
#We are ready to configure the header
CONFIGURE_FILE(cmake/KokkosCore_config.h.in KokkosCore_config.h @ONLY)
ENDMACRO()
## KOKKOS_INSTALL_ADDITIONAL_FILES - instruct cmake to install files in target destination.
## Includes generated header files, scripts such as nvcc_wrapper and hpcbind,
## as well as other files provided through plugins.
MACRO(KOKKOS_INSTALL_ADDITIONAL_FILES)
# kokkos_launch_compiler is used by Kokkos to prefix compiler commands so that they forward to nvcc_wrapper
INSTALL(PROGRAMS
"${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper"
"${CMAKE_CURRENT_SOURCE_DIR}/bin/hpcbind"
"${CMAKE_CURRENT_SOURCE_DIR}/bin/kokkos_launch_compiler"
DESTINATION ${CMAKE_INSTALL_BINDIR})
INSTALL(FILES
"${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_config.h"
"${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_FwdBackend.hpp"
"${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_SetupBackend.hpp"
"${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_DeclareBackend.hpp"
"${CMAKE_CURRENT_BINARY_DIR}/KokkosCore_Config_PostInclude.hpp"
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
ENDMACRO()
FUNCTION(KOKKOS_SET_LIBRARY_PROPERTIES LIBRARY_NAME)
CMAKE_PARSE_ARGUMENTS(PARSE
"PLAIN_STYLE"

35
lib/kokkos/cmake/tpls/FindTPLCUSPARSE.cmake
View File

@ -1,14 +1,16 @@
# @HEADER
# ************************************************************************
#
# Trilinos: An Object-Oriented Solver Framework
# Copyright (2001) Sandia Corporation
# Kokkos v. 3.0
# Copyright (2020) National Technology & Engineering
# Solutions of Sandia, LLC (NTESS).
#
# Under the terms of Contract DE-NA0003525 with NTESS,
# the U.S. Government retains certain rights in this software.
#
# Copyright (2001) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
# work by or on behalf of the U.S. Government. Export of this program
# may require a license from the United States Government.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
@ -21,10 +23,10 @@
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
@ -33,22 +35,7 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# NOTICE: The United States Government is granted for itself and others
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
# license in this data to reproduce, prepare derivative works, and
# perform publicly and display publicly. Beginning five (5) years from
# July 25, 2001, the United States Government is granted for itself and
# others acting on its behalf a paid-up, nonexclusive, irrevocable
# worldwide license in this data to reproduce, prepare derivative works,
# distribute copies to the public, perform publicly and display
# publicly, and to permit others to do so.
#
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
#
# ************************************************************************
# @HEADER

35
lib/kokkos/cmake/tpls/FindTPLHWLOC.cmake
View File

@ -1,14 +1,16 @@
# @HEADER
# ************************************************************************
#
# Trilinos: An Object-Oriented Solver Framework
# Copyright (2001) Sandia Corporation
# Kokkos v. 3.0
# Copyright (2020) National Technology & Engineering
# Solutions of Sandia, LLC (NTESS).
#
# Under the terms of Contract DE-NA0003525 with NTESS,
# the U.S. Government retains certain rights in this software.
#
# Copyright (2001) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
# work by or on behalf of the U.S. Government. Export of this program
# may require a license from the United States Government.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
@ -21,10 +23,10 @@
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
@ -33,22 +35,7 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# NOTICE: The United States Government is granted for itself and others
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
# license in this data to reproduce, prepare derivative works, and
# perform publicly and display publicly. Beginning five (5) years from
# July 25, 2001, the United States Government is granted for itself and
# others acting on its behalf a paid-up, nonexclusive, irrevocable
# worldwide license in this data to reproduce, prepare derivative works,
# distribute copies to the public, perform publicly and display
# publicly, and to permit others to do so.
#
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
#
# ************************************************************************
# @HEADER

35
lib/kokkos/cmake/tpls/FindTPLPthread.cmake
View File

@ -1,14 +1,16 @@
# @HEADER
# ************************************************************************
#
# Trilinos: An Object-Oriented Solver Framework
# Copyright (2001) Sandia Corporation
# Kokkos v. 3.0
# Copyright (2020) National Technology & Engineering
# Solutions of Sandia, LLC (NTESS).
#
# Under the terms of Contract DE-NA0003525 with NTESS,
# the U.S. Government retains certain rights in this software.
#
# Copyright (2001) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000, there is a non-exclusive license for use of this
# work by or on behalf of the U.S. Government. Export of this program
# may require a license from the United States Government.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
@ -21,10 +23,10 @@
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY SANDIA CORPORATION "AS IS" AND ANY
# THIS SOFTWARE IS PROVIDED BY NTESS "AS IS" AND ANY
# EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION OR THE
# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL NTESS OR THE
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
@ -33,22 +35,7 @@
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# NOTICE: The United States Government is granted for itself and others
# acting on its behalf a paid-up, nonexclusive, irrevocable worldwide
# license in this data to reproduce, prepare derivative works, and
# perform publicly and display publicly. Beginning five (5) years from
# July 25, 2001, the United States Government is granted for itself and
# others acting on its behalf a paid-up, nonexclusive, irrevocable
# worldwide license in this data to reproduce, prepare derivative works,
# distribute copies to the public, perform publicly and display
# publicly, and to permit others to do so.
#
# NEITHER THE UNITED STATES GOVERNMENT, NOR THE UNITED STATES DEPARTMENT
# OF ENERGY, NOR SANDIA CORPORATION, NOR ANY OF THEIR EMPLOYEES, MAKES
# ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LEGAL LIABILITY OR
# RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR USEFULNESS OF ANY
# INFORMATION, APPARATUS, PRODUCT, OR PROCESS DISCLOSED, OR REPRESENTS
# THAT ITS USE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS.
# Questions? Contact Christian R. Trott (crtrott@sandia.gov)
#
# ************************************************************************
# @HEADER

54
lib/kokkos/containers/performance_tests/CMakeLists.txt
View File

@ -3,44 +3,26 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
KOKKOS_INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR})
KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/../src )
IF(Kokkos_ENABLE_CUDA)
SET(SOURCES
foreach(Tag Threads;OpenMP;Cuda;HPX;HIP)
# Because there is always an exception to the rule
if(Tag STREQUAL "Threads")
set(DEVICE "PTHREAD")
else()
string(TOUPPER ${Tag} DEVICE)
endif()
string(TOLOWER ${Tag} dir)
if(Kokkos_ENABLE_${DEVICE})
message(STATUS "Sources Test${Tag}.cpp")
set(SOURCES
TestMain.cpp
TestCuda.cpp
Test${Tag}.cpp
)
KOKKOS_ADD_EXECUTABLE_AND_TEST( PerformanceTest_Cuda
KOKKOS_ADD_EXECUTABLE_AND_TEST(
PerformanceTest_${Tag}
SOURCES ${SOURCES}
)
ENDIF()
IF(Kokkos_ENABLE_PTHREAD)
SET(SOURCES
TestMain.cpp
TestThreads.cpp
)
KOKKOS_ADD_EXECUTABLE_AND_TEST( PerformanceTest_Threads
SOURCES ${SOURCES}
)
ENDIF()
IF(Kokkos_ENABLE_OPENMP)
SET(SOURCES
TestMain.cpp
TestOpenMP.cpp
)
KOKKOS_ADD_EXECUTABLE_AND_TEST( PerformanceTest_OpenMP
SOURCES ${SOURCES}
)
ENDIF()
IF(Kokkos_ENABLE_HPX)
SET(SOURCES
TestMain.cpp
TestHPX.cpp
)
KOKKOS_ADD_EXECUTABLE_AND_TEST( PerformanceTest_HPX
SOURCES ${SOURCES}
)
ENDIF()
endif()
endforeach()

8
lib/kokkos/containers/performance_tests/Makefile
View File

@ -58,8 +58,8 @@ endif
KokkosContainers_PerformanceTest_Cuda: $(OBJ_CUDA) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_CUDA) $(KOKKOS_LIBS) $(LIB) -o KokkosContainers_PerformanceTest_Cuda
KokkosContainers_PerformanceTest_ROCm: $(OBJ_ROCM) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_ROCM) $(KOKKOS_LIBS) $(LIB) -o KokkosContainers_PerformanceTest_ROCm
KokkosContainers_PerformanceTest_HIP: $(OBJ_HIP) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_HIP) $(KOKKOS_LIBS) $(LIB) -o KokkosContainers_PerformanceTest_HIP
KokkosContainers_PerformanceTest_Threads: $(OBJ_THREADS) $(KOKKOS_LINK_DEPENDS)
$(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_THREADS) $(KOKKOS_LIBS) $(LIB) -o KokkosContainers_PerformanceTest_Threads
@ -73,8 +73,8 @@ KokkosContainers_PerformanceTest_HPX: $(OBJ_HPX) $(KOKKOS_LINK_DEPENDS)
test-cuda: KokkosContainers_PerformanceTest_Cuda
./KokkosContainers_PerformanceTest_Cuda
test-rocm: KokkosContainers_PerformanceTest_ROCm
./KokkosContainers_PerformanceTest_ROCm
test-hip: KokkosContainers_PerformanceTest_HIP
./KokkosContainers_PerformanceTest_HIP
test-threads: KokkosContainers_PerformanceTest_Threads
./KokkosContainers_PerformanceTest_Threads

22
lib/kokkos/containers/performance_tests/TestCuda.cpp
View File

@ -43,7 +43,6 @@
*/
#include <Kokkos_Macros.hpp>
#if defined(KOKKOS_ENABLE_CUDA)
#include <cstdint>
#include <string>
@ -66,23 +65,13 @@
namespace Performance {
class cuda : public ::testing::Test {
protected:
static void SetUpTestCase() {
std::cout << std::setprecision(5) << std::scientific;
Kokkos::InitArguments args(-1, -1, 0);
Kokkos::initialize(args);
}
static void TearDownTestCase() { Kokkos::finalize(); }
};
TEST_F(cuda, dynrankview_perf) {
TEST(TEST_CATEGORY, dynrankview_perf) {
std::cout << "Cuda" << std::endl;
std::cout << " DynRankView vs View: Initialization Only " << std::endl;
test_dynrankview_op_perf<Kokkos::Cuda>(40960);
}
TEST_F(cuda, global_2_local) {
TEST(TEST_CATEGORY, global_2_local) {
std::cout << "Cuda" << std::endl;
std::cout << "size, create, generate, fill, find" << std::endl;
for (unsigned i = Performance::begin_id_size; i <= Performance::end_id_size;
@ -90,15 +79,12 @@ TEST_F(cuda, global_2_local) {
test_global_to_local_ids<Kokkos::Cuda>(i);
}
TEST_F(cuda, unordered_map_performance_near) {
TEST(TEST_CATEGORY, unordered_map_performance_near) {
Perf::run_performance_tests<Kokkos::Cuda, true>("cuda-near");
}
TEST_F(cuda, unordered_map_performance_far) {
TEST(TEST_CATEGORY, unordered_map_performance_far) {
Perf::run_performance_tests<Kokkos::Cuda, false>("cuda-far");
}
} // namespace Performance
#else
void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTCUDA_PREVENT_EMPTY_LINK_ERROR() {}
#endif /* #if defined( KOKKOS_ENABLE_CUDA ) */

45
lib/kokkos/containers/performance_tests/TestROCm.cpp → lib/kokkos/containers/performance_tests/TestHIP.cpp
View File

@ -43,7 +43,6 @@
*/
#include <Kokkos_Macros.hpp>
#if defined(KOKKOS_ENABLE_ROCM)
#include <cstdint>
#include <string>
@ -66,46 +65,26 @@
namespace Performance {
class rocm : public ::testing::Test {
protected:
static void SetUpTestCase() {
std::cout << std::setprecision(5) << std::scientific;
Kokkos::HostSpace::execution_space::initialize();
Kokkos::Experimental::ROCm::initialize(
Kokkos::Experimental::ROCm::SelectDevice(0));
}
static void TearDownTestCase() {
Kokkos::Experimental::ROCm::finalize();
Kokkos::HostSpace::execution_space::finalize();
}
};
#if 0
// issue 1089
TEST_F( rocm, dynrankview_perf )
{
std::cout << "ROCm" << std::endl;
TEST(TEST_CATEGORY, dynrankview_perf) {
std::cout << "HIP" << std::endl;
std::cout << " DynRankView vs View: Initialization Only " << std::endl;
test_dynrankview_op_perf<Kokkos::Experimental::ROCm>( 40960 );
test_dynrankview_op_perf<Kokkos::Experimental::HIP>(40960);
}
TEST_F( rocm, global_2_local)
{
std::cout << "ROCm" << std::endl;
TEST(TEST_CATEGORY, global_2_local) {
std::cout << "HIP" << std::endl;
std::cout << "size, create, generate, fill, find" << std::endl;
for (unsigned i=Performance::begin_id_size; i<=Performance::end_id_size; i *= Performance::id_step)
test_global_to_local_ids<Kokkos::Experimental::ROCm>(i);
for (unsigned i = Performance::begin_id_size; i <= Performance::end_id_size;
i *= Performance::id_step)
test_global_to_local_ids<Kokkos::Experimental::HIP>(i);
}
#endif
TEST_F(rocm, unordered_map_performance_near) {
Perf::run_performance_tests<Kokkos::Experimental::ROCm, true>("rocm-near");
TEST(TEST_CATEGORY, unordered_map_performance_near) {
Perf::run_performance_tests<Kokkos::Experimental::HIP, true>("hip-near");
}
TEST_F(rocm, unordered_map_performance_far) {
Perf::run_performance_tests<Kokkos::Experimental::ROCm, false>("rocm-far");
TEST(TEST_CATEGORY, unordered_map_performance_far) {
Perf::run_performance_tests<Kokkos::Experimental::HIP, false>("hip-far");
}
} // namespace Performance
#else
void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTROCM_PREVENT_EMPTY_LINK_ERROR() {}
#endif /* #if defined( KOKKOS_ENABLE_ROCM ) */

26
lib/kokkos/containers/performance_tests/TestHPX.cpp
View File

@ -43,7 +43,6 @@
*/
#include <Kokkos_Macros.hpp>
#if defined(KOKKOS_ENABLE_HPX)
#include <gtest/gtest.h>
@ -64,25 +63,13 @@
namespace Performance {
class hpx : public ::testing::Test {
protected:
static void SetUpTestCase() {
std::cout << std::setprecision(5) << std::scientific;
Kokkos::initialize();
Kokkos::print_configuration(std::cout);
}
static void TearDownTestCase() { Kokkos::finalize(); }
};
TEST_F(hpx, dynrankview_perf) {
TEST(TEST_CATEGORY, dynrankview_perf) {
std::cout << "HPX" << std::endl;
std::cout << " DynRankView vs View: Initialization Only " << std::endl;
test_dynrankview_op_perf<Kokkos::Experimental::HPX>(8192);
}
TEST_F(hpx, global_2_local) {
TEST(TEST_CATEGORY, global_2_local) {
std::cout << "HPX" << std::endl;
std::cout << "size, create, generate, fill, find" << std::endl;
for (unsigned i = Performance::begin_id_size; i <= Performance::end_id_size;
@ -90,7 +77,7 @@ TEST_F(hpx, global_2_local) {
test_global_to_local_ids<Kokkos::Experimental::HPX>(i);
}
TEST_F(hpx, unordered_map_performance_near) {
TEST(TEST_CATEGORY, unordered_map_performance_near) {
unsigned num_hpx = 4;
std::ostringstream base_file_name;
base_file_name << "hpx-" << num_hpx << "-near";
@ -98,7 +85,7 @@ TEST_F(hpx, unordered_map_performance_near) {
base_file_name.str());
}
TEST_F(hpx, unordered_map_performance_far) {
TEST(TEST_CATEGORY, unordered_map_performance_far) {
unsigned num_hpx = 4;
std::ostringstream base_file_name;
base_file_name << "hpx-" << num_hpx << "-far";
@ -106,7 +93,7 @@ TEST_F(hpx, unordered_map_performance_far) {
base_file_name.str());
}
TEST_F(hpx, scatter_view) {
TEST(TEST_CATEGORY, scatter_view) {
std::cout << "ScatterView data-duplicated test:\n";
Perf::test_scatter_view<Kokkos::Experimental::HPX, Kokkos::LayoutRight,
Kokkos::Experimental::ScatterDuplicated,
@ -119,6 +106,3 @@ TEST_F(hpx, scatter_view) {
}
} // namespace Performance
#else
void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTHPX_PREVENT_EMPTY_LINK_ERROR() {}
#endif

8
lib/kokkos/containers/performance_tests/TestMain.cpp
View File

@ -45,9 +45,13 @@
#include <gtest/gtest.h>
#include <cstdlib>
#include <Kokkos_Macros.hpp>
#include <Kokkos_Core.hpp>
int main(int argc, char *argv[]) {
Kokkos::initialize(argc, argv);
::testing::InitGoogleTest(&argc, argv);
return RUN_ALL_TESTS();
int result = RUN_ALL_TESTS();
Kokkos::finalize();
return result;
}

27
lib/kokkos/containers/performance_tests/TestOpenMP.cpp
View File

@ -43,7 +43,6 @@
*/
#include <Kokkos_Macros.hpp>
#if defined(KOKKOS_ENABLE_OPENMP)
#include <gtest/gtest.h>
@ -64,25 +63,13 @@
namespace Performance {
class openmp : public ::testing::Test {
protected:
static void SetUpTestCase() {
std::cout << std::setprecision(5) << std::scientific;
Kokkos::initialize();
Kokkos::OpenMP::print_configuration(std::cout);
}
static void TearDownTestCase() { Kokkos::finalize(); }
};
TEST_F(openmp, dynrankview_perf) {
TEST(TEST_CATEGORY, dynrankview_perf) {
std::cout << "OpenMP" << std::endl;
std::cout << " DynRankView vs View: Initialization Only " << std::endl;
test_dynrankview_op_perf<Kokkos::OpenMP>(8192);
}
TEST_F(openmp, global_2_local) {
TEST(TEST_CATEGORY, global_2_local) {
std::cout << "OpenMP" << std::endl;
std::cout << "size, create, generate, fill, find" << std::endl;
for (unsigned i = Performance::begin_id_size; i <= Performance::end_id_size;
@ -90,7 +77,7 @@ TEST_F(openmp, global_2_local) {
test_global_to_local_ids<Kokkos::OpenMP>(i);
}
TEST_F(openmp, unordered_map_performance_near) {
TEST(TEST_CATEGORY, unordered_map_performance_near) {
unsigned num_openmp = 4;
if (Kokkos::hwloc::available()) {
num_openmp = Kokkos::hwloc::get_available_numa_count() *
@ -102,7 +89,7 @@ TEST_F(openmp, unordered_map_performance_near) {
Perf::run_performance_tests<Kokkos::OpenMP, true>(base_file_name.str());
}
TEST_F(openmp, unordered_map_performance_far) {
TEST(TEST_CATEGORY, unordered_map_performance_far) {
unsigned num_openmp = 4;
if (Kokkos::hwloc::available()) {
num_openmp = Kokkos::hwloc::get_available_numa_count() *
@ -114,7 +101,7 @@ TEST_F(openmp, unordered_map_performance_far) {
Perf::run_performance_tests<Kokkos::OpenMP, false>(base_file_name.str());
}
TEST_F(openmp, scatter_view) {
TEST(TEST_CATEGORY, scatter_view) {
std::cout << "ScatterView data-duplicated test:\n";
Perf::test_scatter_view<Kokkos::OpenMP, Kokkos::LayoutRight,
Kokkos::Experimental::ScatterDuplicated,
@ -127,7 +114,3 @@ TEST_F(openmp, scatter_view) {
}
} // namespace Performance
#else
void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTOPENMP_PREVENT_EMPTY_LINK_ERROR() {
}
#endif

35
lib/kokkos/containers/performance_tests/TestThreads.cpp
View File

@ -43,7 +43,6 @@
*/
#include <Kokkos_Macros.hpp>
#if defined(KOKKOS_ENABLE_THREADS)
#include <gtest/gtest.h>
@ -65,34 +64,13 @@
namespace Performance {
class threads : public ::testing::Test {
protected:
static void SetUpTestCase() {
std::cout << std::setprecision(5) << std::scientific;
unsigned num_threads = 4;
if (Kokkos::hwloc::available()) {
num_threads = Kokkos::hwloc::get_available_numa_count() *
Kokkos::hwloc::get_available_cores_per_numa() *
Kokkos::hwloc::get_available_threads_per_core();
}
std::cout << "Threads: " << num_threads << std::endl;
Kokkos::initialize(Kokkos::InitArguments(num_threads));
}
static void TearDownTestCase() { Kokkos::finalize(); }
};
TEST_F(threads, dynrankview_perf) {
TEST(threads, dynrankview_perf) {
std::cout << "Threads" << std::endl;
std::cout << " DynRankView vs View: Initialization Only " << std::endl;
test_dynrankview_op_perf<Kokkos::Threads>(8192);
}
TEST_F(threads, global_2_local) {
TEST(threads, global_2_local) {
std::cout << "Threads" << std::endl;
std::cout << "size, create, generate, fill, find" << std::endl;
for (unsigned i = Performance::begin_id_size; i <= Performance::end_id_size;
@ -100,7 +78,7 @@ TEST_F(threads, global_2_local) {
test_global_to_local_ids<Kokkos::Threads>(i);
}
TEST_F(threads, unordered_map_performance_near) {
TEST(threads, unordered_map_performance_near) {
unsigned num_threads = 4;
if (Kokkos::hwloc::available()) {
num_threads = Kokkos::hwloc::get_available_numa_count() *
@ -112,7 +90,7 @@ TEST_F(threads, unordered_map_performance_near) {
Perf::run_performance_tests<Kokkos::Threads, true>(base_file_name.str());
}
TEST_F(threads, unordered_map_performance_far) {
TEST(threads, unordered_map_performance_far) {
unsigned num_threads = 4;
if (Kokkos::hwloc::available()) {
num_threads = Kokkos::hwloc::get_available_numa_count() *
@ -125,8 +103,3 @@ TEST_F(threads, unordered_map_performance_far) {
}
} // namespace Performance
#else
void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTTHREADS_PREVENT_EMPTY_LINK_ERROR() {
}
#endif

4
lib/kokkos/containers/src/Kokkos_Bitset.hpp
View File

@ -74,7 +74,7 @@ template <typename Device>
class Bitset {
public:
using execution_space = Device;
using size_type = unsigned;
using size_type = unsigned int;
enum { BIT_SCAN_REVERSE = 1u };
enum { MOVE_HINT_BACKWARD = 2u };
@ -309,7 +309,7 @@ template <typename Device>
class ConstBitset {
public:
using execution_space = Device;
using size_type = unsigned;
using size_type = unsigned int;
private:
enum { block_size = static_cast<unsigned>(sizeof(unsigned) * CHAR_BIT) };

70
lib/kokkos/containers/src/Kokkos_DualView.hpp
View File

@ -162,7 +162,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
/// \brief The type of a const, random-access View host mirror of
/// \c t_dev_const_randomread.
using t_host_const_randomread_um =
typename t_dev_const_randomread::HostMirror;
typename t_dev_const_randomread_um::HostMirror;
//@}
//! \name Counters to keep track of changes ("modified" flags)
@ -245,21 +245,6 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
h_view(create_mirror_view(d_view)) // without UVM, host View mirrors
{}
explicit inline DualView(const ViewAllocateWithoutInitializing& arg_prop,
const size_t arg_N0 = KOKKOS_IMPL_CTOR_DEFAULT_ARG,
const size_t arg_N1 = KOKKOS_IMPL_CTOR_DEFAULT_ARG,
const size_t arg_N2 = KOKKOS_IMPL_CTOR_DEFAULT_ARG,
const size_t arg_N3 = KOKKOS_IMPL_CTOR_DEFAULT_ARG,
const size_t arg_N4 = KOKKOS_IMPL_CTOR_DEFAULT_ARG,
const size_t arg_N5 = KOKKOS_IMPL_CTOR_DEFAULT_ARG,
const size_t arg_N6 = KOKKOS_IMPL_CTOR_DEFAULT_ARG,
const size_t arg_N7 = KOKKOS_IMPL_CTOR_DEFAULT_ARG)
: DualView(Impl::ViewCtorProp<std::string,
Kokkos::Impl::WithoutInitializing_t>(
arg_prop.label, Kokkos::WithoutInitializing),
arg_N0, arg_N1, arg_N2, arg_N3, arg_N4, arg_N5, arg_N6,
arg_N7) {}
//! Copy constructor (shallow copy)
template <class SS, class LS, class DS, class MS>
DualView(const DualView<SS, LS, DS, MS>& src)
@ -457,7 +442,27 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
}
return dev;
}
static constexpr const int view_header_size = 128;
void impl_report_host_sync() const noexcept {
if (Kokkos::Tools::Experimental::get_callbacks().sync_dual_view !=
nullptr) {
Kokkos::Tools::syncDualView(
h_view.label(),
reinterpret_cast<void*>(reinterpret_cast<uintptr_t>(h_view.data()) -
view_header_size),
false);
}
}
void impl_report_device_sync() const noexcept {
if (Kokkos::Tools::Experimental::get_callbacks().sync_dual_view !=
nullptr) {
Kokkos::Tools::syncDualView(
d_view.label(),
reinterpret_cast<void*>(reinterpret_cast<uintptr_t>(d_view.data()) -
view_header_size),
true);
}
}
/// \brief Update data on device or host only if data in the other
/// space has been marked as modified.
///
@ -499,6 +504,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
deep_copy(d_view, h_view);
modified_flags(0) = modified_flags(1) = 0;
impl_report_device_sync();
}
}
if (dev == 0) { // hopefully Device is the same as DualView's host type
@ -515,6 +521,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
deep_copy(h_view, d_view);
modified_flags(0) = modified_flags(1) = 0;
impl_report_host_sync();
}
}
if (std::is_same<typename t_host::memory_space,
@ -539,12 +546,14 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
Impl::throw_runtime_exception(
"Calling sync on a DualView with a const datatype.");
}
impl_report_device_sync();
}
if (dev == 0) { // hopefully Device is the same as DualView's host type
if ((modified_flags(1) > 0) && (modified_flags(1) >= modified_flags(0))) {
Impl::throw_runtime_exception(
"Calling sync on a DualView with a const datatype.");
}
impl_report_host_sync();
}
}
@ -567,6 +576,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
deep_copy(h_view, d_view);
modified_flags(1) = modified_flags(0) = 0;
impl_report_host_sync();
}
}
@ -589,6 +599,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
deep_copy(d_view, h_view);
modified_flags(1) = modified_flags(0) = 0;
impl_report_device_sync();
}
}
@ -619,7 +630,26 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
if (modified_flags.data() == nullptr) return false;
return modified_flags(1) < modified_flags(0);
}
void impl_report_device_modification() {
if (Kokkos::Tools::Experimental::get_callbacks().modify_dual_view !=
nullptr) {
Kokkos::Tools::modifyDualView(
d_view.label(),
reinterpret_cast<void*>(reinterpret_cast<uintptr_t>(d_view.data()) -
view_header_size),
true);
}
}
void impl_report_host_modification() {
if (Kokkos::Tools::Experimental::get_callbacks().modify_dual_view !=
nullptr) {
Kokkos::Tools::modifyDualView(
h_view.label(),
reinterpret_cast<void*>(reinterpret_cast<uintptr_t>(h_view.data()) -
view_header_size),
false);
}
}
/// \brief Mark data as modified on the given device \c Device.
///
/// If \c Device is the same as this DualView's device type, then
@ -636,6 +666,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
(modified_flags(1) > modified_flags(0) ? modified_flags(1)
: modified_flags(0)) +
1;
impl_report_device_modification();
}
if (dev == 0) { // hopefully Device is the same as DualView's host type
// Increment the host's modified count.
@ -643,6 +674,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
(modified_flags(1) > modified_flags(0) ? modified_flags(1)
: modified_flags(0)) +
1;
impl_report_host_modification();
}
#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK
@ -663,6 +695,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
(modified_flags(1) > modified_flags(0) ? modified_flags(1)
: modified_flags(0)) +
1;
impl_report_host_modification();
#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK
if (modified_flags(0) && modified_flags(1)) {
std::string msg = "Kokkos::DualView::modify_host ERROR: ";
@ -682,6 +715,7 @@ class DualView : public ViewTraits<DataType, Arg1Type, Arg2Type, Arg3Type> {
(modified_flags(1) > modified_flags(0) ? modified_flags(1)
: modified_flags(0)) +
1;
impl_report_device_modification();
#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK
if (modified_flags(0) && modified_flags(1)) {
std::string msg = "Kokkos::DualView::modify_device ERROR: ";

34
lib/kokkos/containers/src/Kokkos_DynRankView.hpp
View File

@ -245,10 +245,13 @@ KOKKOS_INLINE_FUNCTION bool dyn_rank_view_verify_operator_bounds(
return (size_t(i) < map.extent(R)) &&
dyn_rank_view_verify_operator_bounds<R + 1>(rank, map, args...);
} else if (i != 0) {
// FIXME_SYCL SYCL doesn't allow printf in kernels
#ifndef KOKKOS_ENABLE_SYCL
printf(
"DynRankView Debug Bounds Checking Error: at rank %u\n Extra "
"arguments beyond the rank must be zero \n",
R);
#endif
return (false) &&
dyn_rank_view_verify_operator_bounds<R + 1>(rank, map, args...);
} else {
@ -1264,33 +1267,6 @@ class DynRankView : public ViewTraits<DataType, Properties...> {
typename traits::array_layout(arg_N0, arg_N1, arg_N2, arg_N3,
arg_N4, arg_N5, arg_N6, arg_N7)) {}
// For backward compatibility
// NDE This ctor does not take ViewCtorProp argument - should not use
// alternative createLayout call
explicit inline DynRankView(const ViewAllocateWithoutInitializing& arg_prop,
const typename traits::array_layout& arg_layout)
: DynRankView(
Kokkos::Impl::ViewCtorProp<std::string,
Kokkos::Impl::WithoutInitializing_t>(
arg_prop.label, Kokkos::WithoutInitializing),
arg_layout) {}
explicit inline DynRankView(const ViewAllocateWithoutInitializing& arg_prop,
const size_t arg_N0 = KOKKOS_INVALID_INDEX,
const size_t arg_N1 = KOKKOS_INVALID_INDEX,
const size_t arg_N2 = KOKKOS_INVALID_INDEX,
const size_t arg_N3 = KOKKOS_INVALID_INDEX,
const size_t arg_N4 = KOKKOS_INVALID_INDEX,
const size_t arg_N5 = KOKKOS_INVALID_INDEX,
const size_t arg_N6 = KOKKOS_INVALID_INDEX,
const size_t arg_N7 = KOKKOS_INVALID_INDEX)
: DynRankView(
Kokkos::Impl::ViewCtorProp<std::string,
Kokkos::Impl::WithoutInitializing_t>(
arg_prop.label, Kokkos::WithoutInitializing),
typename traits::array_layout(arg_N0, arg_N1, arg_N2, arg_N3,
arg_N4, arg_N5, arg_N6, arg_N7)) {}
//----------------------------------------
// Memory span required to wrap these dimensions.
static constexpr size_t required_allocation_size(
@ -1401,7 +1377,7 @@ struct DynRankSubviewTag {};
namespace Impl {
template <class SrcTraits, class... Args>
struct ViewMapping<
class ViewMapping<
typename std::enable_if<
(std::is_same<typename SrcTraits::specialize, void>::value &&
(std::is_same<typename SrcTraits::array_layout,
@ -2052,7 +2028,7 @@ create_mirror_view_and_copy(
nullptr) {
using Mirror = typename Impl::MirrorDRViewType<Space, T, P...>::view_type;
std::string label = name.empty() ? src.label() : name;
auto mirror = Mirror(Kokkos::ViewAllocateWithoutInitializing(label),
auto mirror = Mirror(view_alloc(WithoutInitializing, label),
Impl::reconstructLayout(src.layout(), src.rank()));
deep_copy(mirror, src);
return mirror;

16
lib/kokkos/containers/src/Kokkos_OffsetView.hpp
View File

@ -1940,7 +1940,7 @@ create_mirror(
const Kokkos::Experimental::OffsetView<T, P...>& src,
typename std::enable_if<
!std::is_same<typename Kokkos::ViewTraits<T, P...>::array_layout,
Kokkos::LayoutStride>::value>::type* = 0) {
Kokkos::LayoutStride>::value>::type* = nullptr) {
using src_type = Experimental::OffsetView<T, P...>;
using dst_type = typename src_type::HostMirror;
@ -1960,7 +1960,7 @@ create_mirror(
const Kokkos::Experimental::OffsetView<T, P...>& src,
typename std::enable_if<
std::is_same<typename Kokkos::ViewTraits<T, P...>::array_layout,
Kokkos::LayoutStride>::value>::type* = 0) {
Kokkos::LayoutStride>::value>::type* = nullptr) {
using src_type = Experimental::OffsetView<T, P...>;
using dst_type = typename src_type::HostMirror;
@ -2028,7 +2028,7 @@ create_mirror_view(
std::is_same<
typename Kokkos::Experimental::OffsetView<T, P...>::data_type,
typename Kokkos::Experimental::OffsetView<
T, P...>::HostMirror::data_type>::value)>::type* = 0) {
T, P...>::HostMirror::data_type>::value)>::type* = nullptr) {
return Kokkos::create_mirror(src);
}
@ -2038,7 +2038,7 @@ typename Kokkos::Impl::MirrorOffsetViewType<Space, T, P...>::view_type
create_mirror_view(const Space&,
const Kokkos::Experimental::OffsetView<T, P...>& src,
typename std::enable_if<Impl::MirrorOffsetViewType<
Space, T, P...>::is_same_memspace>::type* = 0) {
Space, T, P...>::is_same_memspace>::type* = nullptr) {
return src;
}
@ -2048,7 +2048,7 @@ typename Kokkos::Impl::MirrorOffsetViewType<Space, T, P...>::view_type
create_mirror_view(const Space&,
const Kokkos::Experimental::OffsetView<T, P...>& src,
typename std::enable_if<!Impl::MirrorOffsetViewType<
Space, T, P...>::is_same_memspace>::type* = 0) {
Space, T, P...>::is_same_memspace>::type* = nullptr) {
return typename Kokkos::Impl::MirrorOffsetViewType<Space, T, P...>::view_type(
src.label(), src.layout(),
{src.begin(0), src.begin(1), src.begin(2), src.begin(3), src.begin(4),
@ -2063,7 +2063,7 @@ create_mirror_view(const Space&,
// , std::string const& name = ""
// , typename
// std::enable_if<Impl::MirrorViewType<Space,T,P
// ...>::is_same_memspace>::type* = 0 ) {
// ...>::is_same_memspace>::type* = nullptr) {
// (void)name;
// return src;
// }
@ -2076,11 +2076,11 @@ create_mirror_view(const Space&,
// , std::string const& name = ""
// , typename
// std::enable_if<!Impl::MirrorViewType<Space,T,P
// ...>::is_same_memspace>::type* = 0 ) {
// ...>::is_same_memspace>::type* = nullptr) {
// using Mirror = typename
// Kokkos::Experimental::Impl::MirrorViewType<Space,T,P ...>::view_type;
// std::string label = name.empty() ? src.label() : name;
// auto mirror = Mirror(ViewAllocateWithoutInitializing(label), src.layout(),
// auto mirror = Mirror(view_alloc(WithoutInitializing, label), src.layout(),
// { src.begin(0), src.begin(1), src.begin(2),
// src.begin(3), src.begin(4),
// src.begin(5), src.begin(6), src.begin(7) });

67
lib/kokkos/containers/src/Kokkos_ScatterView.hpp
View File

@ -206,6 +206,23 @@ struct DefaultContribution<Kokkos::Experimental::HIP,
};
#endif
#ifdef KOKKOS_ENABLE_SYCL
template <>
struct DefaultDuplication<Kokkos::Experimental::SYCL> {
using type = Kokkos::Experimental::ScatterNonDuplicated;
};
template <>
struct DefaultContribution<Kokkos::Experimental::SYCL,
Kokkos::Experimental::ScatterNonDuplicated> {
using type = Kokkos::Experimental::ScatterAtomic;
};
template <>
struct DefaultContribution<Kokkos::Experimental::SYCL,
Kokkos::Experimental::ScatterDuplicated> {
using type = Kokkos::Experimental::ScatterAtomic;
};
#endif
// FIXME All these scatter values need overhaul:
// - like should they be copyable at all?
// - what is the internal handle type
@ -636,19 +653,10 @@ struct ReduceDuplicatesBase {
size_t stride_in, size_t start_in, size_t n_in,
std::string const& name)
: src(src_in), dst(dest_in), stride(stride_in), start(start_in), n(n_in) {
uint64_t kpID = 0;
if (Kokkos::Profiling::profileLibraryLoaded()) {
Kokkos::Profiling::beginParallelFor(std::string("reduce_") + name, 0,
&kpID);
}
using policy_type = RangePolicy<ExecSpace, size_t>;
using closure_type = Kokkos::Impl::ParallelFor<Derived, policy_type>;
const closure_type closure(*(static_cast<Derived*>(this)),
policy_type(0, stride));
closure.execute();
if (Kokkos::Profiling::profileLibraryLoaded()) {
Kokkos::Profiling::endParallelFor(kpID);
}
parallel_for(
std::string("Kokkos::ScatterView::ReduceDuplicates [") + name + "]",
RangePolicy<ExecSpace, size_t>(0, stride),
static_cast<Derived const&>(*this));
}
};
@ -682,19 +690,10 @@ struct ResetDuplicatesBase {
ResetDuplicatesBase(ValueType* data_in, size_t size_in,
std::string const& name)
: data(data_in) {
uint64_t kpID = 0;
if (Kokkos::Profiling::profileLibraryLoaded()) {
Kokkos::Profiling::beginParallelFor(std::string("reduce_") + name, 0,
&kpID);
}
using policy_type = RangePolicy<ExecSpace, size_t>;
using closure_type = Kokkos::Impl::ParallelFor<Derived, policy_type>;
const closure_type closure(*(static_cast<Derived*>(this)),
policy_type(0, size_in));
closure.execute();
if (Kokkos::Profiling::profileLibraryLoaded()) {
Kokkos::Profiling::endParallelFor(kpID);
}
parallel_for(
std::string("Kokkos::ScatterView::ResetDuplicates [") + name + "]",
RangePolicy<ExecSpace, size_t>(0, size_in),
static_cast<Derived const&>(*this));
}
};
@ -931,8 +930,8 @@ class ScatterView<DataType, Kokkos::LayoutRight, DeviceType, Op,
ScatterView(View<RT, RP...> const& original_view)
: unique_token(),
internal_view(
Kokkos::ViewAllocateWithoutInitializing(std::string("duplicated_") +
original_view.label()),
view_alloc(WithoutInitializing,
std::string("duplicated_") + original_view.label()),
unique_token.size(),
original_view.rank_dynamic > 0 ? original_view.extent(0)
: KOKKOS_IMPL_CTOR_DEFAULT_ARG,
@ -955,7 +954,7 @@ class ScatterView<DataType, Kokkos::LayoutRight, DeviceType, Op,
template <typename... Dims>
ScatterView(std::string const& name, Dims... dims)
: internal_view(Kokkos::ViewAllocateWithoutInitializing(name),
: internal_view(view_alloc(WithoutInitializing, name),
unique_token.size(), dims...) {
reset();
}
@ -1094,8 +1093,8 @@ class ScatterView<DataType, Kokkos::LayoutLeft, DeviceType, Op,
KOKKOS_IMPL_CTOR_DEFAULT_ARG};
arg_N[internal_view_type::rank - 1] = unique_token.size();
internal_view = internal_view_type(
Kokkos::ViewAllocateWithoutInitializing(std::string("duplicated_") +
original_view.label()),
view_alloc(WithoutInitializing,
std::string("duplicated_") + original_view.label()),
arg_N[0], arg_N[1], arg_N[2], arg_N[3], arg_N[4], arg_N[5], arg_N[6],
arg_N[7]);
reset();
@ -1121,9 +1120,9 @@ class ScatterView<DataType, Kokkos::LayoutLeft, DeviceType, Op,
KOKKOS_IMPL_CTOR_DEFAULT_ARG};
Kokkos::Impl::Experimental::args_to_array(arg_N, 0, dims...);
arg_N[internal_view_type::rank - 1] = unique_token.size();
internal_view = internal_view_type(
Kokkos::ViewAllocateWithoutInitializing(name), arg_N[0], arg_N[1],
arg_N[2], arg_N[3], arg_N[4], arg_N[5], arg_N[6], arg_N[7]);
internal_view = internal_view_type(view_alloc(WithoutInitializing, name),
arg_N[0], arg_N[1], arg_N[2], arg_N[3],
arg_N[4], arg_N[5], arg_N[6], arg_N[7]);
reset();
}

15
lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp
View File

@ -306,9 +306,9 @@ class UnorderedMap {
m_equal_to(equal_to),
m_size(),
m_available_indexes(calculate_capacity(capacity_hint)),
m_hash_lists(ViewAllocateWithoutInitializing("UnorderedMap hash list"),
m_hash_lists(view_alloc(WithoutInitializing, "UnorderedMap hash list"),
Impl::find_hash_size(capacity())),
m_next_index(ViewAllocateWithoutInitializing("UnorderedMap next index"),
m_next_index(view_alloc(WithoutInitializing, "UnorderedMap next index"),
capacity() + 1) // +1 so that the *_at functions can
// always return a valid reference
,
@ -540,7 +540,10 @@ class UnorderedMap {
// Previously claimed an unused entry that was not inserted.
// Release this unused entry immediately.
if (!m_available_indexes.reset(new_index)) {
// FIXME_SYCL SYCL doesn't allow printf in kernels
#ifndef KOKKOS_ENABLE_SYCL
printf("Unable to free existing\n");
#endif
}
}
@ -729,16 +732,16 @@ class UnorderedMap {
tmp.m_size = src.size();
tmp.m_available_indexes = bitset_type(src.capacity());
tmp.m_hash_lists = size_type_view(
ViewAllocateWithoutInitializing("UnorderedMap hash list"),
view_alloc(WithoutInitializing, "UnorderedMap hash list"),
src.m_hash_lists.extent(0));
tmp.m_next_index = size_type_view(
ViewAllocateWithoutInitializing("UnorderedMap next index"),
view_alloc(WithoutInitializing, "UnorderedMap next index"),
src.m_next_index.extent(0));
tmp.m_keys =
key_type_view(ViewAllocateWithoutInitializing("UnorderedMap keys"),
key_type_view(view_alloc(WithoutInitializing, "UnorderedMap keys"),
src.m_keys.extent(0));
tmp.m_values = value_type_view(
ViewAllocateWithoutInitializing("UnorderedMap values"),
view_alloc(WithoutInitializing, "UnorderedMap values"),
src.m_values.extent(0));
tmp.m_scalars = scalars_view("UnorderedMap scalars");

12
lib/kokkos/containers/unit_tests/CMakeLists.txt
View File

@ -3,7 +3,7 @@ KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
KOKKOS_INCLUDE_DIRECTORIES(REQUIRED_DURING_INSTALLATION_TESTING ${CMAKE_CURRENT_SOURCE_DIR})
KOKKOS_INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/../src )
foreach(Tag Threads;Serial;OpenMP;HPX;Cuda;HIP)
foreach(Tag Threads;Serial;OpenMP;HPX;Cuda;HIP;SYCL)
# Because there is always an exception to the rule
if(Tag STREQUAL "Threads")
set(DEVICE "PTHREAD")
@ -31,13 +31,21 @@ foreach(Tag Threads;Serial;OpenMP;HPX;Cuda;HIP)
Vector
ViewCtorPropEmbeddedDim
)
# Write to a temporary intermediate file and call configure_file to avoid
# updating timestamps triggering unnecessary rebuilds on subsequent cmake runs.
set(file ${dir}/Test${Tag}_${Name}.cpp)
file(WRITE ${file}
file(WRITE ${dir}/dummy.cpp
"#include <Test${Tag}_Category.hpp>\n"
"#include <Test${Name}.hpp>\n"
)
configure_file(${dir}/dummy.cpp ${file})
list(APPEND UnitTestSources ${file})
endforeach()
list(REMOVE_ITEM UnitTestSources
${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_Bitset.cpp
${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_ScatterView.cpp
${CMAKE_CURRENT_BINARY_DIR}/sycl/TestSYCL_UnorderedMap.cpp
)
KOKKOS_ADD_EXECUTABLE_AND_TEST(UnitTest_${Tag} SOURCES ${UnitTestSources})
endif()
endforeach()

2
lib/kokkos/containers/unit_tests/Makefile
View File

@ -7,7 +7,7 @@ vpath %.cpp ${KOKKOS_PATH}/containers/unit_tests/openmp
vpath %.cpp ${KOKKOS_PATH}/containers/unit_tests/hpx
vpath %.cpp ${KOKKOS_PATH}/containers/unit_tests/serial
vpath %.cpp ${KOKKOS_PATH}/containers/unit_tests/threads
vpath %.cpp ${KOKKOS_PATH}/containers/unit_tests/rocm
vpath %.cpp ${KOKKOS_PATH}/containers/unit_tests/hip
vpath %.cpp ${KOKKOS_PATH}/containers/unit_tests/cuda
vpath %.cpp ${CURDIR}
default: build_all

8
lib/kokkos/containers/unit_tests/TestDualView.hpp
View File

@ -108,7 +108,7 @@ struct test_dualview_combinations {
if (with_init) {
a = ViewType("A", n, m);
} else {
a = ViewType(Kokkos::ViewAllocateWithoutInitializing("A"), n, m);
a = ViewType(Kokkos::view_alloc(Kokkos::WithoutInitializing, "A"), n, m);
}
Kokkos::deep_copy(a.d_view, 1);
@ -404,14 +404,19 @@ void test_dualview_resize() {
Impl::test_dualview_resize<Scalar, Device>();
}
// FIXME_SYCL requires MDRange policy
#ifndef KOKKOS_ENABLE_SYCL
TEST(TEST_CATEGORY, dualview_combination) {
test_dualview_combinations<int, TEST_EXECSPACE>(10, true);
}
#endif
TEST(TEST_CATEGORY, dualview_alloc) {
test_dualview_alloc<int, TEST_EXECSPACE>(10);
}
// FIXME_SYCL requires MDRange policy
#ifndef KOKKOS_ENABLE_SYCL
TEST(TEST_CATEGORY, dualview_combinations_without_init) {
test_dualview_combinations<int, TEST_EXECSPACE>(10, false);
}
@ -428,6 +433,7 @@ TEST(TEST_CATEGORY, dualview_realloc) {
TEST(TEST_CATEGORY, dualview_resize) {
test_dualview_resize<int, TEST_EXECSPACE>();
}
#endif
} // namespace Test

6
lib/kokkos/containers/unit_tests/TestDynViewAPI.hpp
View File

@ -1063,8 +1063,8 @@ class TestDynViewAPI {
(void)thing;
}
dView0 d_uninitialized(Kokkos::ViewAllocateWithoutInitializing("uninit"),
10, 20);
dView0 d_uninitialized(
Kokkos::view_alloc(Kokkos::WithoutInitializing, "uninit"), 10, 20);
ASSERT_TRUE(d_uninitialized.data() != nullptr);
ASSERT_EQ(d_uninitialized.rank(), 2);
ASSERT_EQ(d_uninitialized.extent(0), 10);
@ -1532,7 +1532,7 @@ class TestDynViewAPI {
ASSERT_EQ(ds5.extent(5), ds5plus.extent(5));
#if (!defined(KOKKOS_ENABLE_CUDA) || defined(KOKKOS_ENABLE_CUDA_UVM)) && \
!defined(KOKKOS_ENABLE_HIP)
!defined(KOKKOS_ENABLE_HIP) && !defined(KOKKOS_ENABLE_SYCL)
ASSERT_EQ(&ds5(1, 1, 1, 1, 0) - &ds5plus(1, 1, 1, 1, 0), 0);
ASSERT_EQ(&ds5(1, 1, 1, 1, 0, 0) - &ds5plus(1, 1, 1, 1, 0, 0),
0); // passing argument to rank beyond the view's rank is allowed

3
lib/kokkos/containers/unit_tests/TestDynamicView.hpp
View File

@ -243,6 +243,8 @@ struct TestDynamicView {
}
};
// FIXME_SYCL needs resize_serial
#ifndef KOKKOS_ENABLE_SYCL
TEST(TEST_CATEGORY, dynamic_view) {
using TestDynView = TestDynamicView<double, TEST_EXECSPACE>;
@ -250,6 +252,7 @@ TEST(TEST_CATEGORY, dynamic_view) {
TestDynView::run(100000 + 100 * i);
}
}
#endif
} // namespace Test

27
lib/kokkos/containers/unit_tests/TestOffsetView.hpp
View File

@ -95,10 +95,6 @@ void test_offsetview_construction() {
ASSERT_EQ(ov.extent(1), 5);
#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA)
const int ovmin0 = ov.begin(0);
const int ovend0 = ov.end(0);
const int ovmin1 = ov.begin(1);
const int ovend1 = ov.end(1);
{
Kokkos::Experimental::OffsetView<Scalar*, Device> offsetV1("OneDOffsetView",
range0);
@ -134,6 +130,13 @@ void test_offsetview_construction() {
}
}
// FIXME_SYCL requires MDRange policy
#ifndef KOKKOS_ENABLE_SYCL
const int ovmin0 = ov.begin(0);
const int ovend0 = ov.end(0);
const int ovmin1 = ov.begin(1);
const int ovend1 = ov.end(1);
using range_type =
Kokkos::MDRangePolicy<Device, Kokkos::Rank<2>, Kokkos::IndexType<int> >;
using point_type = typename range_type::point_type;
@ -175,6 +178,7 @@ void test_offsetview_construction() {
}
ASSERT_EQ(OVResult, answer) << "Bad data found in OffsetView";
#endif
#endif
{
@ -211,6 +215,8 @@ void test_offsetview_construction() {
point3_type{{extent0, extent1, extent2}});
#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA)
// FIXME_SYCL requires MDRange policy
#ifdef KOKKOS_ENABLE_SYCL
int view3DSum = 0;
Kokkos::parallel_reduce(
rangePolicy3DZero,
@ -233,6 +239,7 @@ void test_offsetview_construction() {
ASSERT_EQ(view3DSum, offsetView3DSum)
<< "construction of OffsetView from View and begins array broken.";
#endif
#endif
}
view_type viewFromOV = ov.view();
@ -259,6 +266,8 @@ void test_offsetview_construction() {
Kokkos::deep_copy(aView, ov);
#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA)
// FIXME_SYCL requires MDRange policy
#ifndef KOKKOS_ENABLE_SYCL
int sum = 0;
Kokkos::parallel_reduce(
rangePolicy2D,
@ -268,6 +277,7 @@ void test_offsetview_construction() {
sum);
ASSERT_EQ(sum, 0) << "deep_copy(view, offsetView) broken.";
#endif
#endif
}
@ -278,6 +288,8 @@ void test_offsetview_construction() {
Kokkos::deep_copy(ov, aView);
#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA)
// FIXME_SYCL requires MDRange policy
#ifndef KOKKOS_ENABLE_SYCL
int sum = 0;
Kokkos::parallel_reduce(
rangePolicy2D,
@ -287,6 +299,7 @@ void test_offsetview_construction() {
sum);
ASSERT_EQ(sum, 0) << "deep_copy(offsetView, view) broken.";
#endif
#endif
}
}
@ -458,6 +471,8 @@ void test_offsetview_subview() {
ASSERT_EQ(offsetSubview.end(1), 9);
#if defined(KOKKOS_ENABLE_CUDA_LAMBDA) || !defined(KOKKOS_ENABLE_CUDA)
// FIXME_SYCL requires MDRange policy
#ifndef KOKKOS_ENABLE_SYCL
using range_type = Kokkos::MDRangePolicy<Device, Kokkos::Rank<2>,
Kokkos::IndexType<int> >;
using point_type = typename range_type::point_type;
@ -483,6 +498,7 @@ void test_offsetview_subview() {
sum);
ASSERT_EQ(sum, 6 * (e0 - b0) * (e1 - b1));
#endif
#endif
}
@ -685,9 +701,12 @@ void test_offsetview_offsets_rank3() {
}
#endif
// FIXME_SYCL needs MDRangePolicy
#ifndef KOKKOS_ENABLE_SYCL
TEST(TEST_CATEGORY, offsetview_construction) {
test_offsetview_construction<int, TEST_EXECSPACE>();
}
#endif
TEST(TEST_CATEGORY, offsetview_unmanaged_construction) {
test_offsetview_unmanaged_construction<int, TEST_EXECSPACE>();

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