git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12592 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -165,8 +165,8 @@ coprocessors.
|
||||
</P>
|
||||
<P>All of these commands are in packages provided with LAMMPS. An
|
||||
overview of packages is give in <A HREF = "Section_packages.html">Section
|
||||
packages</A>. Currently, there are 6 accelerator
|
||||
packages in LAMMPS, either as standard or user packages:
|
||||
packages</A>. These are the accelerator packages
|
||||
currently in LAMMPS, either as standard or user packages:
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR><TD ><A HREF = "accelerate_cuda.html">USER-CUDA</A> </TD><TD > for NVIDIA GPUs</TD></TR>
|
||||
@ -201,8 +201,8 @@ for that style.
|
||||
</P>
|
||||
<P>To use an accelerator package in LAMMPS, and one or more of the styles
|
||||
it provides, follow these general steps. Details vary from package to
|
||||
package and are explained in the individual accelerator sub-section
|
||||
doc pages, listed above:
|
||||
package and are explained in the individual accelerator doc pages,
|
||||
listed above:
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR><TD >build the accelerator library </TD><TD > only for USER-CUDA and GPU packages </TD></TR>
|
||||
@ -215,26 +215,46 @@ doc pages, listed above:
|
||||
<TR><TD >use accelerated styles in your input script </TD><TD > via "-sf" <A HREF = "Section_start.html#start_7">command-line switch</A> or <A HREF = "suffix.html">suffix</A> command
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>The first 4 steps typically only need to be done once, to create an
|
||||
executable that uses one or more accelerator packages. We are working
|
||||
to create a "make" tool that will perform all these 4 steps in a
|
||||
single command.
|
||||
<P>The first 4 steps can be done as a single command, using the
|
||||
src/Make.py tool. The Make.py tool is discussed in <A HREF = "Section_start.html#start_4">Section
|
||||
2.4</A> of the manual, and its use is
|
||||
illustrated in the individual accelerator sections. Typically these
|
||||
steps only need to be done once, to create an executable that uses one
|
||||
or more accelerator packages.
|
||||
</P>
|
||||
<P>The last 4 steps can all be done from the command-line when LAMMPS is
|
||||
launched, without changing your input script. Or you can add
|
||||
launched, without changing your input script, as illustrated in the
|
||||
individual accelerator sections. Or you can add
|
||||
<A HREF = "package.html">package</A> and <A HREF = "suffix.html">suffix</A> commands to your input
|
||||
script.
|
||||
</P>
|
||||
<P>The examples directory has several sub-directories with scripts and
|
||||
README files for how to use the following accelerator packages:
|
||||
<P>IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
|
||||
executable with all its accelerator packages installed. Note that the
|
||||
USER-INTEL and KOKKOS packages require you to choose one of their
|
||||
options when building. I.e. CPU or Phi for USER-INTEL. OpenMP, Cuda,
|
||||
or Phi for KOKKOS. Here are the exceptions; you cannot build a single
|
||||
executable with:
|
||||
</P>
|
||||
<UL><LI>examples/cuda for USER-CUDA package
|
||||
<LI>examples/gpu for GPU package
|
||||
<LI>examples/intel for USER-INTEL package
|
||||
<LI>examples/kokkos for KOKKOS package
|
||||
<UL><LI>both the USER-INTEL Phi and KOKKOS Phi options
|
||||
<LI>the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages
|
||||
</UL>
|
||||
<P>Likewise, the bench directory has FERMI and KEPLER sub-directories
|
||||
with scripts and README files for using all the accelerator packages.
|
||||
<P>See the examples/accelerate/README and make.list files for sample
|
||||
Make.py commands that build LAMMPS with any or all of the accelerator
|
||||
packages. As an example, here is a command that builds with all the
|
||||
GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
|
||||
including settings to build the needed auxiliary USER-CUDA and GPU
|
||||
libraries for Kepler GPUs:
|
||||
</P>
|
||||
<PRE>Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi -cuda mode=double arch=35 -gpu mode=double arch=35 \ -kokkos cuda arch=35 lib-all file mpi
|
||||
</PRE>
|
||||
<P>The examples/accelerate directory also has input scripts that can be
|
||||
used with all of the accelerator packages. See its README file for
|
||||
details.
|
||||
</P>
|
||||
<P>Likewise, the bench directory has FERMI and KEPLER and PHI
|
||||
sub-directories with Make.py commands and input scripts for using all
|
||||
the accelerator packages on various machines. See the README files in
|
||||
those dirs.
|
||||
</P>
|
||||
<P>As mentioned above, the <A HREF = "http://lammps.sandia.gov/bench.html">Benchmark
|
||||
page</A> of the LAMMPS web site gives
|
||||
@ -243,23 +263,25 @@ of the standard LAMMPS benchmark problems, as a function of problem
|
||||
size and number of compute nodes, on different hardware platforms.
|
||||
</P>
|
||||
<P>Here is a brief summary of what the various packages provide. Details
|
||||
are in the individual package sub-sections listed above.
|
||||
are in the individual accelerator sections.
|
||||
</P>
|
||||
<UL><LI>Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU
|
||||
packages, and can be run on NVIDIA GPUs. The speed-up on a GPU
|
||||
depends on a variety of factors, as discussed below.
|
||||
depends on a variety of factors, discussed in the accelerator
|
||||
sections.
|
||||
|
||||
<LI>Styles with an "intel" suffix are part of the USER-INTEL
|
||||
package. These styles support vectorized single and mixed precision
|
||||
calculations, in addition to full double precision. In extreme cases,
|
||||
this can provide speedups over 3.5x on CPUs. The package also
|
||||
supports acceleration with offload to Intel(R) Xeon Phi(TM)
|
||||
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
|
||||
coprocessors. This can result in additional speedup over 2x depending
|
||||
on the hardware configuration.
|
||||
|
||||
<LI>Styles with a "kk" suffix are part of the KOKKOS package, and can be
|
||||
run using OpenMP, on an NVIDIA GPU, or on an Intel Xeon Phi. The
|
||||
speed-up depends on a variety of factors, as discussed below.
|
||||
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
|
||||
Xeon Phi in "native" mode. The speed-up depends on a variety of
|
||||
factors, as discussed on the KOKKOS accelerator page.
|
||||
|
||||
<LI>Styles with an "omp" suffix are part of the USER-OMP package and allow
|
||||
a pair-style to be run in multi-threaded mode using OpenMP. This can
|
||||
@ -272,7 +294,7 @@ overload the available bandwidth for communication.
|
||||
speed-up the pairwise calculations of your simulation by 5-25% on a
|
||||
CPU.
|
||||
</UL>
|
||||
<P>The individual accelerator package sub-sections explain:
|
||||
<P>The individual accelerator package doc pages explain:
|
||||
</P>
|
||||
<UL><LI>what hardware and software the accelerated package requires
|
||||
<LI>how to build LAMMPS with the accelerated package
|
||||
|
||||
@ -152,8 +152,8 @@ coprocessors.
|
||||
|
||||
All of these commands are in packages provided with LAMMPS. An
|
||||
overview of packages is give in "Section
|
||||
packages"_Section_packages.html. Currently, there are 6 accelerator
|
||||
packages in LAMMPS, either as standard or user packages:
|
||||
packages"_Section_packages.html. These are the accelerator packages
|
||||
currently in LAMMPS, either as standard or user packages:
|
||||
|
||||
"USER-CUDA"_accelerate_cuda.html : for NVIDIA GPUs
|
||||
"GPU"_accelerate_gpu.html : for NVIDIA GPUs as well as OpenCL support
|
||||
@ -186,8 +186,8 @@ for that style.
|
||||
|
||||
To use an accelerator package in LAMMPS, and one or more of the styles
|
||||
it provides, follow these general steps. Details vary from package to
|
||||
package and are explained in the individual accelerator sub-section
|
||||
doc pages, listed above:
|
||||
package and are explained in the individual accelerator doc pages,
|
||||
listed above:
|
||||
|
||||
build the accelerator library |
|
||||
only for USER-CUDA and GPU packages |
|
||||
@ -211,26 +211,48 @@ use accelerated styles in your input script |
|
||||
via "-sf" "command-line switch"_Section_start.html#start_7 or
|
||||
"suffix"_suffix.html command :tb(c=2,s=|)
|
||||
|
||||
The first 4 steps typically only need to be done once, to create an
|
||||
executable that uses one or more accelerator packages. We are working
|
||||
to create a "make" tool that will perform all these 4 steps in a
|
||||
single command.
|
||||
The first 4 steps can be done as a single command, using the
|
||||
src/Make.py tool. The Make.py tool is discussed in "Section
|
||||
2.4"_Section_start.html#start_4 of the manual, and its use is
|
||||
illustrated in the individual accelerator sections. Typically these
|
||||
steps only need to be done once, to create an executable that uses one
|
||||
or more accelerator packages.
|
||||
|
||||
The last 4 steps can all be done from the command-line when LAMMPS is
|
||||
launched, without changing your input script. Or you can add
|
||||
launched, without changing your input script, as illustrated in the
|
||||
individual accelerator sections. Or you can add
|
||||
"package"_package.html and "suffix"_suffix.html commands to your input
|
||||
script.
|
||||
|
||||
The examples directory has several sub-directories with scripts and
|
||||
README files for how to use the following accelerator packages:
|
||||
IMPORTANT NOTE: With a few exceptions, you can build a single LAMMPS
|
||||
executable with all its accelerator packages installed. Note that the
|
||||
USER-INTEL and KOKKOS packages require you to choose one of their
|
||||
options when building. I.e. CPU or Phi for USER-INTEL. OpenMP, Cuda,
|
||||
or Phi for KOKKOS. Here are the exceptions; you cannot build a single
|
||||
executable with:
|
||||
|
||||
examples/cuda for USER-CUDA package
|
||||
examples/gpu for GPU package
|
||||
examples/intel for USER-INTEL package
|
||||
examples/kokkos for KOKKOS package :ul
|
||||
both the USER-INTEL Phi and KOKKOS Phi options
|
||||
the USER-INTEL Phi or Kokkos Phi option, and either the USER-CUDA or GPU packages :ul
|
||||
|
||||
Likewise, the bench directory has FERMI and KEPLER sub-directories
|
||||
with scripts and README files for using all the accelerator packages.
|
||||
See the examples/accelerate/README and make.list files for sample
|
||||
Make.py commands that build LAMMPS with any or all of the accelerator
|
||||
packages. As an example, here is a command that builds with all the
|
||||
GPU related packages installed (USER-CUDA, GPU, KOKKOS with Cuda),
|
||||
including settings to build the needed auxiliary USER-CUDA and GPU
|
||||
libraries for Kepler GPUs:
|
||||
|
||||
Make.py -j 16 -p omp gpu cuda kokkos -cc nvcc wrap=mpi \
|
||||
-cuda mode=double arch=35 -gpu mode=double arch=35 \\
|
||||
-kokkos cuda arch=35 lib-all file mpi :pre
|
||||
|
||||
The examples/accelerate directory also has input scripts that can be
|
||||
used with all of the accelerator packages. See its README file for
|
||||
details.
|
||||
|
||||
Likewise, the bench directory has FERMI and KEPLER and PHI
|
||||
sub-directories with Make.py commands and input scripts for using all
|
||||
the accelerator packages on various machines. See the README files in
|
||||
those dirs.
|
||||
|
||||
As mentioned above, the "Benchmark
|
||||
page"_http://lammps.sandia.gov/bench.html of the LAMMPS web site gives
|
||||
@ -239,23 +261,25 @@ of the standard LAMMPS benchmark problems, as a function of problem
|
||||
size and number of compute nodes, on different hardware platforms.
|
||||
|
||||
Here is a brief summary of what the various packages provide. Details
|
||||
are in the individual package sub-sections listed above.
|
||||
are in the individual accelerator sections.
|
||||
|
||||
Styles with a "cuda" or "gpu" suffix are part of the USER-CUDA or GPU
|
||||
packages, and can be run on NVIDIA GPUs. The speed-up on a GPU
|
||||
depends on a variety of factors, as discussed below. :ulb,l
|
||||
depends on a variety of factors, discussed in the accelerator
|
||||
sections. :ulb,l
|
||||
|
||||
Styles with an "intel" suffix are part of the USER-INTEL
|
||||
package. These styles support vectorized single and mixed precision
|
||||
calculations, in addition to full double precision. In extreme cases,
|
||||
this can provide speedups over 3.5x on CPUs. The package also
|
||||
supports acceleration with offload to Intel(R) Xeon Phi(TM)
|
||||
supports acceleration in "offload" mode to Intel(R) Xeon Phi(TM)
|
||||
coprocessors. This can result in additional speedup over 2x depending
|
||||
on the hardware configuration. :l
|
||||
|
||||
Styles with a "kk" suffix are part of the KOKKOS package, and can be
|
||||
run using OpenMP, on an NVIDIA GPU, or on an Intel Xeon Phi. The
|
||||
speed-up depends on a variety of factors, as discussed below. :l
|
||||
run using OpenMP on multicore CPUs, on an NVIDIA GPU, or on an Intel
|
||||
Xeon Phi in "native" mode. The speed-up depends on a variety of
|
||||
factors, as discussed on the KOKKOS accelerator page. :l
|
||||
|
||||
Styles with an "omp" suffix are part of the USER-OMP package and allow
|
||||
a pair-style to be run in multi-threaded mode using OpenMP. This can
|
||||
@ -268,7 +292,7 @@ Styles with an "opt" suffix are part of the OPT package and typically
|
||||
speed-up the pairwise calculations of your simulation by 5-25% on a
|
||||
CPU. :l,ule
|
||||
|
||||
The individual accelerator package sub-sections explain:
|
||||
The individual accelerator package doc pages explain:
|
||||
|
||||
what hardware and software the accelerated package requires
|
||||
how to build LAMMPS with the accelerated package
|
||||
|
||||
@ -85,14 +85,27 @@ launch a LAMMPS Windows executable on a Windows box.
|
||||
|
||||
<A NAME = "start_2_1"></A><B><I>Read this first:</I></B>
|
||||
|
||||
<P>If you want to avoid building LAMMPS, read the preceeding section
|
||||
about options available for downloading and installing executables.
|
||||
Details are discussed on the <A HREF = "download">download</A> page.
|
||||
<P>If you want to avoid building LAMMPS yourself, read the preceeding
|
||||
section about options available for downloading and installing
|
||||
executables. Details are discussed on the <A HREF = "download">download</A> page.
|
||||
</P>
|
||||
<P>Building LAMMPS can be simple or not-so-simple. If MPI is already
|
||||
installed on your machine (or you just want to run LAMMPS in serial)
|
||||
and you can use one of the provided machine Makefiles and the build
|
||||
works on your platform, then it's simple.
|
||||
<P>Building LAMMPS can be simple or not-so-simple. If all you need are
|
||||
the default packages installed in LAMMPS, and MPI is already installed
|
||||
on your machine, or you just want to run LAMMPS in serial, then you
|
||||
can typically use the Makefile.mpi or Makefile.serial files in
|
||||
src/MAKE and type one of these lines (from the src dir):
|
||||
</P>
|
||||
<PRE>make mpi
|
||||
make serial
|
||||
</PRE>
|
||||
<P>Or if one of the other Makefile.machine files in the src/MAKE
|
||||
sub-directories matches your system (type "make" to see a list), you
|
||||
can use it as-is by typing (for example):
|
||||
</P>
|
||||
<PRE>make stampede
|
||||
</PRE>
|
||||
<P>If any of these builds with an existing Makefile.machine works on your
|
||||
system, then you're done!
|
||||
</P>
|
||||
<P>If you want to do one of these:
|
||||
</P>
|
||||
@ -105,7 +118,14 @@ works on your platform, then it's simple.
|
||||
auxiliary libraries exist on your machine or install them if they
|
||||
don't. You may need to build additional libraries that are part of
|
||||
the LAMMPS package, before building LAMMPS. You may need to edit a
|
||||
machine Makefile to make it compatible with your system.
|
||||
Makefile.machine file to make it compatible with your system.
|
||||
</P>
|
||||
<P>Note that there is a Make.py tool in the src directory that automates
|
||||
several of these steps, but you still have to know what you are doing.
|
||||
<A HREF = "#start_4">Section 2.4</A> below describes the tool. It is a convenient
|
||||
way to work with installing/un-installing various packages, the
|
||||
Makefile.machine changes required by some packages, and the auxiliary
|
||||
libraries some of them use.
|
||||
</P>
|
||||
<P>Please read the following sections carefully. If you are not
|
||||
comfortable with makefiles, or building codes on a Unix platform, or
|
||||
@ -121,7 +141,7 @@ please post the issue to the <A HREF = "http://lammps.sandia.gov/mail.html">LAMM
|
||||
list</A>.
|
||||
</P>
|
||||
<P>If you succeed in building LAMMPS on a new kind of machine, for which
|
||||
there isn't a similar machine Makefile included in the src/MAKE
|
||||
there isn't a similar machine Makefile included in the src/MAKE/MORE
|
||||
directory, then send it to the developers and we can include it in the
|
||||
LAMMPS distribution.
|
||||
</P>
|
||||
@ -133,21 +153,43 @@ LAMMPS distribution.
|
||||
</P>
|
||||
<P>The src directory contains the C++ source and header files for LAMMPS.
|
||||
It also contains a top-level Makefile and a MAKE sub-directory with
|
||||
low-level Makefile.* files for many machines. From within the src
|
||||
directory, type "make" or "gmake". You should see a list of available
|
||||
choices. If one of those is the machine and options you want, you can
|
||||
type a command like:
|
||||
low-level Makefile.* files for many systems and machines. See the
|
||||
src/MAKE/README file for a quick overview of what files are available
|
||||
and what sub-directories they are in.
|
||||
</P>
|
||||
<PRE>make linux
|
||||
<P>The src/MAKE dir has a few files that should work as-is on many
|
||||
platforms. The src/MAKE/OPTIONS dir has more that inovke additional
|
||||
compiler, MPI, and other setting options commonly used by LAMMPS, to
|
||||
illustrate their syntax. The src/MAKE/MACHINES dir has many more that
|
||||
have been tweaked or optimized for specific machines. These files are
|
||||
all good starting points if you find you need to change them for your
|
||||
machine. Put any file you edit into the src/MAKE/MINE directory and
|
||||
it will be never be touched by any LAMMPS updates.
|
||||
</P>
|
||||
<P>From within the src directory, type "make" or "gmake". You should see
|
||||
a list of available choices from src/MAKE and all of its
|
||||
sub-directories. If one of those has the options you want or is the
|
||||
machine you want, you can type a command like:
|
||||
</P>
|
||||
<PRE>make mpi
|
||||
or
|
||||
make serial_icc
|
||||
or
|
||||
gmake mac
|
||||
</PRE>
|
||||
<P>Note that the corresponding Makefile.machine can exist in src/MAKE or
|
||||
any of its sub-directories. If a file with the same name appears in
|
||||
multiple places (not a good idea), the order they are used is as
|
||||
follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.
|
||||
This gives preference to a file you have created/edited and put in
|
||||
src/MAKE/MINE.
|
||||
</P>
|
||||
<P>Note that on a multi-processor or multi-core platform you can launch a
|
||||
parallel make, by using the "-j" switch with the make command, which
|
||||
will build LAMMPS more quickly.
|
||||
</P>
|
||||
<P>If you get no errors and an executable like lmp_linux or lmp_mac is
|
||||
produced, you're done; it's your lucky day.
|
||||
<P>If you get no errors and an executable like lmp_mpi or lmp_g++_serial
|
||||
or lmp_mac is produced, then you're done; it's your lucky day.
|
||||
</P>
|
||||
<P>Note that by default only a few of LAMMPS optional packages are
|
||||
installed. To build LAMMPS with optional packages, see <A HREF = "#start_3">this
|
||||
@ -157,43 +199,47 @@ section</A> below.
|
||||
</P>
|
||||
<P>If Step 0 did not work, you will need to create a low-level Makefile
|
||||
for your machine, like Makefile.foo. You should make a copy of an
|
||||
existing src/MAKE/Makefile.* as a starting point. The only portions
|
||||
of the file you need to edit are the first line, the "compiler/linker
|
||||
settings" section, and the "LAMMPS-specific settings" section.
|
||||
existing Makefile.* in src/MAKE or one of its sub-directories as a
|
||||
starting point. The only portions of the file you need to edit are
|
||||
the first line, the "compiler/linker settings" section, and the
|
||||
"LAMMPS-specific settings" section. When it works, put the edited
|
||||
file in src/MAKE/MINE and it will not be altered by any future LAMMPS
|
||||
updates.
|
||||
</P>
|
||||
<P><B>Step 2</B>
|
||||
</P>
|
||||
<P>Change the first line of src/MAKE/Makefile.foo to list the word "foo"
|
||||
after the "#", and whatever other options it will set. This is the
|
||||
line you will see if you just type "make".
|
||||
<P>Change the first line of Makefile.foo to list the word "foo" after the
|
||||
"#", and whatever other options it will set. This is the line you
|
||||
will see if you just type "make".
|
||||
</P>
|
||||
<P><B>Step 3</B>
|
||||
</P>
|
||||
<P>The "compiler/linker settings" section lists compiler and linker
|
||||
settings for your C++ compiler, including optimization flags. You can
|
||||
use g++, the open-source GNU compiler, which is available on all Unix
|
||||
systems. You can also use mpicc which will typically be available if
|
||||
systems. You can also use mpicxx which will typically be available if
|
||||
MPI is installed on your system, though you should check which actual
|
||||
compiler it wraps. Vendor compilers often produce faster code. On
|
||||
boxes with Intel CPUs, we suggest using the commercial Intel icc
|
||||
compiler, which can be downloaded from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
|
||||
boxes with Intel CPUs, we suggest using the Intel icc compiler, which
|
||||
can be downloaded from <A HREF = "http://www.intel.com/software/products/noncom">Intel's compiler site</A>.
|
||||
</P>
|
||||
|
||||
|
||||
<P>If building a C++ code on your machine requires additional libraries,
|
||||
then you should list them as part of the LIB variable.
|
||||
then you should list them as part of the LIB variable. You should
|
||||
not need to do this if you use mpicxx.
|
||||
</P>
|
||||
<P>The DEPFLAGS setting is what triggers the C++ compiler to create a
|
||||
dependency list for a source file. This speeds re-compilation when
|
||||
source (*.cpp) or header (*.h) files are edited. Some compilers do
|
||||
not support dependency file creation, or may use a different switch
|
||||
than -D. GNU g++ works with -D. If your compiler can't create
|
||||
dependency files, then you'll need to create a Makefile.foo patterned
|
||||
after Makefile.storm, which uses different rules that do not involve
|
||||
dependency files. Note that when you build LAMMPS for the first time
|
||||
on a new platform, a long list of *.d files will be printed out
|
||||
rapidly. This is not an error; it is the Makefile doing its normal
|
||||
creation of dependencies.
|
||||
than -D. GNU g++ and Intel icc works with -D. If your compiler can't
|
||||
create dependency files, then you'll need to create a Makefile.foo
|
||||
patterned after Makefile.storm, which uses different rules that do not
|
||||
involve dependency files. Note that when you build LAMMPS for the
|
||||
first time on a new platform, a long list of *.d files will be printed
|
||||
out rapidly. This is not an error; it is the Makefile doing its
|
||||
normal creation of dependencies.
|
||||
</P>
|
||||
<P><B>Step 4</B>
|
||||
</P>
|
||||
@ -277,20 +323,21 @@ Step 6 below for info about building LAMMPS with an FFT library.
|
||||
<P><B>Step 5</B>
|
||||
</P>
|
||||
<P>The 3 MPI variables are used to specify an MPI library to build LAMMPS
|
||||
with.
|
||||
with. Note that you do not need to set these if you use the MPI
|
||||
compiler mpicxx for your CC and LINK setting in the section above.
|
||||
The MPI wrapper knows where to find the needed files.
|
||||
</P>
|
||||
<P>If you want LAMMPS to run in parallel, you must have an MPI library
|
||||
installed on your platform. If you use an MPI-wrapped compiler, such
|
||||
as "mpicc" to build LAMMPS, you should be able to leave these 3
|
||||
variables blank; the MPI wrapper knows where to find the needed files.
|
||||
If not, and MPI is installed on your system in the usual place (under
|
||||
/usr/local), you also may not need to specify these 3 variables. On
|
||||
some large parallel machines which use "modules" for their
|
||||
compile/link environements, you may simply need to include the correct
|
||||
module in your build environment. Or the parallel machine may have a
|
||||
vendor-provided MPI which the compiler has no trouble finding.
|
||||
installed on your platform. If MPI is installed on your system in the
|
||||
usual place (under /usr/local), you also may not need to specify these
|
||||
3 variables, assuming /usr/local is in your path. On some large
|
||||
parallel machines which use "modules" for their compile/link
|
||||
environements, you may simply need to include the correct module in
|
||||
your build environment, before building LAMMPS. Or the parallel
|
||||
machine may have a vendor-provided MPI which the compiler has no
|
||||
trouble finding.
|
||||
</P>
|
||||
<P>Failing this, with these 3 variables you can specify where the mpi.h
|
||||
<P>Failing this, these 3 variables can be used to specify where the mpi.h
|
||||
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
|
||||
name of the library file (MPI_LIB).
|
||||
</P>
|
||||
@ -310,20 +357,22 @@ arise when linking LAMMPS to the MPI library.
|
||||
</P>
|
||||
<P>If you just want to run LAMMPS on a single processor, you can use the
|
||||
dummy MPI library provided in src/STUBS, since you don't need a true
|
||||
MPI library installed on your system. See the
|
||||
src/MAKE/Makefile.serial file for how to specify the 3 MPI variables
|
||||
in this case. You will also need to build the STUBS library for your
|
||||
platform before making LAMMPS itself. To build from the src
|
||||
directory, type "make stubs", or from the STUBS dir, type "make".
|
||||
This should create a libmpi_stubs.a file suitable for linking to
|
||||
LAMMPS. If the build fails, you will need to edit the STUBS/Makefile
|
||||
for your platform.
|
||||
MPI library installed on your system. See src/MAKE/Makefile.serial
|
||||
for how to specify the 3 MPI variables in this case. You will also
|
||||
need to build the STUBS library for your platform before making LAMMPS
|
||||
itself. Note that if you are building with src/MAKE/Makefile.serial,
|
||||
e.g. by typing "make serial", then the STUBS library is built for you.
|
||||
</P>
|
||||
<P>The file STUBS/mpi.c provides a CPU timer function called
|
||||
MPI_Wtime() that calls gettimeofday() . If your system doesn't
|
||||
support gettimeofday() , you'll need to insert code to call another
|
||||
timer. Note that the ANSI-standard function clock() rolls over after
|
||||
an hour or so, and is therefore insufficient for timing long LAMMPS
|
||||
<P>To build the STUBS library from the src directory, type "make stubs",
|
||||
or from the src/STUBS dir, type "make". This should create a
|
||||
libmpi_stubs.a file suitable for linking to LAMMPS. If the build
|
||||
fails, you will need to edit the STUBS/Makefile for your platform.
|
||||
</P>
|
||||
<P>The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
|
||||
that calls gettimeofday() . If your system doesn't support
|
||||
gettimeofday() , you'll need to insert code to call another timer.
|
||||
Note that the ANSI-standard function clock() rolls over after an hour
|
||||
or so, and is therefore insufficient for timing long LAMMPS
|
||||
simulations.
|
||||
</P>
|
||||
<P><B>Step 6</B>
|
||||
@ -410,11 +459,9 @@ section</A> below, before proceeding to Step 9.
|
||||
</P>
|
||||
<P><B>Step 9</B>
|
||||
</P>
|
||||
<P>That's it. Once you have a correct Makefile.foo, you have installed
|
||||
the optional LAMMPS packages you want to include in your build, and
|
||||
you have pre-built any other needed libraries (e.g. MPI, FFT, package
|
||||
libraries), all you need to do from the src directory is type
|
||||
something like this:
|
||||
<P>That's it. Once you have a correct Makefile.foo, and you have
|
||||
pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
|
||||
to do from the src directory is type something like this:
|
||||
</P>
|
||||
<PRE>make foo
|
||||
or
|
||||
@ -530,7 +577,7 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
|
||||
<A NAME = "start_2_5"></A><B><I>Building for a Mac:</I></B>
|
||||
|
||||
<P>OS X is BSD Unix, so it should just work. See the
|
||||
src/MAKE/Makefile.mac file.
|
||||
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
@ -559,7 +606,7 @@ excluded, you can build it yourself.
|
||||
</P>
|
||||
<P>One way to do this is install and use cygwin to build LAMMPS with a
|
||||
standard unix style make program, just as you would on a Linux box;
|
||||
see src/MAKE/Makefile.cygwin.
|
||||
see src/MAKE/MACHINES/Makefile.cygwin.
|
||||
</P>
|
||||
<P>The other way to do this is using Visual Studio and project files.
|
||||
See the src/WINDOWS directory and its README.txt file for instructions
|
||||
@ -574,8 +621,13 @@ on both a basic build and a customized build with pacakges you select.
|
||||
<UL><LI><A HREF = "#start_3_1">Package basics</A>
|
||||
<LI><A HREF = "#start_3_2">Including/excluding packages</A>
|
||||
<LI><A HREF = "#start_3_3">Packages that require extra libraries</A>
|
||||
<LI><A HREF = "#start_3_4">Packages that use make variable settings</A>
|
||||
<LI><A HREF = "#start_3_4">Packages that require Makefile.machine settings</A>
|
||||
</UL>
|
||||
<P>Note that the following <A HREF = "#start_4">Section 2.4</A> describes the Make.py
|
||||
tool which can be used to install/un-install packages and build the
|
||||
auxiliary libraries which some of them use. It can also auto-edit a
|
||||
Makefile.machine to add settings needed by some packages.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "start_3_1"></A><B><I>Package basics:</I></B>
|
||||
@ -583,9 +635,11 @@ on both a basic build and a customized build with pacakges you select.
|
||||
<P>The source code for LAMMPS is structured as a set of core files which
|
||||
are always included, plus optional packages. Packages are groups of
|
||||
files that enable a specific set of features. For example, force
|
||||
fields for molecular systems or granular systems are in packages. You
|
||||
can see the list of all packages by typing "make package" from within
|
||||
the src directory of the LAMMPS distribution.
|
||||
fields for molecular systems or granular systems are in packages.
|
||||
</P>
|
||||
<P>You can see the list of all packages by typing "make package" from
|
||||
within the src directory of the LAMMPS distribution. This also lists
|
||||
various make commands that can be used to manipulate packages.
|
||||
</P>
|
||||
<P>If you use a command in a LAMMPS input script that is specific to a
|
||||
particular package, you must have built LAMMPS with that package, else
|
||||
@ -652,10 +706,11 @@ I.e. individual files are only included if their dependencies are
|
||||
already included. Likewise, if a package is excluded, other files
|
||||
dependent on that package are also excluded.
|
||||
</P>
|
||||
<P>The reason to exclude packages is if you will never run certain kinds
|
||||
of simulations. For some packages, this will keep you from having to
|
||||
build auxiliary libraries (see below), and will also produce a smaller
|
||||
executable which may run a bit faster.
|
||||
<P>If you will never run simulations that use the features in a
|
||||
particular packages, there is no reason to include it in your build.
|
||||
For some packages, this will keep you from having to build auxiliary
|
||||
libraries (see below), and will also produce a smaller executable
|
||||
which may run a bit faster.
|
||||
</P>
|
||||
<P>When you download a LAMMPS tarball, these packages are pre-installed
|
||||
in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
|
||||
@ -666,9 +721,10 @@ pre-installed.
|
||||
no-name", where "name" is the name of the package in lower-case, e.g.
|
||||
name = kspace for the KSPACE package or name = user-atc for the
|
||||
USER-ATC package. You can also type "make yes-standard", "make
|
||||
no-standard", "make yes-user", "make no-user", "make yes-all" or "make
|
||||
no-all" to include/exclude various sets of packages. Type "make
|
||||
package" to see the all of the package-related make options.
|
||||
no-standard", "make yes-std", "make no-std", "make yes-user", "make
|
||||
no-user", "make yes-all" or "make no-all" to include/exclude various
|
||||
sets of packages. Type "make package" to see the all of the
|
||||
package-related make options.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
|
||||
moving files back and forth between the main src directory and
|
||||
@ -682,18 +738,19 @@ sub-directories. You do not normally need to use these commands
|
||||
unless you are editing LAMMPS files or have downloaded a patch from
|
||||
the LAMMPS WWW site.
|
||||
</P>
|
||||
<P>Typing "make package-update" will overwrite src files with files from
|
||||
the package sub-directories if the package has been included. It
|
||||
should be used after a patch is installed, since patches only update
|
||||
the files in the package sub-directory, but not the src files. Typing
|
||||
"make package-overwrite" will overwrite files in the package
|
||||
sub-directories with src files.
|
||||
<P>Typing "make package-update" or "make pu" will overwrite src files
|
||||
with files from the package sub-directories if the package has been
|
||||
included. It should be used after a patch is installed, since patches
|
||||
only update the files in the package sub-directory, but not the src
|
||||
files. Typing "make package-overwrite" will overwrite files in the
|
||||
package sub-directories with src files.
|
||||
</P>
|
||||
<P>Typing "make package-status" will show which packages are currently
|
||||
included. Of those that are included, it will list files that are
|
||||
different in the src directory and package sub-directory. Typing
|
||||
"make package-diff" lists all differences between these files. Again,
|
||||
type "make package" to see all of the package-related make options.
|
||||
<P>Typing "make package-status" or "make ps" will show which packages are
|
||||
currently included. Of those that are included, it will list files
|
||||
that are different in the src directory and package sub-directory.
|
||||
Typing "make package-diff" lists all differences between these files.
|
||||
Again, type "make package" to see all of the package-related make
|
||||
options.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
@ -705,16 +762,16 @@ you get a LAMMPS build error about a missing library, this is likely
|
||||
the reason. See the <A HREF = "Section_packages.html">Section_packages</A> doc page
|
||||
for a list of packages that have auxiliary libraries.
|
||||
</P>
|
||||
<P>Code for some of these auxiliary libraries is included in the LAMMPS
|
||||
<P>Code for most of these auxiliary libraries is included in the LAMMPS
|
||||
distribution under the lib directory. Examples are the USER-ATC and
|
||||
MEAM packages. Some auxiliary libraries are NOT included with LAMMPS;
|
||||
to use the associated package you must download and install the
|
||||
auxiliary library yourself. Examples are the KIM and VORONOI and
|
||||
MEAM packages. A few auxiliary libraries are NOT included with
|
||||
LAMMPS; to use the associated package you must download and install
|
||||
the auxiliary library yourself. Examples are the KIM and VORONOI and
|
||||
USER-MOLFILE packages.
|
||||
</P>
|
||||
<P>For libraries with provided source code, each lib directory has a
|
||||
README file (e.g. lib/reax/README) with instructions on how to build
|
||||
that library. Typically this is done by typing something like:
|
||||
<P>For provided libraries, each lib directory has a README file
|
||||
(e.g. lib/reax/README) with instructions on how to build that library.
|
||||
Typically this is done by typing something like:
|
||||
</P>
|
||||
<PRE>make -f Makefile.g++
|
||||
</PRE>
|
||||
@ -746,168 +803,205 @@ is built with, typically requires additional Fortran-to-C libraries be
|
||||
included in the link. Another example are the BLAS and LAPACK
|
||||
libraries needed to use the USER-ATC or USER-AWPMD packages.
|
||||
</P>
|
||||
<P>For libraries without provided source code, see the
|
||||
src/package/Makefile.lammps file for information on where to find the
|
||||
library and how to build it. E.g. the file src/KIM/Makefile.lammps or
|
||||
src/VORONOI/Makefile.lammps or src/UESR-MOLFILE/Makefile.lammps.
|
||||
These files serve the same purpose as the lib/package/Makefile.lammps
|
||||
files described above. The files have settings needed when LAMMPS is
|
||||
built to link with the corresponding auxiliary library.
|
||||
<P>For libraries without provided source code, the file
|
||||
src/package/README has information on where to find the library and
|
||||
how to build it, e.g. src/VORONOI/README. There is also a
|
||||
Makefile.lammps file in the src/package directory. E.g. files
|
||||
src/KIM/Makefile.lammps or src/VORONOI/Makefile.lammps or
|
||||
src/UESR-MOLFILE/Makefile.lammps. These files serve the same purpose
|
||||
as the lib/package/Makefile.lammps files described above. The files
|
||||
have settings needed when LAMMPS is built to link with the
|
||||
corresponding auxiliary library.
|
||||
</P>
|
||||
<P>Again, you must insure that the settings in
|
||||
src/package/Makefile.lammps are appropriate for your system and where
|
||||
you installed the auxiliary library. If they are not, the LAMMPS
|
||||
build will fail.
|
||||
build will typically fail.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "start_3_4"></A><B><I>Packages that use make variable settings</I></B>
|
||||
<A NAME = "start_3_4"></A><B><I>Packages that require Makefile.machine settings</I></B>
|
||||
|
||||
<P>One package, the KOKKOS package, allows its build options to be
|
||||
specified by setting variables via the "make" command, rather than by
|
||||
first building an auxiliary library and editing a Makefile.lammps
|
||||
file, as discussed in the previous sub-section for other packages.
|
||||
This is for convenience since it is common to want to experiment with
|
||||
different Kokkos library options. Using variables enables a direct
|
||||
re-build of LAMMPS and its Kokkos dependencies, so that a benchmark
|
||||
test with different Kokkos options can be quickly performed.
|
||||
<P>A few packages require specific settings in Makefile.machine, to
|
||||
either build or use the package effectively. These are the
|
||||
USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what
|
||||
flags to add or what variables to define are given on the doc pages
|
||||
that describe each of these accelerator packages in detail:
|
||||
</P>
|
||||
<P>The syntax for setting make variables is as follows. You must
|
||||
use a GNU-compatible make command for this to work. Try "gmake"
|
||||
if your system's standard make complains.
|
||||
</P>
|
||||
<PRE>make yes-kokkos
|
||||
make g++ VAR1=value VAR2=value ...
|
||||
</PRE>
|
||||
<P>The first line installs the KOKKOS package, which only needs to be
|
||||
done once. The second line builds LAMMPS with src/MAKE/Makefile.g++
|
||||
and optionally sets one or more variables that affect the build. Each
|
||||
variable is specified in upper-case; its value follows an equal sign
|
||||
with no spaces. The second line can be repeated with different
|
||||
variable settings, though a "clean" must be done before the rebuild.
|
||||
Type "make clean" to see options for this operation.
|
||||
</P>
|
||||
<P>These are the variables that can be specified. Each takes a value of
|
||||
<I>yes</I> or <I>no</I>. The default value is listed, which is set in the
|
||||
lib/kokkos/Makefile.lammps file. See <A HREF = "Section_accelerate.html#acc_8">this
|
||||
section</A> for a discussion of what is
|
||||
meant by "host" and "device" in the Kokkos context.
|
||||
</P>
|
||||
<UL><LI>OMP, default = <I>yes</I>
|
||||
<LI>CUDA, default = <I>no</I>
|
||||
<LI>HWLOC, default = <I>no</I>
|
||||
<LI>AVX, default = <I>no</I>
|
||||
<LI>MIC, default = <I>no</I>
|
||||
<LI>LIBRT, default = <I>no</I>
|
||||
<LI>DEBUG, default = <I>no</I>
|
||||
<UL><LI><A HREF = "accelerate_intel.html">USER-INTEL package</A>
|
||||
<LI><A HREF = "accelerate_kokkos.html">KOKKOS package</A>
|
||||
<LI><A HREF = "accelerate_omp.html">USER-OMP package</A>
|
||||
<LI><A HREF = "accelerate_opt.html">OPT package</A>
|
||||
</UL>
|
||||
<P>OMP sets the parallelization method used for Kokkos code (within
|
||||
LAMMPS) that runs on the host. OMP=yes means that OpenMP will be
|
||||
used. OMP=no means that pthreads will be used.
|
||||
<P>Here is a brief summary of what Makefile.machine changes are needed.
|
||||
Note that the Make.py tool, described in the next <A HREF = "#start_4">Section
|
||||
2.4</A> can automatically add the needed info to an existing
|
||||
machine Makefile, using simple command-line arguments.
|
||||
</P>
|
||||
<P>CUDA sets the parallelization method used for Kokkos code (within
|
||||
LAMMPS) that runs on the device. CUDA=yes means an NVIDIA GPU running
|
||||
CUDA will be used. CUDA=no means that the OMP=yes or OMP=no setting
|
||||
will be used for the device as well as the host.
|
||||
<P>In src/MAKE/OPTIONS see the following Makefiles for examples of the
|
||||
changes described below:
|
||||
</P>
|
||||
<P>If CUDA=yes, then the lo-level Makefile in the src/MAKE directory must
|
||||
use "nvcc" as its compiler, via its CC setting. For best performance
|
||||
its CCFLAGS setting should use -O3 and have an -arch setting that
|
||||
matches the compute capability of your NVIDIA hardware and software
|
||||
installation, e.g. -arch=sm_20. Generally Fermi Generation GPUs are
|
||||
sm_20, while Kepler generation GPUs are sm_30 or sm_35 and Maxwell
|
||||
cards are sm_50. A complete list can be found on
|
||||
<A HREF = "http://en.wikipedia.org/wiki/CUDA#Supported_GPUs">wikipedia</A>. You can
|
||||
also use the deviceQuery tool that comes with the CUDA samples. Note
|
||||
the minimal required compute capability is 2.0, but this will give
|
||||
signicantly reduced performance compared to Kepler generation GPUs
|
||||
with compute capability 3.x. For the LINK setting, "nvcc" should not
|
||||
be used; instead use g++ or another compiler suitable for linking C++
|
||||
applications. Often you will want to use your MPI compiler wrapper
|
||||
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
|
||||
also have a "Compilation rule" for creating *.o files from *.cu files.
|
||||
See src/Makefile.cuda for an example of a lo-level Makefile with all
|
||||
of these settings.
|
||||
<UL><LI>Makefile.intel_cpu
|
||||
<LI>Makefile.intel_phi
|
||||
<LI>Makefile.kokkos_omp
|
||||
<LI>Makefile.kokkos_cuda
|
||||
<LI>Makefile.kokkos_phi
|
||||
<LI>Makefile.omp
|
||||
</UL>
|
||||
<P>For the USER-INTEL package, you have 2 choices when building. You can
|
||||
build with CPU or Phi support. The latter uses Xeon Phi chips in
|
||||
"offload" mode. Each of these modes requires additional settings in
|
||||
your Makefile.machine for CCFLAGS and LINKFLAGS.
|
||||
</P>
|
||||
<P>HWLOC binds threads to hardware cores, so they do not migrate during a
|
||||
simulation. HWLOC=yes should always be used if running with OMP=no
|
||||
for pthreads. It is not necessary for OMP=yes for OpenMP, because
|
||||
OpenMP provides alternative methods via environment variables for
|
||||
binding threads to hardware cores. More info on binding threads to
|
||||
cores is given in <A HREF = "Section_accelerate.html#acc_8">this section</A>.
|
||||
<P>For CPU mode (if using an Intel compiler):
|
||||
</P>
|
||||
<P>AVX enables Intel advanced vector extensions when compiling for an
|
||||
Intel-compatible chip. AVX=yes should only be set if your host
|
||||
hardware supports AVX. If it does not support it, this will cause a
|
||||
run-time crash.
|
||||
<UL><LI>CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
|
||||
<LI>LINKFLAGS: add -fopenmp
|
||||
</UL>
|
||||
<P>For Phi mode add the following in addition to the CPU mode flags:
|
||||
</P>
|
||||
<P>MIC enables compiler switches needed when compling for an Intel Phi
|
||||
processor.
|
||||
<UL><LI>CCFLAGS: add -DLMP_INTEL_OFFLOAD and
|
||||
<LI>LINKFLAGS: add -offload
|
||||
</UL>
|
||||
<P>And also add this to CCFLAGS:
|
||||
</P>
|
||||
<P>LIBRT enables use of a more accurate timer mechanism on most Unix
|
||||
platforms. This library is not available on all platforms.
|
||||
<PRE>-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\""
|
||||
</PRE>
|
||||
<P>For the KOKKOS package, you have 3 choices when building. You can
|
||||
build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
|
||||
chips in "native" mode. This can be done by setting the following
|
||||
variables in your Makefile.machine:
|
||||
</P>
|
||||
<P>DEBUG is only useful when developing a Kokkos-enabled style within
|
||||
LAMMPS. DEBUG=yes enables printing of run-time debugging information
|
||||
that can be useful. It also enables runtime bounds checking on Kokkos
|
||||
data structures.
|
||||
<UL><LI>for OMP support, set OMP = yes
|
||||
<LI>for Cuda support, set OMP = yes and CUDA = yes
|
||||
<LI>for Phi support, set OMP = yes and MIC = yes
|
||||
</UL>
|
||||
<P>These can also be set as additional arguments to the make command, e.g.
|
||||
</P>
|
||||
<PRE>make g++ OMP=yes MIC=yes
|
||||
</PRE>
|
||||
<P>Building the KOKKOS package with CUDA support requires a Makefile
|
||||
machine that uses the NVIDIA "nvcc" compiler, as well as an
|
||||
appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
|
||||
software you have on your machine. See
|
||||
src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
|
||||
Makefile.
|
||||
</P>
|
||||
<P>For the USER-OMP package, your Makefile.machine needs additional
|
||||
settings for CCFLAGS and LINKFLAGS.
|
||||
</P>
|
||||
<UL><LI>CCFLAGS: add -fopenmp and -restrict
|
||||
<LI>LINKFLAGS: add -fopenmp
|
||||
</UL>
|
||||
<P>For the OPT package, your Makefile.machine needs an additional
|
||||
settings for CCFLAGS.
|
||||
</P>
|
||||
<UL><LI>CCFLAGS: add -restrict
|
||||
</UL>
|
||||
<HR>
|
||||
|
||||
<H4><A NAME = "start_4"></A>2.4 Building LAMMPS via the Make.py script
|
||||
</H4>
|
||||
<P>The src directory includes a Make.py script, written
|
||||
in Python, which can be used to automate various steps
|
||||
of the build process.
|
||||
<P>The src directory includes a Make.py script, written in Python, which
|
||||
can be used to automate various steps of the build process. It is
|
||||
particularly useful for working with the accelerator packages, as well
|
||||
as other packages which require auxiliary libraries to be built.
|
||||
</P>
|
||||
<P>You can run the script from the src directory by typing either:
|
||||
<P>You can run Make.py from the src directory by typing either:
|
||||
</P>
|
||||
<PRE>Make.py
|
||||
python Make.py
|
||||
<PRE>Make.py -h
|
||||
python Make.py -h
|
||||
</PRE>
|
||||
<P>which will give you info about the tool. For the former to work, you
|
||||
may need to edit the 1st line of the script to point to your local
|
||||
<P>which will give you help info about the tool. For the former to work,
|
||||
you may need to edit the first line of Make.py to point to your local
|
||||
Python. And you may need to insure the script is executable:
|
||||
</P>
|
||||
<PRE>chmod +x Make.py
|
||||
</PRE>
|
||||
<P>The following options are supported as switches:
|
||||
<P>Here are examples of build tasks you can perform with Make.py:
|
||||
</P>
|
||||
<UL><LI>-i file1 file2 ...
|
||||
<LI>-p package1 package2 ...
|
||||
<LI>-u package1 package2 ...
|
||||
<LI>-e package1 arg1 arg2 package2 ...
|
||||
<LI>-o dir
|
||||
<LI>-b machine
|
||||
<LI>-s suffix1 suffix2 ...
|
||||
<LI>-l dir
|
||||
<LI>-j N
|
||||
<LI>-h switch1 switch2 ...
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR><TD >Install/uninstall packages</TD><TD > Make.py -p no-lib kokkos omp intel</TD></TR>
|
||||
<TR><TD >Build specific auxiliary libs</TD><TD > Make.py lib-atc lib-meam</TD></TR>
|
||||
<TR><TD >Build libs for all installed packages</TD><TD > Make.py -p cuda gpu -gpu mode=double arch=31 lib-all</TD></TR>
|
||||
<TR><TD >Create a Makefile from scratch with a compiler and MPI</TD><TD > Make.py -m none -cc g++ -mpi mpich file</TD></TR>
|
||||
<TR><TD >Augment Makefile.serial with settings for installed packages</TD><TD > Make.py -p intel -intel cpu -m serial file</TD></TR>
|
||||
<TR><TD >Add JPG and FFTW support to Makefile.mpi</TD><TD > Make.py -m mpi -jpg -fft fftw file</TD></TR>
|
||||
<TR><TD >Build LAMMPS with a parallel make using Makefile.mpi</TD><TD > Make.py -j 16 -m mpi exe</TD></TR>
|
||||
<TR><TD >Build LAMMPS and libs it needs using Makefile.serial with accelerator settings</TD><TD > Make.py -p gpu intel -intel cpu lib-all file serial
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>The bench and examples directories give Make.py commands that can be
|
||||
used to build LAMMPS with the various packages and options needed to
|
||||
run all the benchmark and example input scripts. See these files for
|
||||
more details:
|
||||
</P>
|
||||
<UL><LI>bench/README
|
||||
<LI>bench/FERMI/README
|
||||
<LI>bench/KEPLER/README
|
||||
<LI>bench/PHI/README
|
||||
<LI>examples/README
|
||||
<LI>examples/accelerate/README
|
||||
<LI>examples/accelerate/make.list
|
||||
</UL>
|
||||
<P>Help on any switch can be listed by using -h, e.g.
|
||||
<P>All of the Make.py options and syntax help can be accessed by using
|
||||
the "-h" switch.
|
||||
</P>
|
||||
<PRE>Make.py -h -i -p
|
||||
<P>E.g. typing "Make.py -h" gives
|
||||
</P>
|
||||
<PRE>Syntax: Make.py switch args ... <I>action1</I> <I>action2</I> ...
|
||||
actions:
|
||||
lib-all, lib-dir, clean, file, exe or machine
|
||||
zero or more actions, in any order (machine must be last)
|
||||
switches:
|
||||
-d (dir), -j (jmake), -m (makefile), -o (output),
|
||||
-p (packages), -r (redo), -s (settings), -v (verbose)
|
||||
switches for libs:
|
||||
-atc, -awpmd, -colvars, -cuda
|
||||
-gpu, -meam, -poems, -qmmm, -reax
|
||||
switches for build and makefile options:
|
||||
-intel, -kokkos, -cc, -mpi, -fft, -jpg, -png
|
||||
</PRE>
|
||||
<P>At a hi-level, these are the kinds of package management
|
||||
and build tasks that can be performed easily, using
|
||||
the Make.py tool:
|
||||
<P>Using the "-h" switch with other switches and actions gives additional
|
||||
info on all the other specified switches or actions. The "-h" can be
|
||||
anywhere in the command-line and the other switches do not need their
|
||||
arguments. E.g. type "Make.py -h -d -atc -intel" will print:
|
||||
</P>
|
||||
<UL><LI>install/uninstall packages and build the associated external libs (use -p and -u and -e)
|
||||
<LI>install packages needed for one or more input scripts (use -i and -p)
|
||||
<LI>build LAMMPS, either in the src dir or new dir (use -b)
|
||||
<LI>create a new dir with only the source code needed for one or more input scripts (use -i and -o)
|
||||
</UL>
|
||||
<P>The last bullet can be useful when you wish to build a stripped-down
|
||||
version of LAMMPS to run a specific script(s). Or when you wish to
|
||||
move the minimal amount of files to another platform for a remote
|
||||
LAMMPS build.
|
||||
<PRE>-d dir
|
||||
dir = LAMMPS home dir
|
||||
if -d not specified, working dir must be lammps/src
|
||||
</PRE>
|
||||
<PRE>-atc make=suffix lammps=suffix2
|
||||
all args are optional and can be in any order
|
||||
make = use Makefile.suffix (def = g++)
|
||||
lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile)
|
||||
</PRE>
|
||||
<PRE>-intel mode
|
||||
mode = cpu or phi (def = cpu)
|
||||
build Intel package for CPU or Xeon Phi
|
||||
</PRE>
|
||||
<P>Note that Make.py never overwrites an existing Makefile.machine.
|
||||
Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
|
||||
rename if desired. Likewise it creates an executable named
|
||||
src/lmp_auto, which you can rename using the -o switch if desired.
|
||||
</P>
|
||||
<P>Note that using Make.py is not a substitute for insuring you have a
|
||||
valid src/MAKE/Makefile.foo for your system, or that external library
|
||||
Makefiles in any lib/* directories you use are also valid for your
|
||||
system. But once you have done that, you can use Make.py to quickly
|
||||
include/exclude the packages and external libraries needed by your
|
||||
input scripts.
|
||||
<P>The most recently executed Make.py commmand is saved in
|
||||
src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
|
||||
the last command, or you can save a sequence of one or more Make.py
|
||||
commands to a file and invoke the file of commands using "-r". You
|
||||
can also label the commands in the file and invoke one or more of them
|
||||
by name.
|
||||
</P>
|
||||
<P>A typical use of Make.py is to start with a valid Makefile.machine for
|
||||
your system, that works for a vanilla LAMMPS build, i.e. when optional
|
||||
packages are not installed. You can then use Make.py to add various
|
||||
settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
|
||||
compiler and MPI options. You can also add additional packages to the
|
||||
build, as well as build the needed supporting libraries.
|
||||
</P>
|
||||
<P>You can also use Make.py to create a new Makefile.machine from
|
||||
scratch, using the "-m none" switch, if you also specify what compiler
|
||||
and MPI options to use, via the "-cc" and "-mpi" switches.
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
|
||||
@ -79,14 +79,27 @@ This section has the following sub-sections:
|
||||
|
||||
[{Read this first:}] :link(start_2_1)
|
||||
|
||||
If you want to avoid building LAMMPS, read the preceeding section
|
||||
about options available for downloading and installing executables.
|
||||
Details are discussed on the "download"_download page.
|
||||
If you want to avoid building LAMMPS yourself, read the preceeding
|
||||
section about options available for downloading and installing
|
||||
executables. Details are discussed on the "download"_download page.
|
||||
|
||||
Building LAMMPS can be simple or not-so-simple. If MPI is already
|
||||
installed on your machine (or you just want to run LAMMPS in serial)
|
||||
and you can use one of the provided machine Makefiles and the build
|
||||
works on your platform, then it's simple.
|
||||
Building LAMMPS can be simple or not-so-simple. If all you need are
|
||||
the default packages installed in LAMMPS, and MPI is already installed
|
||||
on your machine, or you just want to run LAMMPS in serial, then you
|
||||
can typically use the Makefile.mpi or Makefile.serial files in
|
||||
src/MAKE and type one of these lines (from the src dir):
|
||||
|
||||
make mpi
|
||||
make serial :pre
|
||||
|
||||
Or if one of the other Makefile.machine files in the src/MAKE
|
||||
sub-directories matches your system (type "make" to see a list), you
|
||||
can use it as-is by typing (for example):
|
||||
|
||||
make stampede :pre
|
||||
|
||||
If any of these builds with an existing Makefile.machine works on your
|
||||
system, then you're done!
|
||||
|
||||
If you want to do one of these:
|
||||
|
||||
@ -99,7 +112,14 @@ then building LAMMPS is more complicated. You may need to find where
|
||||
auxiliary libraries exist on your machine or install them if they
|
||||
don't. You may need to build additional libraries that are part of
|
||||
the LAMMPS package, before building LAMMPS. You may need to edit a
|
||||
machine Makefile to make it compatible with your system.
|
||||
Makefile.machine file to make it compatible with your system.
|
||||
|
||||
Note that there is a Make.py tool in the src directory that automates
|
||||
several of these steps, but you still have to know what you are doing.
|
||||
"Section 2.4"_#start_4 below describes the tool. It is a convenient
|
||||
way to work with installing/un-installing various packages, the
|
||||
Makefile.machine changes required by some packages, and the auxiliary
|
||||
libraries some of them use.
|
||||
|
||||
Please read the following sections carefully. If you are not
|
||||
comfortable with makefiles, or building codes on a Unix platform, or
|
||||
@ -115,7 +135,7 @@ please post the issue to the "LAMMPS mail
|
||||
list"_http://lammps.sandia.gov/mail.html.
|
||||
|
||||
If you succeed in building LAMMPS on a new kind of machine, for which
|
||||
there isn't a similar machine Makefile included in the src/MAKE
|
||||
there isn't a similar machine Makefile included in the src/MAKE/MORE
|
||||
directory, then send it to the developers and we can include it in the
|
||||
LAMMPS distribution.
|
||||
|
||||
@ -127,21 +147,43 @@ LAMMPS distribution.
|
||||
|
||||
The src directory contains the C++ source and header files for LAMMPS.
|
||||
It also contains a top-level Makefile and a MAKE sub-directory with
|
||||
low-level Makefile.* files for many machines. From within the src
|
||||
directory, type "make" or "gmake". You should see a list of available
|
||||
choices. If one of those is the machine and options you want, you can
|
||||
type a command like:
|
||||
low-level Makefile.* files for many systems and machines. See the
|
||||
src/MAKE/README file for a quick overview of what files are available
|
||||
and what sub-directories they are in.
|
||||
|
||||
make linux
|
||||
The src/MAKE dir has a few files that should work as-is on many
|
||||
platforms. The src/MAKE/OPTIONS dir has more that inovke additional
|
||||
compiler, MPI, and other setting options commonly used by LAMMPS, to
|
||||
illustrate their syntax. The src/MAKE/MACHINES dir has many more that
|
||||
have been tweaked or optimized for specific machines. These files are
|
||||
all good starting points if you find you need to change them for your
|
||||
machine. Put any file you edit into the src/MAKE/MINE directory and
|
||||
it will be never be touched by any LAMMPS updates.
|
||||
|
||||
From within the src directory, type "make" or "gmake". You should see
|
||||
a list of available choices from src/MAKE and all of its
|
||||
sub-directories. If one of those has the options you want or is the
|
||||
machine you want, you can type a command like:
|
||||
|
||||
make mpi
|
||||
or
|
||||
make serial_icc
|
||||
or
|
||||
gmake mac :pre
|
||||
|
||||
Note that the corresponding Makefile.machine can exist in src/MAKE or
|
||||
any of its sub-directories. If a file with the same name appears in
|
||||
multiple places (not a good idea), the order they are used is as
|
||||
follows: src/MAKE/MINE, src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.
|
||||
This gives preference to a file you have created/edited and put in
|
||||
src/MAKE/MINE.
|
||||
|
||||
Note that on a multi-processor or multi-core platform you can launch a
|
||||
parallel make, by using the "-j" switch with the make command, which
|
||||
will build LAMMPS more quickly.
|
||||
|
||||
If you get no errors and an executable like lmp_linux or lmp_mac is
|
||||
produced, you're done; it's your lucky day.
|
||||
If you get no errors and an executable like lmp_mpi or lmp_g++_serial
|
||||
or lmp_mac is produced, then you're done; it's your lucky day.
|
||||
|
||||
Note that by default only a few of LAMMPS optional packages are
|
||||
installed. To build LAMMPS with optional packages, see "this
|
||||
@ -151,43 +193,47 @@ section"_#start_3 below.
|
||||
|
||||
If Step 0 did not work, you will need to create a low-level Makefile
|
||||
for your machine, like Makefile.foo. You should make a copy of an
|
||||
existing src/MAKE/Makefile.* as a starting point. The only portions
|
||||
of the file you need to edit are the first line, the "compiler/linker
|
||||
settings" section, and the "LAMMPS-specific settings" section.
|
||||
existing Makefile.* in src/MAKE or one of its sub-directories as a
|
||||
starting point. The only portions of the file you need to edit are
|
||||
the first line, the "compiler/linker settings" section, and the
|
||||
"LAMMPS-specific settings" section. When it works, put the edited
|
||||
file in src/MAKE/MINE and it will not be altered by any future LAMMPS
|
||||
updates.
|
||||
|
||||
[Step 2]
|
||||
|
||||
Change the first line of src/MAKE/Makefile.foo to list the word "foo"
|
||||
after the "#", and whatever other options it will set. This is the
|
||||
line you will see if you just type "make".
|
||||
Change the first line of Makefile.foo to list the word "foo" after the
|
||||
"#", and whatever other options it will set. This is the line you
|
||||
will see if you just type "make".
|
||||
|
||||
[Step 3]
|
||||
|
||||
The "compiler/linker settings" section lists compiler and linker
|
||||
settings for your C++ compiler, including optimization flags. You can
|
||||
use g++, the open-source GNU compiler, which is available on all Unix
|
||||
systems. You can also use mpicc which will typically be available if
|
||||
systems. You can also use mpicxx which will typically be available if
|
||||
MPI is installed on your system, though you should check which actual
|
||||
compiler it wraps. Vendor compilers often produce faster code. On
|
||||
boxes with Intel CPUs, we suggest using the commercial Intel icc
|
||||
compiler, which can be downloaded from "Intel's compiler site"_intel.
|
||||
boxes with Intel CPUs, we suggest using the Intel icc compiler, which
|
||||
can be downloaded from "Intel's compiler site"_intel.
|
||||
|
||||
:link(intel,http://www.intel.com/software/products/noncom)
|
||||
|
||||
If building a C++ code on your machine requires additional libraries,
|
||||
then you should list them as part of the LIB variable.
|
||||
then you should list them as part of the LIB variable. You should
|
||||
not need to do this if you use mpicxx.
|
||||
|
||||
The DEPFLAGS setting is what triggers the C++ compiler to create a
|
||||
dependency list for a source file. This speeds re-compilation when
|
||||
source (*.cpp) or header (*.h) files are edited. Some compilers do
|
||||
not support dependency file creation, or may use a different switch
|
||||
than -D. GNU g++ works with -D. If your compiler can't create
|
||||
dependency files, then you'll need to create a Makefile.foo patterned
|
||||
after Makefile.storm, which uses different rules that do not involve
|
||||
dependency files. Note that when you build LAMMPS for the first time
|
||||
on a new platform, a long list of *.d files will be printed out
|
||||
rapidly. This is not an error; it is the Makefile doing its normal
|
||||
creation of dependencies.
|
||||
than -D. GNU g++ and Intel icc works with -D. If your compiler can't
|
||||
create dependency files, then you'll need to create a Makefile.foo
|
||||
patterned after Makefile.storm, which uses different rules that do not
|
||||
involve dependency files. Note that when you build LAMMPS for the
|
||||
first time on a new platform, a long list of *.d files will be printed
|
||||
out rapidly. This is not an error; it is the Makefile doing its
|
||||
normal creation of dependencies.
|
||||
|
||||
[Step 4]
|
||||
|
||||
@ -271,20 +317,21 @@ Step 6 below for info about building LAMMPS with an FFT library.
|
||||
[Step 5]
|
||||
|
||||
The 3 MPI variables are used to specify an MPI library to build LAMMPS
|
||||
with.
|
||||
with. Note that you do not need to set these if you use the MPI
|
||||
compiler mpicxx for your CC and LINK setting in the section above.
|
||||
The MPI wrapper knows where to find the needed files.
|
||||
|
||||
If you want LAMMPS to run in parallel, you must have an MPI library
|
||||
installed on your platform. If you use an MPI-wrapped compiler, such
|
||||
as "mpicc" to build LAMMPS, you should be able to leave these 3
|
||||
variables blank; the MPI wrapper knows where to find the needed files.
|
||||
If not, and MPI is installed on your system in the usual place (under
|
||||
/usr/local), you also may not need to specify these 3 variables. On
|
||||
some large parallel machines which use "modules" for their
|
||||
compile/link environements, you may simply need to include the correct
|
||||
module in your build environment. Or the parallel machine may have a
|
||||
vendor-provided MPI which the compiler has no trouble finding.
|
||||
installed on your platform. If MPI is installed on your system in the
|
||||
usual place (under /usr/local), you also may not need to specify these
|
||||
3 variables, assuming /usr/local is in your path. On some large
|
||||
parallel machines which use "modules" for their compile/link
|
||||
environements, you may simply need to include the correct module in
|
||||
your build environment, before building LAMMPS. Or the parallel
|
||||
machine may have a vendor-provided MPI which the compiler has no
|
||||
trouble finding.
|
||||
|
||||
Failing this, with these 3 variables you can specify where the mpi.h
|
||||
Failing this, these 3 variables can be used to specify where the mpi.h
|
||||
file (MPI_INC) and the MPI library file (MPI_PATH) are found and the
|
||||
name of the library file (MPI_LIB).
|
||||
|
||||
@ -304,20 +351,22 @@ arise when linking LAMMPS to the MPI library.
|
||||
|
||||
If you just want to run LAMMPS on a single processor, you can use the
|
||||
dummy MPI library provided in src/STUBS, since you don't need a true
|
||||
MPI library installed on your system. See the
|
||||
src/MAKE/Makefile.serial file for how to specify the 3 MPI variables
|
||||
in this case. You will also need to build the STUBS library for your
|
||||
platform before making LAMMPS itself. To build from the src
|
||||
directory, type "make stubs", or from the STUBS dir, type "make".
|
||||
This should create a libmpi_stubs.a file suitable for linking to
|
||||
LAMMPS. If the build fails, you will need to edit the STUBS/Makefile
|
||||
for your platform.
|
||||
MPI library installed on your system. See src/MAKE/Makefile.serial
|
||||
for how to specify the 3 MPI variables in this case. You will also
|
||||
need to build the STUBS library for your platform before making LAMMPS
|
||||
itself. Note that if you are building with src/MAKE/Makefile.serial,
|
||||
e.g. by typing "make serial", then the STUBS library is built for you.
|
||||
|
||||
The file STUBS/mpi.c provides a CPU timer function called
|
||||
MPI_Wtime() that calls gettimeofday() . If your system doesn't
|
||||
support gettimeofday() , you'll need to insert code to call another
|
||||
timer. Note that the ANSI-standard function clock() rolls over after
|
||||
an hour or so, and is therefore insufficient for timing long LAMMPS
|
||||
To build the STUBS library from the src directory, type "make stubs",
|
||||
or from the src/STUBS dir, type "make". This should create a
|
||||
libmpi_stubs.a file suitable for linking to LAMMPS. If the build
|
||||
fails, you will need to edit the STUBS/Makefile for your platform.
|
||||
|
||||
The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
|
||||
that calls gettimeofday() . If your system doesn't support
|
||||
gettimeofday() , you'll need to insert code to call another timer.
|
||||
Note that the ANSI-standard function clock() rolls over after an hour
|
||||
or so, and is therefore insufficient for timing long LAMMPS
|
||||
simulations.
|
||||
|
||||
[Step 6]
|
||||
@ -404,11 +453,9 @@ section"_#start_3 below, before proceeding to Step 9.
|
||||
|
||||
[Step 9]
|
||||
|
||||
That's it. Once you have a correct Makefile.foo, you have installed
|
||||
the optional LAMMPS packages you want to include in your build, and
|
||||
you have pre-built any other needed libraries (e.g. MPI, FFT, package
|
||||
libraries), all you need to do from the src directory is type
|
||||
something like this:
|
||||
That's it. Once you have a correct Makefile.foo, and you have
|
||||
pre-built any other needed libraries (e.g. MPI, FFT, etc) all you need
|
||||
to do from the src directory is type something like this:
|
||||
|
||||
make foo
|
||||
or
|
||||
@ -524,7 +571,7 @@ neighbor lists and would run very slowly in terms of CPU secs/timestep.
|
||||
[{Building for a Mac:}] :link(start_2_5)
|
||||
|
||||
OS X is BSD Unix, so it should just work. See the
|
||||
src/MAKE/Makefile.mac file.
|
||||
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.
|
||||
|
||||
:line
|
||||
|
||||
@ -553,7 +600,7 @@ excluded, you can build it yourself.
|
||||
|
||||
One way to do this is install and use cygwin to build LAMMPS with a
|
||||
standard unix style make program, just as you would on a Linux box;
|
||||
see src/MAKE/Makefile.cygwin.
|
||||
see src/MAKE/MACHINES/Makefile.cygwin.
|
||||
|
||||
The other way to do this is using Visual Studio and project files.
|
||||
See the src/WINDOWS directory and its README.txt file for instructions
|
||||
@ -568,7 +615,12 @@ This section has the following sub-sections:
|
||||
"Package basics"_#start_3_1
|
||||
"Including/excluding packages"_#start_3_2
|
||||
"Packages that require extra libraries"_#start_3_3
|
||||
"Packages that use make variable settings"_#start_3_4 :ul
|
||||
"Packages that require Makefile.machine settings"_#start_3_4 :ul
|
||||
|
||||
Note that the following "Section 2.4"_#start_4 describes the Make.py
|
||||
tool which can be used to install/un-install packages and build the
|
||||
auxiliary libraries which some of them use. It can also auto-edit a
|
||||
Makefile.machine to add settings needed by some packages.
|
||||
|
||||
:line
|
||||
|
||||
@ -577,9 +629,11 @@ This section has the following sub-sections:
|
||||
The source code for LAMMPS is structured as a set of core files which
|
||||
are always included, plus optional packages. Packages are groups of
|
||||
files that enable a specific set of features. For example, force
|
||||
fields for molecular systems or granular systems are in packages. You
|
||||
can see the list of all packages by typing "make package" from within
|
||||
the src directory of the LAMMPS distribution.
|
||||
fields for molecular systems or granular systems are in packages.
|
||||
|
||||
You can see the list of all packages by typing "make package" from
|
||||
within the src directory of the LAMMPS distribution. This also lists
|
||||
various make commands that can be used to manipulate packages.
|
||||
|
||||
If you use a command in a LAMMPS input script that is specific to a
|
||||
particular package, you must have built LAMMPS with that package, else
|
||||
@ -646,10 +700,11 @@ I.e. individual files are only included if their dependencies are
|
||||
already included. Likewise, if a package is excluded, other files
|
||||
dependent on that package are also excluded.
|
||||
|
||||
The reason to exclude packages is if you will never run certain kinds
|
||||
of simulations. For some packages, this will keep you from having to
|
||||
build auxiliary libraries (see below), and will also produce a smaller
|
||||
executable which may run a bit faster.
|
||||
If you will never run simulations that use the features in a
|
||||
particular packages, there is no reason to include it in your build.
|
||||
For some packages, this will keep you from having to build auxiliary
|
||||
libraries (see below), and will also produce a smaller executable
|
||||
which may run a bit faster.
|
||||
|
||||
When you download a LAMMPS tarball, these packages are pre-installed
|
||||
in the src directory: KSPACE, MANYBODY,MOLECULE. When you download
|
||||
@ -660,9 +715,10 @@ Packages are included or excluded by typing "make yes-name" or "make
|
||||
no-name", where "name" is the name of the package in lower-case, e.g.
|
||||
name = kspace for the KSPACE package or name = user-atc for the
|
||||
USER-ATC package. You can also type "make yes-standard", "make
|
||||
no-standard", "make yes-user", "make no-user", "make yes-all" or "make
|
||||
no-all" to include/exclude various sets of packages. Type "make
|
||||
package" to see the all of the package-related make options.
|
||||
no-standard", "make yes-std", "make no-std", "make yes-user", "make
|
||||
no-user", "make yes-all" or "make no-all" to include/exclude various
|
||||
sets of packages. Type "make package" to see the all of the
|
||||
package-related make options.
|
||||
|
||||
IMPORTANT NOTE: Inclusion/exclusion of a package works by simply
|
||||
moving files back and forth between the main src directory and
|
||||
@ -676,18 +732,19 @@ sub-directories. You do not normally need to use these commands
|
||||
unless you are editing LAMMPS files or have downloaded a patch from
|
||||
the LAMMPS WWW site.
|
||||
|
||||
Typing "make package-update" will overwrite src files with files from
|
||||
the package sub-directories if the package has been included. It
|
||||
should be used after a patch is installed, since patches only update
|
||||
the files in the package sub-directory, but not the src files. Typing
|
||||
"make package-overwrite" will overwrite files in the package
|
||||
sub-directories with src files.
|
||||
Typing "make package-update" or "make pu" will overwrite src files
|
||||
with files from the package sub-directories if the package has been
|
||||
included. It should be used after a patch is installed, since patches
|
||||
only update the files in the package sub-directory, but not the src
|
||||
files. Typing "make package-overwrite" will overwrite files in the
|
||||
package sub-directories with src files.
|
||||
|
||||
Typing "make package-status" will show which packages are currently
|
||||
included. Of those that are included, it will list files that are
|
||||
different in the src directory and package sub-directory. Typing
|
||||
"make package-diff" lists all differences between these files. Again,
|
||||
type "make package" to see all of the package-related make options.
|
||||
Typing "make package-status" or "make ps" will show which packages are
|
||||
currently included. Of those that are included, it will list files
|
||||
that are different in the src directory and package sub-directory.
|
||||
Typing "make package-diff" lists all differences between these files.
|
||||
Again, type "make package" to see all of the package-related make
|
||||
options.
|
||||
|
||||
:line
|
||||
|
||||
@ -699,16 +756,16 @@ you get a LAMMPS build error about a missing library, this is likely
|
||||
the reason. See the "Section_packages"_Section_packages.html doc page
|
||||
for a list of packages that have auxiliary libraries.
|
||||
|
||||
Code for some of these auxiliary libraries is included in the LAMMPS
|
||||
Code for most of these auxiliary libraries is included in the LAMMPS
|
||||
distribution under the lib directory. Examples are the USER-ATC and
|
||||
MEAM packages. Some auxiliary libraries are NOT included with LAMMPS;
|
||||
to use the associated package you must download and install the
|
||||
auxiliary library yourself. Examples are the KIM and VORONOI and
|
||||
MEAM packages. A few auxiliary libraries are NOT included with
|
||||
LAMMPS; to use the associated package you must download and install
|
||||
the auxiliary library yourself. Examples are the KIM and VORONOI and
|
||||
USER-MOLFILE packages.
|
||||
|
||||
For libraries with provided source code, each lib directory has a
|
||||
README file (e.g. lib/reax/README) with instructions on how to build
|
||||
that library. Typically this is done by typing something like:
|
||||
For provided libraries, each lib directory has a README file
|
||||
(e.g. lib/reax/README) with instructions on how to build that library.
|
||||
Typically this is done by typing something like:
|
||||
|
||||
make -f Makefile.g++ :pre
|
||||
|
||||
@ -740,168 +797,203 @@ is built with, typically requires additional Fortran-to-C libraries be
|
||||
included in the link. Another example are the BLAS and LAPACK
|
||||
libraries needed to use the USER-ATC or USER-AWPMD packages.
|
||||
|
||||
For libraries without provided source code, see the
|
||||
src/package/Makefile.lammps file for information on where to find the
|
||||
library and how to build it. E.g. the file src/KIM/Makefile.lammps or
|
||||
src/VORONOI/Makefile.lammps or src/UESR-MOLFILE/Makefile.lammps.
|
||||
These files serve the same purpose as the lib/package/Makefile.lammps
|
||||
files described above. The files have settings needed when LAMMPS is
|
||||
built to link with the corresponding auxiliary library.
|
||||
For libraries without provided source code, the file
|
||||
src/package/README has information on where to find the library and
|
||||
how to build it, e.g. src/VORONOI/README. There is also a
|
||||
Makefile.lammps file in the src/package directory. E.g. files
|
||||
src/KIM/Makefile.lammps or src/VORONOI/Makefile.lammps or
|
||||
src/UESR-MOLFILE/Makefile.lammps. These files serve the same purpose
|
||||
as the lib/package/Makefile.lammps files described above. The files
|
||||
have settings needed when LAMMPS is built to link with the
|
||||
corresponding auxiliary library.
|
||||
|
||||
Again, you must insure that the settings in
|
||||
src/package/Makefile.lammps are appropriate for your system and where
|
||||
you installed the auxiliary library. If they are not, the LAMMPS
|
||||
build will fail.
|
||||
build will typically fail.
|
||||
|
||||
:line
|
||||
|
||||
[{Packages that use make variable settings}] :link(start_3_4)
|
||||
[{Packages that require Makefile.machine settings}] :link(start_3_4)
|
||||
|
||||
One package, the KOKKOS package, allows its build options to be
|
||||
specified by setting variables via the "make" command, rather than by
|
||||
first building an auxiliary library and editing a Makefile.lammps
|
||||
file, as discussed in the previous sub-section for other packages.
|
||||
This is for convenience since it is common to want to experiment with
|
||||
different Kokkos library options. Using variables enables a direct
|
||||
re-build of LAMMPS and its Kokkos dependencies, so that a benchmark
|
||||
test with different Kokkos options can be quickly performed.
|
||||
A few packages require specific settings in Makefile.machine, to
|
||||
either build or use the package effectively. These are the
|
||||
USER-INTEL, KOKKOS, USER-OMP, and OPT packages. The details of what
|
||||
flags to add or what variables to define are given on the doc pages
|
||||
that describe each of these accelerator packages in detail:
|
||||
|
||||
The syntax for setting make variables is as follows. You must
|
||||
use a GNU-compatible make command for this to work. Try "gmake"
|
||||
if your system's standard make complains.
|
||||
"USER-INTEL package"_accelerate_intel.html
|
||||
"KOKKOS package"_accelerate_kokkos.html
|
||||
"USER-OMP package"_accelerate_omp.html
|
||||
"OPT package"_accelerate_opt.html :ul
|
||||
|
||||
make yes-kokkos
|
||||
make g++ VAR1=value VAR2=value ... :pre
|
||||
Here is a brief summary of what Makefile.machine changes are needed.
|
||||
Note that the Make.py tool, described in the next "Section
|
||||
2.4"_#start_4 can automatically add the needed info to an existing
|
||||
machine Makefile, using simple command-line arguments.
|
||||
|
||||
The first line installs the KOKKOS package, which only needs to be
|
||||
done once. The second line builds LAMMPS with src/MAKE/Makefile.g++
|
||||
and optionally sets one or more variables that affect the build. Each
|
||||
variable is specified in upper-case; its value follows an equal sign
|
||||
with no spaces. The second line can be repeated with different
|
||||
variable settings, though a "clean" must be done before the rebuild.
|
||||
Type "make clean" to see options for this operation.
|
||||
In src/MAKE/OPTIONS see the following Makefiles for examples of the
|
||||
changes described below:
|
||||
|
||||
These are the variables that can be specified. Each takes a value of
|
||||
{yes} or {no}. The default value is listed, which is set in the
|
||||
lib/kokkos/Makefile.lammps file. See "this
|
||||
section"_Section_accelerate.html#acc_8 for a discussion of what is
|
||||
meant by "host" and "device" in the Kokkos context.
|
||||
Makefile.intel_cpu
|
||||
Makefile.intel_phi
|
||||
Makefile.kokkos_omp
|
||||
Makefile.kokkos_cuda
|
||||
Makefile.kokkos_phi
|
||||
Makefile.omp :ul
|
||||
|
||||
OMP, default = {yes}
|
||||
CUDA, default = {no}
|
||||
HWLOC, default = {no}
|
||||
AVX, default = {no}
|
||||
MIC, default = {no}
|
||||
LIBRT, default = {no}
|
||||
DEBUG, default = {no} :ul
|
||||
For the USER-INTEL package, you have 2 choices when building. You can
|
||||
build with CPU or Phi support. The latter uses Xeon Phi chips in
|
||||
"offload" mode. Each of these modes requires additional settings in
|
||||
your Makefile.machine for CCFLAGS and LINKFLAGS.
|
||||
|
||||
OMP sets the parallelization method used for Kokkos code (within
|
||||
LAMMPS) that runs on the host. OMP=yes means that OpenMP will be
|
||||
used. OMP=no means that pthreads will be used.
|
||||
For CPU mode (if using an Intel compiler):
|
||||
|
||||
CUDA sets the parallelization method used for Kokkos code (within
|
||||
LAMMPS) that runs on the device. CUDA=yes means an NVIDIA GPU running
|
||||
CUDA will be used. CUDA=no means that the OMP=yes or OMP=no setting
|
||||
will be used for the device as well as the host.
|
||||
CCFLAGS: add -fopenmp, -DLAMMPS_MEMALIGN=64, -restrict, -xHost, -fno-alias, -ansi-alias, -override-limits
|
||||
LINKFLAGS: add -fopenmp :ul
|
||||
|
||||
If CUDA=yes, then the lo-level Makefile in the src/MAKE directory must
|
||||
use "nvcc" as its compiler, via its CC setting. For best performance
|
||||
its CCFLAGS setting should use -O3 and have an -arch setting that
|
||||
matches the compute capability of your NVIDIA hardware and software
|
||||
installation, e.g. -arch=sm_20. Generally Fermi Generation GPUs are
|
||||
sm_20, while Kepler generation GPUs are sm_30 or sm_35 and Maxwell
|
||||
cards are sm_50. A complete list can be found on
|
||||
"wikipedia"_http://en.wikipedia.org/wiki/CUDA#Supported_GPUs. You can
|
||||
also use the deviceQuery tool that comes with the CUDA samples. Note
|
||||
the minimal required compute capability is 2.0, but this will give
|
||||
signicantly reduced performance compared to Kepler generation GPUs
|
||||
with compute capability 3.x. For the LINK setting, "nvcc" should not
|
||||
be used; instead use g++ or another compiler suitable for linking C++
|
||||
applications. Often you will want to use your MPI compiler wrapper
|
||||
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
|
||||
also have a "Compilation rule" for creating *.o files from *.cu files.
|
||||
See src/Makefile.cuda for an example of a lo-level Makefile with all
|
||||
of these settings.
|
||||
For Phi mode add the following in addition to the CPU mode flags:
|
||||
|
||||
HWLOC binds threads to hardware cores, so they do not migrate during a
|
||||
simulation. HWLOC=yes should always be used if running with OMP=no
|
||||
for pthreads. It is not necessary for OMP=yes for OpenMP, because
|
||||
OpenMP provides alternative methods via environment variables for
|
||||
binding threads to hardware cores. More info on binding threads to
|
||||
cores is given in "this section"_Section_accelerate.html#acc_8.
|
||||
CCFLAGS: add -DLMP_INTEL_OFFLOAD and
|
||||
LINKFLAGS: add -offload :ul
|
||||
|
||||
AVX enables Intel advanced vector extensions when compiling for an
|
||||
Intel-compatible chip. AVX=yes should only be set if your host
|
||||
hardware supports AVX. If it does not support it, this will cause a
|
||||
run-time crash.
|
||||
And also add this to CCFLAGS:
|
||||
|
||||
MIC enables compiler switches needed when compling for an Intel Phi
|
||||
processor.
|
||||
-offload-option,mic,compiler,"-fp-model fast=2 -mGLOB_default_function_attrs=\"gather_scatter_loop_unroll=4\"" :pre
|
||||
|
||||
LIBRT enables use of a more accurate timer mechanism on most Unix
|
||||
platforms. This library is not available on all platforms.
|
||||
For the KOKKOS package, you have 3 choices when building. You can
|
||||
build with OMP or Cuda or Phi support. Phi support uses Xeon Phi
|
||||
chips in "native" mode. This can be done by setting the following
|
||||
variables in your Makefile.machine:
|
||||
|
||||
DEBUG is only useful when developing a Kokkos-enabled style within
|
||||
LAMMPS. DEBUG=yes enables printing of run-time debugging information
|
||||
that can be useful. It also enables runtime bounds checking on Kokkos
|
||||
data structures.
|
||||
for OMP support, set OMP = yes
|
||||
for Cuda support, set OMP = yes and CUDA = yes
|
||||
for Phi support, set OMP = yes and MIC = yes :ul
|
||||
|
||||
These can also be set as additional arguments to the make command, e.g.
|
||||
|
||||
make g++ OMP=yes MIC=yes :pre
|
||||
|
||||
Building the KOKKOS package with CUDA support requires a Makefile
|
||||
machine that uses the NVIDIA "nvcc" compiler, as well as an
|
||||
appropriate "arch" setting appropriate to the GPU hardware and NVIDIA
|
||||
software you have on your machine. See
|
||||
src/MAKE/OPTIONS/Makefile.kokkos_cuda for an example of such a machine
|
||||
Makefile.
|
||||
|
||||
For the USER-OMP package, your Makefile.machine needs additional
|
||||
settings for CCFLAGS and LINKFLAGS.
|
||||
|
||||
CCFLAGS: add -fopenmp and -restrict
|
||||
LINKFLAGS: add -fopenmp :ul
|
||||
|
||||
For the OPT package, your Makefile.machine needs an additional
|
||||
settings for CCFLAGS.
|
||||
|
||||
CCFLAGS: add -restrict :ul
|
||||
|
||||
:line
|
||||
|
||||
2.4 Building LAMMPS via the Make.py script :h4,link(start_4)
|
||||
|
||||
The src directory includes a Make.py script, written
|
||||
in Python, which can be used to automate various steps
|
||||
of the build process.
|
||||
The src directory includes a Make.py script, written in Python, which
|
||||
can be used to automate various steps of the build process. It is
|
||||
particularly useful for working with the accelerator packages, as well
|
||||
as other packages which require auxiliary libraries to be built.
|
||||
|
||||
You can run the script from the src directory by typing either:
|
||||
You can run Make.py from the src directory by typing either:
|
||||
|
||||
Make.py
|
||||
python Make.py :pre
|
||||
Make.py -h
|
||||
python Make.py -h :pre
|
||||
|
||||
which will give you info about the tool. For the former to work, you
|
||||
may need to edit the 1st line of the script to point to your local
|
||||
which will give you help info about the tool. For the former to work,
|
||||
you may need to edit the first line of Make.py to point to your local
|
||||
Python. And you may need to insure the script is executable:
|
||||
|
||||
chmod +x Make.py :pre
|
||||
|
||||
The following options are supported as switches:
|
||||
Here are examples of build tasks you can perform with Make.py:
|
||||
|
||||
-i file1 file2 ...
|
||||
-p package1 package2 ...
|
||||
-u package1 package2 ...
|
||||
-e package1 arg1 arg2 package2 ...
|
||||
-o dir
|
||||
-b machine
|
||||
-s suffix1 suffix2 ...
|
||||
-l dir
|
||||
-j N
|
||||
-h switch1 switch2 ... :ul
|
||||
Install/uninstall packages: Make.py -p no-lib kokkos omp intel
|
||||
Build specific auxiliary libs: Make.py lib-atc lib-meam
|
||||
Build libs for all installed packages: Make.py -p cuda gpu -gpu mode=double arch=31 lib-all
|
||||
Create a Makefile from scratch with a compiler and MPI: Make.py -m none -cc g++ -mpi mpich file
|
||||
Augment Makefile.serial with settings for installed packages: Make.py -p intel -intel cpu -m serial file
|
||||
Add JPG and FFTW support to Makefile.mpi: Make.py -m mpi -jpg -fft fftw file
|
||||
Build LAMMPS with a parallel make using Makefile.mpi: Make.py -j 16 -m mpi exe
|
||||
Build LAMMPS and libs it needs using Makefile.serial with accelerator settings: Make.py -p gpu intel -intel cpu lib-all file serial :tb(s=:)
|
||||
|
||||
Help on any switch can be listed by using -h, e.g.
|
||||
The bench and examples directories give Make.py commands that can be
|
||||
used to build LAMMPS with the various packages and options needed to
|
||||
run all the benchmark and example input scripts. See these files for
|
||||
more details:
|
||||
|
||||
Make.py -h -i -p :pre
|
||||
bench/README
|
||||
bench/FERMI/README
|
||||
bench/KEPLER/README
|
||||
bench/PHI/README
|
||||
examples/README
|
||||
examples/accelerate/README
|
||||
examples/accelerate/make.list :ul
|
||||
|
||||
At a hi-level, these are the kinds of package management
|
||||
and build tasks that can be performed easily, using
|
||||
the Make.py tool:
|
||||
All of the Make.py options and syntax help can be accessed by using
|
||||
the "-h" switch.
|
||||
|
||||
install/uninstall packages and build the associated external libs (use -p and -u and -e)
|
||||
install packages needed for one or more input scripts (use -i and -p)
|
||||
build LAMMPS, either in the src dir or new dir (use -b)
|
||||
create a new dir with only the source code needed for one or more input scripts (use -i and -o) :ul
|
||||
E.g. typing "Make.py -h" gives
|
||||
|
||||
The last bullet can be useful when you wish to build a stripped-down
|
||||
version of LAMMPS to run a specific script(s). Or when you wish to
|
||||
move the minimal amount of files to another platform for a remote
|
||||
LAMMPS build.
|
||||
Syntax: Make.py switch args ... {action1} {action2} ...
|
||||
actions:
|
||||
lib-all, lib-dir, clean, file, exe or machine
|
||||
zero or more actions, in any order (machine must be last)
|
||||
switches:
|
||||
-d (dir), -j (jmake), -m (makefile), -o (output),
|
||||
-p (packages), -r (redo), -s (settings), -v (verbose)
|
||||
switches for libs:
|
||||
-atc, -awpmd, -colvars, -cuda
|
||||
-gpu, -meam, -poems, -qmmm, -reax
|
||||
switches for build and makefile options:
|
||||
-intel, -kokkos, -cc, -mpi, -fft, -jpg, -png :pre
|
||||
|
||||
Note that using Make.py is not a substitute for insuring you have a
|
||||
valid src/MAKE/Makefile.foo for your system, or that external library
|
||||
Makefiles in any lib/* directories you use are also valid for your
|
||||
system. But once you have done that, you can use Make.py to quickly
|
||||
include/exclude the packages and external libraries needed by your
|
||||
input scripts.
|
||||
Using the "-h" switch with other switches and actions gives additional
|
||||
info on all the other specified switches or actions. The "-h" can be
|
||||
anywhere in the command-line and the other switches do not need their
|
||||
arguments. E.g. type "Make.py -h -d -atc -intel" will print:
|
||||
|
||||
-d dir
|
||||
dir = LAMMPS home dir
|
||||
if -d not specified, working dir must be lammps/src :pre
|
||||
|
||||
-atc make=suffix lammps=suffix2
|
||||
all args are optional and can be in any order
|
||||
make = use Makefile.suffix (def = g++)
|
||||
lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile) :pre
|
||||
|
||||
-intel mode
|
||||
mode = cpu or phi (def = cpu)
|
||||
build Intel package for CPU or Xeon Phi :pre
|
||||
|
||||
Note that Make.py never overwrites an existing Makefile.machine.
|
||||
Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
|
||||
rename if desired. Likewise it creates an executable named
|
||||
src/lmp_auto, which you can rename using the -o switch if desired.
|
||||
|
||||
The most recently executed Make.py commmand is saved in
|
||||
src/Make.py.last. You can use the "-r" switch (for redo) to re-invoke
|
||||
the last command, or you can save a sequence of one or more Make.py
|
||||
commands to a file and invoke the file of commands using "-r". You
|
||||
can also label the commands in the file and invoke one or more of them
|
||||
by name.
|
||||
|
||||
A typical use of Make.py is to start with a valid Makefile.machine for
|
||||
your system, that works for a vanilla LAMMPS build, i.e. when optional
|
||||
packages are not installed. You can then use Make.py to add various
|
||||
settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
|
||||
compiler and MPI options. You can also add additional packages to the
|
||||
build, as well as build the needed supporting libraries.
|
||||
|
||||
You can also use Make.py to create a new Makefile.machine from
|
||||
scratch, using the "-m none" switch, if you also specify what compiler
|
||||
and MPI options to use, via the "-cc" and "-mpi" switches.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
@ -74,16 +74,30 @@ projects can be compiled without problems.
|
||||
<P>This requires two steps (a,b): build the USER-CUDA library, then build
|
||||
LAMMPS with the USER-CUDA package.
|
||||
</P>
|
||||
<P>You can do both these steps in one line, using the src/Make.py script,
|
||||
described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
|
||||
Type "Make.py -h" for help. If run from the src directory, this
|
||||
command will create src/lmp_cuda using src/MAKE/Makefile.mpi as the
|
||||
starting Makefile.machine:
|
||||
</P>
|
||||
<PRE>Make.py -p cuda -cuda mode=single arch=20 -o cuda lib-cuda file mpi
|
||||
</PRE>
|
||||
<P>Or you can follow these two (a,b) steps:
|
||||
</P>
|
||||
<P>(a) Build the USER-CUDA library
|
||||
</P>
|
||||
<P>The USER-CUDA library is in lammps/lib/cuda. If your <I>CUDA</I> toolkit
|
||||
is not installed in the default system directoy <I>/usr/local/cuda</I> edit
|
||||
the file <I>lib/cuda/Makefile.common</I> accordingly.
|
||||
</P>
|
||||
<P>To set options for the library build, type "make OPTIONS", where
|
||||
<P>To build the library with the settings in lib/cuda/Makefile.default,
|
||||
simply type:
|
||||
</P>
|
||||
<PRE>make
|
||||
</PRE>
|
||||
<P>To set options when the library is built, type "make OPTIONS", where
|
||||
<I>OPTIONS</I> are one or more of the following. The settings will be
|
||||
written to the <I>lib/cuda/Makefile.defaults</I> and used when
|
||||
the library is built.
|
||||
written to the <I>lib/cuda/Makefile.defaults</I> before the build.
|
||||
</P>
|
||||
<PRE><I>precision=N</I> to set the precision level
|
||||
N = 1 for single precision (default)
|
||||
@ -107,11 +121,8 @@ the library is built.
|
||||
0 = no CUFFT support (default)
|
||||
in the future other CUDA-enabled FFT libraries might be supported
|
||||
</PRE>
|
||||
<P>To build the library, simply type:
|
||||
</P>
|
||||
<PRE>make
|
||||
</PRE>
|
||||
<P>If successful, it will produce the files libcuda.a and Makefile.lammps.
|
||||
<P>If the build is successful, it will produce the files liblammpscuda.a and
|
||||
Makefile.lammps.
|
||||
</P>
|
||||
<P>Note that if you change any of the options (like precision), you need
|
||||
to re-build the entire library. Do a "make clean" first, followed by
|
||||
@ -123,8 +134,7 @@ to re-build the entire library. Do a "make clean" first, followed by
|
||||
make yes-user-cuda
|
||||
make machine
|
||||
</PRE>
|
||||
<P>No additional compile/link flags are needed in your Makefile.machine
|
||||
in src/MAKE.
|
||||
<P>No additional compile/link flags are needed in Makefile.machine.
|
||||
</P>
|
||||
<P>Note that if you change the USER-CUDA library precision (discussed
|
||||
above) and rebuild the USER-CUDA library, then you also need to
|
||||
|
||||
@ -71,16 +71,30 @@ projects can be compiled without problems.
|
||||
This requires two steps (a,b): build the USER-CUDA library, then build
|
||||
LAMMPS with the USER-CUDA package.
|
||||
|
||||
You can do both these steps in one line, using the src/Make.py script,
|
||||
described in "Section 2.4"_Section_start.html#start_4 of the manual.
|
||||
Type "Make.py -h" for help. If run from the src directory, this
|
||||
command will create src/lmp_cuda using src/MAKE/Makefile.mpi as the
|
||||
starting Makefile.machine:
|
||||
|
||||
Make.py -p cuda -cuda mode=single arch=20 -o cuda lib-cuda file mpi :pre
|
||||
|
||||
Or you can follow these two (a,b) steps:
|
||||
|
||||
(a) Build the USER-CUDA library
|
||||
|
||||
The USER-CUDA library is in lammps/lib/cuda. If your {CUDA} toolkit
|
||||
is not installed in the default system directoy {/usr/local/cuda} edit
|
||||
the file {lib/cuda/Makefile.common} accordingly.
|
||||
|
||||
To set options for the library build, type "make OPTIONS", where
|
||||
To build the library with the settings in lib/cuda/Makefile.default,
|
||||
simply type:
|
||||
|
||||
make :pre
|
||||
|
||||
To set options when the library is built, type "make OPTIONS", where
|
||||
{OPTIONS} are one or more of the following. The settings will be
|
||||
written to the {lib/cuda/Makefile.defaults} and used when
|
||||
the library is built.
|
||||
written to the {lib/cuda/Makefile.defaults} before the build.
|
||||
|
||||
{precision=N} to set the precision level
|
||||
N = 1 for single precision (default)
|
||||
@ -104,11 +118,8 @@ the library is built.
|
||||
0 = no CUFFT support (default)
|
||||
in the future other CUDA-enabled FFT libraries might be supported :pre
|
||||
|
||||
To build the library, simply type:
|
||||
|
||||
make :pre
|
||||
|
||||
If successful, it will produce the files libcuda.a and Makefile.lammps.
|
||||
If the build is successful, it will produce the files liblammpscuda.a and
|
||||
Makefile.lammps.
|
||||
|
||||
Note that if you change any of the options (like precision), you need
|
||||
to re-build the entire library. Do a "make clean" first, followed by
|
||||
@ -120,8 +131,7 @@ cd lammps/src
|
||||
make yes-user-cuda
|
||||
make machine :pre
|
||||
|
||||
No additional compile/link flags are needed in your Makefile.machine
|
||||
in src/MAKE.
|
||||
No additional compile/link flags are needed in Makefile.machine.
|
||||
|
||||
Note that if you change the USER-CUDA library precision (discussed
|
||||
above) and rebuild the USER-CUDA library, then you also need to
|
||||
|
||||
@ -76,6 +76,16 @@ install the NVIDIA Cuda software on your system:
|
||||
<P>This requires two steps (a,b): build the GPU library, then build
|
||||
LAMMPS with the GPU package.
|
||||
</P>
|
||||
<P>You can do both these steps in one line, using the src/Make.py script,
|
||||
described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
|
||||
Type "Make.py -h" for help. If run from the src directory, this
|
||||
command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
|
||||
starting Makefile.machine:
|
||||
</P>
|
||||
<PRE>Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi
|
||||
</PRE>
|
||||
<P>Or you can follow these two (a,b) steps:
|
||||
</P>
|
||||
<P>(a) Build the GPU library
|
||||
</P>
|
||||
<P>The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in
|
||||
@ -120,8 +130,7 @@ Makefile.linux clean", followed by the make command above.
|
||||
make yes-gpu
|
||||
make machine
|
||||
</PRE>
|
||||
<P>No additional compile/link flags are needed in your Makefile.machine
|
||||
in src/MAKE.
|
||||
<P>No additional compile/link flags are needed in Makefile.machine.
|
||||
</P>
|
||||
<P>Note that if you change the GPU library precision (discussed above)
|
||||
and rebuild the GPU library, then you also need to re-install the GPU
|
||||
|
||||
@ -73,6 +73,16 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
|
||||
This requires two steps (a,b): build the GPU library, then build
|
||||
LAMMPS with the GPU package.
|
||||
|
||||
You can do both these steps in one line, using the src/Make.py script,
|
||||
described in "Section 2.4"_Section_start.html#start_4 of the manual.
|
||||
Type "Make.py -h" for help. If run from the src directory, this
|
||||
command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
|
||||
starting Makefile.machine:
|
||||
|
||||
Make.py -p gpu -gpu mode=single arch=31 -o gpu lib-gpu file mpi :pre
|
||||
|
||||
Or you can follow these two (a,b) steps:
|
||||
|
||||
(a) Build the GPU library
|
||||
|
||||
The GPU library is in lammps/lib/gpu. Select a Makefile.machine (in
|
||||
@ -117,8 +127,7 @@ cd lammps/src
|
||||
make yes-gpu
|
||||
make machine :pre
|
||||
|
||||
No additional compile/link flags are needed in your Makefile.machine
|
||||
in src/MAKE.
|
||||
No additional compile/link flags are needed in Makefile.machine.
|
||||
|
||||
Note that if you change the GPU library precision (discussed above)
|
||||
and rebuild the GPU library, then you also need to re-install the GPU
|
||||
|
||||
@ -41,6 +41,10 @@ suffix to "omp" so that styles from the USER-OMP package will be used
|
||||
if available, after first testing if a style from the USER-INTEL
|
||||
package is available.
|
||||
</P>
|
||||
<P>When using the USER-INTEL package, you must choose at build time
|
||||
whether you are building for CPU-only acceleration or for using the
|
||||
Xeon Phi in offload mode.
|
||||
</P>
|
||||
<P>Here is a quick overview of how to use the USER-INTEL package
|
||||
for CPU-only acceleration:
|
||||
</P>
|
||||
@ -50,6 +54,9 @@ for CPU-only acceleration:
|
||||
<LI>specify how many OpenMP threads per MPI task to use
|
||||
<LI>use USER-INTEL and (optionally) USER-OMP styles in your input script
|
||||
</UL>
|
||||
<P>Note that many of these settings can only be used with the Intel
|
||||
compiler, as discussed below.
|
||||
</P>
|
||||
<P>Using the USER-INTEL package to offload work to the Intel(R)
|
||||
Xeon Phi(TM) coprocessor is the same except for these additional
|
||||
steps:
|
||||
@ -74,25 +81,41 @@ Phi(TM) coprocessors.
|
||||
Intel(R) compiler. Use of other compilers may not result in
|
||||
vectorization or give poor performance.
|
||||
</P>
|
||||
<P>Use of an Intel C++ compiler is reccommended, but not required. The
|
||||
compiler must support the OpenMP interface.
|
||||
<P>Use of an Intel C++ compiler is recommended, but not required (though
|
||||
g++ will not recognize some of the settings, so they cannot be used).
|
||||
The compiler must support the OpenMP interface.
|
||||
</P>
|
||||
<P><B>Building LAMMPS with the USER-INTEL package:</B>
|
||||
</P>
|
||||
<P>Include the package(s) and build LAMMPS:
|
||||
<P>You must choose at build time whether to build for CPU acceleration or
|
||||
to use the Xeon Phi in offload mode.
|
||||
</P>
|
||||
<P>You can do either in one line, using the src/Make.py script, described
|
||||
in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type
|
||||
"Make.py -h" for help. If run from the src directory, these commands
|
||||
will create src/lmp_intel_cpu and lmp_intel_phi using
|
||||
src/MAKE/Makefile.mpi as the starting Makefile.machine:
|
||||
</P>
|
||||
<PRE>Make.py -p intel omp -intel cpu -o intel_cpu -cc icc file mpi
|
||||
Make.py -p intel omp -intel phi -o intel_phi -cc icc file mpi
|
||||
</PRE>
|
||||
<P>Note that this assumes that your MPI and its mpicxx wrapper
|
||||
is using the Intel compiler. If it is not, you should
|
||||
leave off the "-cc icc" switch.
|
||||
</P>
|
||||
<P>Or you can follow these steps:
|
||||
</P>
|
||||
<PRE>cd lammps/src
|
||||
make yes-user-intel
|
||||
make yes-user-omp (if desired)
|
||||
make machine
|
||||
</PRE>
|
||||
<P>If the USER-OMP package is also installed, you can use styles from
|
||||
both packages, as described below.
|
||||
<P>Note that if the USER-OMP package is also installed, you can use
|
||||
styles from both packages, as described below.
|
||||
</P>
|
||||
<P>The lo-level src/MAKE/Makefile.machine needs a flag for OpenMP support
|
||||
in both the CCFLAGS and LINKFLAGS variables, which is <I>-openmp</I> for
|
||||
Intel compilers. You also need to add -DLAMMPS_MEMALIGN=64 and
|
||||
-restrict to CCFLAGS.
|
||||
<P>The Makefile.machine needs a "-fopenmp" flag for OpenMP support in
|
||||
both the CCFLAGS and LINKFLAGS variables. You also need to add
|
||||
-DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.
|
||||
</P>
|
||||
<P>If you are compiling on the same architecture that will be used for
|
||||
the runs, adding the flag <I>-xHost</I> to CCFLAGS will enable
|
||||
@ -102,10 +125,10 @@ vectorization with the Intel(R) compiler.
|
||||
coprocessor, the flag <I>-offload</I> should be added to the LINKFLAGS line
|
||||
and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.
|
||||
</P>
|
||||
<P>Note that the machine makefiles Makefile.intel and
|
||||
Makefile.intel_offload are included in the src/MAKE directory with
|
||||
options that perform well with the Intel(R) compiler. The latter file
|
||||
has support for offload to coprocessors; the former does not.
|
||||
<P>Example makefiles Makefile.intel_cpu and Makefile.intel_phi are
|
||||
included in the src/MAKE/OPTIONS directory with settings that perform
|
||||
well with the Intel(R) compiler. The latter file has support for
|
||||
offload to coprocessors; the former does not.
|
||||
</P>
|
||||
<P>If using an Intel compiler, it is recommended that Intel(R) Compiler
|
||||
2013 SP1 update 1 be used. Newer versions have some performance
|
||||
|
||||
@ -38,6 +38,10 @@ suffix to "omp" so that styles from the USER-OMP package will be used
|
||||
if available, after first testing if a style from the USER-INTEL
|
||||
package is available.
|
||||
|
||||
When using the USER-INTEL package, you must choose at build time
|
||||
whether you are building for CPU-only acceleration or for using the
|
||||
Xeon Phi in offload mode.
|
||||
|
||||
Here is a quick overview of how to use the USER-INTEL package
|
||||
for CPU-only acceleration:
|
||||
|
||||
@ -47,6 +51,9 @@ include the USER-INTEL package and (optionally) USER-OMP package and build LAMMP
|
||||
specify how many OpenMP threads per MPI task to use
|
||||
use USER-INTEL and (optionally) USER-OMP styles in your input script :ul
|
||||
|
||||
Note that many of these settings can only be used with the Intel
|
||||
compiler, as discussed below.
|
||||
|
||||
Using the USER-INTEL package to offload work to the Intel(R)
|
||||
Xeon Phi(TM) coprocessor is the same except for these additional
|
||||
steps:
|
||||
@ -71,25 +78,41 @@ Optimizations for vectorization have only been tested with the
|
||||
Intel(R) compiler. Use of other compilers may not result in
|
||||
vectorization or give poor performance.
|
||||
|
||||
Use of an Intel C++ compiler is reccommended, but not required. The
|
||||
compiler must support the OpenMP interface.
|
||||
Use of an Intel C++ compiler is recommended, but not required (though
|
||||
g++ will not recognize some of the settings, so they cannot be used).
|
||||
The compiler must support the OpenMP interface.
|
||||
|
||||
[Building LAMMPS with the USER-INTEL package:]
|
||||
|
||||
Include the package(s) and build LAMMPS:
|
||||
You must choose at build time whether to build for CPU acceleration or
|
||||
to use the Xeon Phi in offload mode.
|
||||
|
||||
You can do either in one line, using the src/Make.py script, described
|
||||
in "Section 2.4"_Section_start.html#start_4 of the manual. Type
|
||||
"Make.py -h" for help. If run from the src directory, these commands
|
||||
will create src/lmp_intel_cpu and lmp_intel_phi using
|
||||
src/MAKE/Makefile.mpi as the starting Makefile.machine:
|
||||
|
||||
Make.py -p intel omp -intel cpu -o intel_cpu -cc icc file mpi
|
||||
Make.py -p intel omp -intel phi -o intel_phi -cc icc file mpi :pre
|
||||
|
||||
Note that this assumes that your MPI and its mpicxx wrapper
|
||||
is using the Intel compiler. If it is not, you should
|
||||
leave off the "-cc icc" switch.
|
||||
|
||||
Or you can follow these steps:
|
||||
|
||||
cd lammps/src
|
||||
make yes-user-intel
|
||||
make yes-user-omp (if desired)
|
||||
make machine :pre
|
||||
|
||||
If the USER-OMP package is also installed, you can use styles from
|
||||
both packages, as described below.
|
||||
Note that if the USER-OMP package is also installed, you can use
|
||||
styles from both packages, as described below.
|
||||
|
||||
The lo-level src/MAKE/Makefile.machine needs a flag for OpenMP support
|
||||
in both the CCFLAGS and LINKFLAGS variables, which is {-openmp} for
|
||||
Intel compilers. You also need to add -DLAMMPS_MEMALIGN=64 and
|
||||
-restrict to CCFLAGS.
|
||||
The Makefile.machine needs a "-fopenmp" flag for OpenMP support in
|
||||
both the CCFLAGS and LINKFLAGS variables. You also need to add
|
||||
-DLAMMPS_MEMALIGN=64 and -restrict to CCFLAGS.
|
||||
|
||||
If you are compiling on the same architecture that will be used for
|
||||
the runs, adding the flag {-xHost} to CCFLAGS will enable
|
||||
@ -99,10 +122,10 @@ In order to build with support for an Intel(R) Xeon Phi(TM)
|
||||
coprocessor, the flag {-offload} should be added to the LINKFLAGS line
|
||||
and the flag -DLMP_INTEL_OFFLOAD should be added to the CCFLAGS line.
|
||||
|
||||
Note that the machine makefiles Makefile.intel and
|
||||
Makefile.intel_offload are included in the src/MAKE directory with
|
||||
options that perform well with the Intel(R) compiler. The latter file
|
||||
has support for offload to coprocessors; the former does not.
|
||||
Example makefiles Makefile.intel_cpu and Makefile.intel_phi are
|
||||
included in the src/MAKE/OPTIONS directory with settings that perform
|
||||
well with the Intel(R) compiler. The latter file has support for
|
||||
offload to coprocessors; the former does not.
|
||||
|
||||
If using an Intel compiler, it is recommended that Intel(R) Compiler
|
||||
2013 SP1 update 1 be used. Newer versions have some performance
|
||||
|
||||
@ -61,14 +61,17 @@ one or the other of the two modes. The first mode is called the
|
||||
processor (running in native mode, not offload mode like the
|
||||
USER-INTEL package) are supported. The second mode is called the
|
||||
"device" and is an accelerator chip of some kind. Currently only an
|
||||
NVIDIA GPU is supported. If your compute node does not have a GPU,
|
||||
then there is only one mode of execution, i.e. the host and device are
|
||||
the same.
|
||||
NVIDIA GPU is supported via Cuda. If your compute node does not have
|
||||
a GPU, then there is only one mode of execution, i.e. the host and
|
||||
device are the same.
|
||||
</P>
|
||||
<P>Here is a quick overview of how to use the KOKKOS package
|
||||
for GPU acceleration:
|
||||
<P>When using the KOKKOS package, you must choose at build time whether
|
||||
you are building for OpenMP, GPU, or for using the Xeon Phi in native
|
||||
mode.
|
||||
</P>
|
||||
<UL><LI>specify variables and settings in your Makefile.machine that enable GPU, Phi, or OpenMP support
|
||||
<P>Here is a quick overview of how to use the KOKKOS package:
|
||||
</P>
|
||||
<UL><LI>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
|
||||
<LI>include the KOKKOS package and build LAMMPS
|
||||
<LI>enable the KOKKOS package and its hardware options via the "-k on" command-line switch
|
||||
<LI>use KOKKOS styles in your input script
|
||||
@ -105,14 +108,23 @@ and GPU packages for details of how to check and do this.
|
||||
</P>
|
||||
<P><B>Building LAMMPS with the KOKKOS package:</B>
|
||||
</P>
|
||||
<P>Unlike other acceleration packages discussed in this section, the
|
||||
Kokkos library in lib/kokkos does not have to be pre-built before
|
||||
building LAMMPS itself. Instead, options for the Kokkos library are
|
||||
specified at compile time, when LAMMPS itself is built. This can be
|
||||
done in one of two ways, as discussed below.
|
||||
<P>You must choose at build time whether to build for OpenMP, Cuda, or
|
||||
Phi.
|
||||
</P>
|
||||
<P>Here are examples of how to build LAMMPS for the different compute-node
|
||||
configurations listed above.
|
||||
<P>You can do any of these in one line, using the src/Make.py script,
|
||||
described in <A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual.
|
||||
Type "Make.py -h" for help. If run from the src directory, these
|
||||
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
|
||||
lmp_kokkos_phi. The OMP and PHI options use src/MAKE/Makefile.mpi as
|
||||
the starting Makefile.machine. The CUDA option uses
|
||||
src/MAKE/OPTIONS/Makefile.cuda since the NVIDIA nvcc compiler is
|
||||
required.
|
||||
</P>
|
||||
<P>Make.py -p kokkos -kokkos omp -o kokkos_omp file mpi
|
||||
Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda file kokkos_cuda
|
||||
Make.py -p kokkos -kokkos phi -o kokkos_phi file mpi
|
||||
</P>
|
||||
<P>Or you can follow these steps:
|
||||
</P>
|
||||
<P>CPU-only (run all-MPI or with OpenMP threading):
|
||||
</P>
|
||||
@ -164,15 +176,76 @@ in <A HREF = "Section_start.html#start_3_4">Section 2.3.4</A> of the manual, as
|
||||
as other settings that must be included in the machine makefile, if
|
||||
you create your own.
|
||||
</P>
|
||||
<P>There are other allowed options when building with the KOKKOS package.
|
||||
As above, They can be set either as variables on the make command line
|
||||
or in the machine makefile in the src/MAKE directory. See <A HREF = "Section_start.html#start_3_4">Section
|
||||
2.3.4</A> of the manual for details.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Currently, there are no precision options with the
|
||||
KOKKOS package. All compilation and computation is performed in
|
||||
double precision.
|
||||
</P>
|
||||
<P>There are other allowed options when building with the KOKKOS package.
|
||||
As above, they can be set either as variables on the make command line
|
||||
or in Makefile.machine. This is the full list of options, including
|
||||
those discussed above, Each takes a value of <I>yes</I> or <I>no</I>. The
|
||||
default value is listed, which is set in the
|
||||
lib/kokkos/Makefile.lammps file.
|
||||
</P>
|
||||
<UL><LI>OMP, default = <I>yes</I>
|
||||
<LI>CUDA, default = <I>no</I>
|
||||
<LI>HWLOC, default = <I>no</I>
|
||||
<LI>AVX, default = <I>no</I>
|
||||
<LI>MIC, default = <I>no</I>
|
||||
<LI>LIBRT, default = <I>no</I>
|
||||
<LI>DEBUG, default = <I>no</I>
|
||||
</UL>
|
||||
<P>OMP sets the parallelization method used for Kokkos code (within
|
||||
LAMMPS) that runs on the host. OMP=yes means that OpenMP will be
|
||||
used. OMP=no means that pthreads will be used.
|
||||
</P>
|
||||
<P>CUDA sets the parallelization method used for Kokkos code (within
|
||||
LAMMPS) that runs on the device. CUDA=yes means an NVIDIA GPU running
|
||||
CUDA will be used. CUDA=no means that the OMP=yes or OMP=no setting
|
||||
will be used for the device as well as the host.
|
||||
</P>
|
||||
<P>If CUDA=yes, then the lo-level Makefile in the src/MAKE directory must
|
||||
use "nvcc" as its compiler, via its CC setting. For best performance
|
||||
its CCFLAGS setting should use -O3 and have an -arch setting that
|
||||
matches the compute capability of your NVIDIA hardware and software
|
||||
installation, e.g. -arch=sm_20. Generally Fermi Generation GPUs are
|
||||
sm_20, while Kepler generation GPUs are sm_30 or sm_35 and Maxwell
|
||||
cards are sm_50. A complete list can be found on
|
||||
<A HREF = "http://en.wikipedia.org/wiki/CUDA#Supported_GPUs">wikipedia</A>. You can
|
||||
also use the deviceQuery tool that comes with the CUDA samples. Note
|
||||
the minimal required compute capability is 2.0, but this will give
|
||||
signicantly reduced performance compared to Kepler generation GPUs
|
||||
with compute capability 3.x. For the LINK setting, "nvcc" should not
|
||||
be used; instead use g++ or another compiler suitable for linking C++
|
||||
applications. Often you will want to use your MPI compiler wrapper
|
||||
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
|
||||
also have a "Compilation rule" for creating *.o files from *.cu files.
|
||||
See src/Makefile.cuda for an example of a lo-level Makefile with all
|
||||
of these settings.
|
||||
</P>
|
||||
<P>HWLOC binds threads to hardware cores, so they do not migrate during a
|
||||
simulation. HWLOC=yes should always be used if running with OMP=no
|
||||
for pthreads. It is not necessary for OMP=yes for OpenMP, because
|
||||
OpenMP provides alternative methods via environment variables for
|
||||
binding threads to hardware cores. More info on binding threads to
|
||||
cores is given in <A HREF = "Section_accelerate.html#acc_8">this section</A>.
|
||||
</P>
|
||||
<P>AVX enables Intel advanced vector extensions when compiling for an
|
||||
Intel-compatible chip. AVX=yes should only be set if your host
|
||||
hardware supports AVX. If it does not support it, this will cause a
|
||||
run-time crash.
|
||||
</P>
|
||||
<P>MIC enables compiler switches needed when compling for an Intel Phi
|
||||
processor.
|
||||
</P>
|
||||
<P>LIBRT enables use of a more accurate timer mechanism on most Unix
|
||||
platforms. This library is not available on all platforms.
|
||||
</P>
|
||||
<P>DEBUG is only useful when developing a Kokkos-enabled style within
|
||||
LAMMPS. DEBUG=yes enables printing of run-time debugging information
|
||||
that can be useful. It also enables runtime bounds checking on Kokkos
|
||||
data structures.
|
||||
</P>
|
||||
<P><B>Run with the KOKKOS package from the command line:</B>
|
||||
</P>
|
||||
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
|
||||
|
||||
@ -58,14 +58,17 @@ one or the other of the two modes. The first mode is called the
|
||||
processor (running in native mode, not offload mode like the
|
||||
USER-INTEL package) are supported. The second mode is called the
|
||||
"device" and is an accelerator chip of some kind. Currently only an
|
||||
NVIDIA GPU is supported. If your compute node does not have a GPU,
|
||||
then there is only one mode of execution, i.e. the host and device are
|
||||
the same.
|
||||
NVIDIA GPU is supported via Cuda. If your compute node does not have
|
||||
a GPU, then there is only one mode of execution, i.e. the host and
|
||||
device are the same.
|
||||
|
||||
Here is a quick overview of how to use the KOKKOS package
|
||||
for GPU acceleration:
|
||||
When using the KOKKOS package, you must choose at build time whether
|
||||
you are building for OpenMP, GPU, or for using the Xeon Phi in native
|
||||
mode.
|
||||
|
||||
specify variables and settings in your Makefile.machine that enable GPU, Phi, or OpenMP support
|
||||
Here is a quick overview of how to use the KOKKOS package:
|
||||
|
||||
specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support
|
||||
include the KOKKOS package and build LAMMPS
|
||||
enable the KOKKOS package and its hardware options via the "-k on" command-line switch
|
||||
use KOKKOS styles in your input script :ul
|
||||
@ -102,14 +105,23 @@ and GPU packages for details of how to check and do this.
|
||||
|
||||
[Building LAMMPS with the KOKKOS package:]
|
||||
|
||||
Unlike other acceleration packages discussed in this section, the
|
||||
Kokkos library in lib/kokkos does not have to be pre-built before
|
||||
building LAMMPS itself. Instead, options for the Kokkos library are
|
||||
specified at compile time, when LAMMPS itself is built. This can be
|
||||
done in one of two ways, as discussed below.
|
||||
You must choose at build time whether to build for OpenMP, Cuda, or
|
||||
Phi.
|
||||
|
||||
Here are examples of how to build LAMMPS for the different compute-node
|
||||
configurations listed above.
|
||||
You can do any of these in one line, using the src/Make.py script,
|
||||
described in "Section 2.4"_Section_start.html#start_4 of the manual.
|
||||
Type "Make.py -h" for help. If run from the src directory, these
|
||||
commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
|
||||
lmp_kokkos_phi. The OMP and PHI options use src/MAKE/Makefile.mpi as
|
||||
the starting Makefile.machine. The CUDA option uses
|
||||
src/MAKE/OPTIONS/Makefile.cuda since the NVIDIA nvcc compiler is
|
||||
required.
|
||||
|
||||
Make.py -p kokkos -kokkos omp -o kokkos_omp file mpi
|
||||
Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda file kokkos_cuda
|
||||
Make.py -p kokkos -kokkos phi -o kokkos_phi file mpi
|
||||
|
||||
Or you can follow these steps:
|
||||
|
||||
CPU-only (run all-MPI or with OpenMP threading):
|
||||
|
||||
@ -161,15 +173,76 @@ in "Section 2.3.4"_Section_start.html#start_3_4 of the manual, as well
|
||||
as other settings that must be included in the machine makefile, if
|
||||
you create your own.
|
||||
|
||||
There are other allowed options when building with the KOKKOS package.
|
||||
As above, They can be set either as variables on the make command line
|
||||
or in the machine makefile in the src/MAKE directory. See "Section
|
||||
2.3.4"_Section_start.html#start_3_4 of the manual for details.
|
||||
|
||||
IMPORTANT NOTE: Currently, there are no precision options with the
|
||||
KOKKOS package. All compilation and computation is performed in
|
||||
double precision.
|
||||
|
||||
There are other allowed options when building with the KOKKOS package.
|
||||
As above, they can be set either as variables on the make command line
|
||||
or in Makefile.machine. This is the full list of options, including
|
||||
those discussed above, Each takes a value of {yes} or {no}. The
|
||||
default value is listed, which is set in the
|
||||
lib/kokkos/Makefile.lammps file.
|
||||
|
||||
OMP, default = {yes}
|
||||
CUDA, default = {no}
|
||||
HWLOC, default = {no}
|
||||
AVX, default = {no}
|
||||
MIC, default = {no}
|
||||
LIBRT, default = {no}
|
||||
DEBUG, default = {no} :ul
|
||||
|
||||
OMP sets the parallelization method used for Kokkos code (within
|
||||
LAMMPS) that runs on the host. OMP=yes means that OpenMP will be
|
||||
used. OMP=no means that pthreads will be used.
|
||||
|
||||
CUDA sets the parallelization method used for Kokkos code (within
|
||||
LAMMPS) that runs on the device. CUDA=yes means an NVIDIA GPU running
|
||||
CUDA will be used. CUDA=no means that the OMP=yes or OMP=no setting
|
||||
will be used for the device as well as the host.
|
||||
|
||||
If CUDA=yes, then the lo-level Makefile in the src/MAKE directory must
|
||||
use "nvcc" as its compiler, via its CC setting. For best performance
|
||||
its CCFLAGS setting should use -O3 and have an -arch setting that
|
||||
matches the compute capability of your NVIDIA hardware and software
|
||||
installation, e.g. -arch=sm_20. Generally Fermi Generation GPUs are
|
||||
sm_20, while Kepler generation GPUs are sm_30 or sm_35 and Maxwell
|
||||
cards are sm_50. A complete list can be found on
|
||||
"wikipedia"_http://en.wikipedia.org/wiki/CUDA#Supported_GPUs. You can
|
||||
also use the deviceQuery tool that comes with the CUDA samples. Note
|
||||
the minimal required compute capability is 2.0, but this will give
|
||||
signicantly reduced performance compared to Kepler generation GPUs
|
||||
with compute capability 3.x. For the LINK setting, "nvcc" should not
|
||||
be used; instead use g++ or another compiler suitable for linking C++
|
||||
applications. Often you will want to use your MPI compiler wrapper
|
||||
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
|
||||
also have a "Compilation rule" for creating *.o files from *.cu files.
|
||||
See src/Makefile.cuda for an example of a lo-level Makefile with all
|
||||
of these settings.
|
||||
|
||||
HWLOC binds threads to hardware cores, so they do not migrate during a
|
||||
simulation. HWLOC=yes should always be used if running with OMP=no
|
||||
for pthreads. It is not necessary for OMP=yes for OpenMP, because
|
||||
OpenMP provides alternative methods via environment variables for
|
||||
binding threads to hardware cores. More info on binding threads to
|
||||
cores is given in "this section"_Section_accelerate.html#acc_8.
|
||||
|
||||
AVX enables Intel advanced vector extensions when compiling for an
|
||||
Intel-compatible chip. AVX=yes should only be set if your host
|
||||
hardware supports AVX. If it does not support it, this will cause a
|
||||
run-time crash.
|
||||
|
||||
MIC enables compiler switches needed when compling for an Intel Phi
|
||||
processor.
|
||||
|
||||
LIBRT enables use of a more accurate timer mechanism on most Unix
|
||||
platforms. This library is not available on all platforms.
|
||||
|
||||
DEBUG is only useful when developing a Kokkos-enabled style within
|
||||
LAMMPS. DEBUG=yes enables printing of run-time debugging information
|
||||
that can be useful. It also enables runtime bounds checking on Kokkos
|
||||
data structures.
|
||||
|
||||
[Run with the KOKKOS package from the command line:]
|
||||
|
||||
The mpirun or mpiexec command sets the total number of MPI tasks used
|
||||
|
||||
@ -42,17 +42,27 @@ MPI task running on a CPU.
|
||||
</P>
|
||||
<P><B>Building LAMMPS with the USER-OMP package:</B>
|
||||
</P>
|
||||
<P>Include the package and build LAMMPS:
|
||||
<P>To do this in one line, use the src/Make.py script, described in
|
||||
<A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type "Make.py
|
||||
-h" for help. If run from the src directory, this command will create
|
||||
src/lmp_omp using src/MAKE/Makefile.mpi as the starting
|
||||
Makefile.machine:
|
||||
</P>
|
||||
<PRE>Make.py -p omp -o omp file mpi
|
||||
</PRE>
|
||||
<P>Or you can follow these steps:
|
||||
</P>
|
||||
<PRE>cd lammps/src
|
||||
make yes-user-omp
|
||||
make machine
|
||||
</PRE>
|
||||
<P>The CCFLAGS setting in your src/MAKE/Makefile.machine needs "-fopenmp"
|
||||
to add OpenMP support. This works for both the GNU and Intel
|
||||
compilers. Without this flag the USER-OMP styles will still be
|
||||
compiled and work, but will not support multi-threading. For the
|
||||
Intel compilers the CCFLAGS setting also needs to include "-restrict".
|
||||
<P>The CCFLAGS setting in Makefile.machine needs "-fopenmp" to add OpenMP
|
||||
support. This works for both the GNU and Intel compilers. Without
|
||||
this flag the USER-OMP styles will still be compiled and work, but
|
||||
will not support multi-threading. For the Intel compilers the CCFLAGS
|
||||
setting also needs to include "-restrict".
|
||||
</P>
|
||||
<P><B>Run with the USER-OMP package from the command line:</B>
|
||||
</P>
|
||||
<P>The mpirun or mpiexec command sets the total number of MPI tasks used
|
||||
by LAMMPS (one or multiple per compute node) and the number of MPI
|
||||
|
||||
@ -39,17 +39,27 @@ MPI task running on a CPU.
|
||||
|
||||
[Building LAMMPS with the USER-OMP package:]
|
||||
|
||||
Include the package and build LAMMPS:
|
||||
To do this in one line, use the src/Make.py script, described in
|
||||
"Section 2.4"_Section_start.html#start_4 of the manual. Type "Make.py
|
||||
-h" for help. If run from the src directory, this command will create
|
||||
src/lmp_omp using src/MAKE/Makefile.mpi as the starting
|
||||
Makefile.machine:
|
||||
|
||||
Make.py -p omp -o omp file mpi :pre
|
||||
|
||||
Or you can follow these steps:
|
||||
|
||||
cd lammps/src
|
||||
make yes-user-omp
|
||||
make machine :pre
|
||||
|
||||
The CCFLAGS setting in your src/MAKE/Makefile.machine needs "-fopenmp"
|
||||
to add OpenMP support. This works for both the GNU and Intel
|
||||
compilers. Without this flag the USER-OMP styles will still be
|
||||
compiled and work, but will not support multi-threading. For the
|
||||
Intel compilers the CCFLAGS setting also needs to include "-restrict".
|
||||
The CCFLAGS setting in Makefile.machine needs "-fopenmp" to add OpenMP
|
||||
support. This works for both the GNU and Intel compilers. Without
|
||||
this flag the USER-OMP styles will still be compiled and work, but
|
||||
will not support multi-threading. For the Intel compilers the CCFLAGS
|
||||
setting also needs to include "-restrict".
|
||||
|
||||
[Run with the USER-OMP package from the command line:]
|
||||
|
||||
The mpirun or mpiexec command sets the total number of MPI tasks used
|
||||
by LAMMPS (one or multiple per compute node) and the number of MPI
|
||||
|
||||
@ -38,12 +38,22 @@ input script.
|
||||
</P>
|
||||
<P>Include the package and build LAMMPS:
|
||||
</P>
|
||||
<P>To do this in one line, use the src/Make.py script, described in
|
||||
<A HREF = "Section_start.html#start_4">Section 2.4</A> of the manual. Type "Make.py
|
||||
-h" for help. If run from the src directory, this command will create
|
||||
src/lmp_opt using src/MAKE/Makefile.mpi as the starting
|
||||
Makefile.machine:
|
||||
</P>
|
||||
<PRE>Make.py -p opt -o opt file mpi
|
||||
</PRE>
|
||||
<P>Or you can follow these steps:
|
||||
</P>
|
||||
<PRE>cd lammps/src
|
||||
make yes-opt
|
||||
make machine
|
||||
</PRE>
|
||||
<P>If you are using Intel compilers, then the CCFLAGS setting in your
|
||||
src/MAKE/Makefile.machine needs to include "-restrict".
|
||||
<P>If you are using Intel compilers, then the CCFLAGS setting in
|
||||
Makefile.machine needs to include "-restrict".
|
||||
</P>
|
||||
<P><B>Run with the OPT package from the command line:</B>
|
||||
</P>
|
||||
|
||||
@ -35,12 +35,22 @@ None.
|
||||
|
||||
Include the package and build LAMMPS:
|
||||
|
||||
To do this in one line, use the src/Make.py script, described in
|
||||
"Section 2.4"_Section_start.html#start_4 of the manual. Type "Make.py
|
||||
-h" for help. If run from the src directory, this command will create
|
||||
src/lmp_opt using src/MAKE/Makefile.mpi as the starting
|
||||
Makefile.machine:
|
||||
|
||||
Make.py -p opt -o opt file mpi :pre
|
||||
|
||||
Or you can follow these steps:
|
||||
|
||||
cd lammps/src
|
||||
make yes-opt
|
||||
make machine :pre
|
||||
|
||||
If you are using Intel compilers, then the CCFLAGS setting in your
|
||||
src/MAKE/Makefile.machine needs to include "-restrict".
|
||||
If you are using Intel compilers, then the CCFLAGS setting in
|
||||
Makefile.machine needs to include "-restrict".
|
||||
|
||||
[Run with the OPT package from the command line:]
|
||||
|
||||
|
||||
Reference in New Issue
Block a user