Merge branch 'master' into kim-v2-update
This commit is contained in:
Ryan S. Elliott
@ -45,6 +45,7 @@ This is the list of packages that may require additional steps.
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"USER-INTEL"_#user-intel,
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"USER-MOLFILE"_#user-molfile,
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"USER-NETCDF"_#user-netcdf,
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"USER-PLUMED"_#user-plumed,
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"USER-OMP"_#user-omp,
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"USER-QMMM"_#user-qmmm,
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"USER-QUIP"_#user-quip,
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@ -86,22 +87,30 @@ which GPU hardware to build for.
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# value = double or mixed (default) or single
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-D OCL_TUNE=value # hardware choice for GPU_API=opencl
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# generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
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-D GPU_ARCH=value # hardware choice for GPU_API=cuda
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-D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda
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# value = sm_XX, see below
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# default is Cuda-compiler dependent, but typically sm_20
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-D CUDPP_OPT=value # optimization setting for GPU_API=cudea
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-D CUDPP_OPT=value # optimization setting for GPU_API=cuda
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# enables CUDA Performance Primitives Optimizations
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# yes (default) or no :pre
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GPU_ARCH settings for different GPU hardware is as follows:
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sm_20 for Fermi (C2050/C2070, deprecated as of CUDA 8.0) or GeForce GTX 580 or similar
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sm_30 for Kepler (K10)
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sm_35 for Kepler (K40) or GeForce GTX Titan or similar
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sm_37 for Kepler (dual K80)
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sm_50 for Maxwell
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sm_60 for Pascal (P100)
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sm_70 for Volta :ul
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sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
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sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5)
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sm_50 or sm_52 for Maxwell (supported since CUDA 6)
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sm_60 or sm_61 for Pascal (supported since CUDA 8)
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sm_70 for Volta (supported since CUDA 9)
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sm_75 for Turing (supported since CUDA 10) :ul
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A more detailed list can be found, for example,
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at "Wikipedia's CUDA article"_https://en.wikipedia.org/wiki/CUDA#GPUs_supported
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CMake can detect which version of the CUDA toolkit is used and thus can
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include support for [all] major GPU architectures supported by this toolkit.
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Thus the GPU_ARCH setting is merely an optimization, to have code for
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the preferred GPU architecture directly included rather than having to wait
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for the JIT compiler of the CUDA driver to translate it.
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[Traditional make]:
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@ -136,6 +145,11 @@ CUDA_ARCH = sm_XX, what GPU hardware you have, same as CMake GPU_ARCH above
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CUDA_PRECISION = precision (double, mixed, single)
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EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul
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The file Makefile.linux_multi is set up to include support for multiple
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GPU architectures as supported by the CUDA toolkit in use. This is done
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through using the "--gencode " flag, which can be used multiple times and
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thus support all GPU architectures supported by your CUDA compiler.
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If the library build is successful, 3 files should be created:
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lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and
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lib/gpu/Makefile.lammps. The latter has settings that enable LAMMPS
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@ -149,6 +163,7 @@ re-build LAMMPS. This is because the compilation of files in the GPU
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package uses the library settings from the lib/gpu/Makefile.machine
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used to build the GPU library.
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:line
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KIM package :h4,link(kim)
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@ -176,7 +191,7 @@ package?" page.
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[CMake build]:
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-D DOWNLOAD_KIM=value # download OpenKIM API v1 for build, value = no (default) or yes :pre
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-D DOWNLOAD_KIM=value # download OpenKIM API v2 for build, value = no (default) or yes :pre
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If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
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inside the CMake build directory. If the KIM library is already on
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@ -602,8 +617,8 @@ The USER-ATC package requires the MANYBODY package also be installed.
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[CMake build]:
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No additional settings are needed besides "-D PKG_REAX=yes" and "-D
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PKG_MANYBODY=yes".
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No additional settings are needed besides "-D PKG_USER-ATC=yes"
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and "-D PKG_MANYBODY=yes".
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[Traditional make]:
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@ -708,6 +723,114 @@ a corresponding Makefile.lammps.machine file.
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:line
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USER-PLUMED package :h4,link(user-plumed)
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Before building LAMMPS with this package, you must first build PLUMED.
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PLUMED can be built as part of the LAMMPS build or installed separately
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from LAMMPS using the generic "plumed installation instructions"_plumedinstall.
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:link(plumedinstall,http://plumed.github.io/doc-master/user-doc/html/_installation.html)
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PLUMED can be linked into MD codes in three different modes: static,
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shared, and runtime. With the "static" mode, all the code that PLUMED
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requires is linked statically into LAMMPS. LAMMPS is then fully
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independent from the PLUMED installation, but you have to rebuild/relink
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it in order to update the PLUMED code inside it. With the "shared"
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linkage mode, LAMMPS is linked to a shared library that contains the
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PLUMED code. This library should preferably be installed in a globally
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accessible location. When PLUMED is linked in this way the same library
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can be used by multiple MD packages. Furthermore, the PLUMED library
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LAMMPS uses can be updated without the need for a recompile of LAMMPS
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for as long as the shared PLUMED library is ABI-compatible.
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The third linkage mode is "runtime" which allows the user to specify
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which PLUMED kernel should be used at runtime by using the PLUMED_KERNEL
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environment variable. This variable should point to the location of the
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libplumedKernel.so dynamical shared object, which is then loaded at
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runtime. This mode of linking is particularly convenient for doing
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PLUMED development and comparing multiple PLUMED versions as these sorts
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of comparisons can be done without recompiling the hosting MD code. All
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three linkage modes are supported by LAMMPS on selected operating
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systems (e.g. Linux) and using either CMake or traditional make
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build. The "static" mode should be the most portable, while the
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"runtime" mode support in LAMMPS makes the most assumptions about
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operating system and compiler environment. If one mode does not work,
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try a different one, switch to a different build system, consider a
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global PLUMED installation or consider downloading PLUMED during the
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LAMMPS build.
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[CMake build]:
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When the "-D PKG_USER-PLUMED" flag is included in the cmake command you
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must ensure that GSL is installed in locations that are specified in
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your environment. There are then two additional commands that control
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the manner in which PLUMED is obtained and linked into LAMMPS.
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-D DOWNLOAD_PLUMED=value # download PLUMED for build, value = no (default) or yes
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-D PLUMED_MODE=value # Linkage mode for PLUMED, value = static (default), shared, or runtime :pre
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If DOWNLOAD_PLUMED is set to "yes", the PLUMED library will be
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downloaded (the version of PLUMED that will be downloaded is hard-coded
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to a vetted version of PLUMED, usually a recent stable release version)
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and built inside the CMake build directory. If DOWNLOAD_PLUMED is set
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to "no" (the default), CMake will try to detect and link to an installed
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version of PLUMED. For this to work, the PLUMED library has to be
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installed into a location where the pkg-config tool can find it or the
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PKG_CONFIG_PATH environment variable has to be set up accordingly.
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PLUMED should be installed in such a location if you compile it using
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the default make; make install commands.
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The PLUMED_MODE setting determines the linkage mode for the PLUMED
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library. The allowed values for this flag are "static" (default),
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"shared", or "runtime". For a discussion of PLUMED linkage modes,
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please see above. When DOWNLOAD_PLUMED is enabled the static linkage
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mode is recommended.
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[Traditional make]:
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PLUMED needs to be installed before the USER-PLUMED package is installed
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so that LAMMPS can find the right settings when compiling and linking
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the LAMMPS executable. You can either download and build PLUMED inside
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the LAMMPS plumed library folder or use a previously installed PLUMED
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library and point LAMMPS to its location. You also have to choose the
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linkage mode: "static" (default), "shared" or "runtime". For a
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discussion of PLUMED linkage modes, please see above.
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Download/compilation/configuration of the plumed library can be done
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from the src folder through the following make args:
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make lib-plumed # print help message
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make lib-plumed args="-b" # download and build PLUMED in lib/plumed/plumed2
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make lib-plumed args="-p $HOME/.local" # use existing PLUMED installation in $HOME/.local
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make lib-plumed args="-p /usr/local -m shared" # use existing PLUMED installation in
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# /usr/local and use shared linkage mode
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:pre
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Note that 2 symbolic (soft) links, "includelink" and "liblink" are
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created in lib/plumed that point to the location of the PLUMED build to
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use. A new file lib/plumed/Makefile.lammps is also created with settings
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suitable for LAMMPS to compile and link PLUMED using the desired linkage
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mode. After this step is completed, you can install the USER-PLUMED
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package and compile LAMMPS in the usual manner:
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make yes-user-plumed
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make machine :pre
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Once this compilation completes you should be able to run LAMMPS in the
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usual way. For shared linkage mode, libplumed.so must be found by the
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LAMMPS executable, which on many operating systems means, you have to
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set the LD_LIBRARY_PATH environment variable accordingly.
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Support for the different linkage modes in LAMMPS varies for different
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operating systems, using the static linkage is expected to be the most
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portable, and thus set to be the default.
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If you want to change the linkage mode, you have to re-run "make
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lib-plumed" with the desired settings [and] do a re-install if the
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USER-PLUMED package with "make yes-user-plumed" to update the required
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makefile settings with the changes in the lib/plumed folder.
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:line
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USER-H5MD package :h4,link(user-h5md)
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To build with this package you must have the HDF5 software package
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