PLUMED/2.9.2-cpeGNU-24.03-cray-python-3.11.7 (PLUMED-2.9.2-cpeGNU-24.03-cray-python-3.11.7.eb)
Install with the EasyBuild-user module:
To access module help after installation and get reminded for which stacks and partitions the module is installed, usemodule spider PLUMED/2.9.2-cpeGNU-24.03-cray-python-3.11.7.
EasyConfig:
# by Ward Poelmans <wpoely86@gmail.com>
# Modified by Luca Marsella (CSCS)
# Adapted by Kurt Lust (kurt.lust@uantwerpen.be) for the LUMI consortium
#
# Instructions to run regression tests at the bottom of this file.
#
#DOC PLUMED with the Python plugin. Only in cpeGNU as Cray Python is compiled
#DOC with the GNU compilers and not compatible with libraries compiled with
#DOC other compilers that use or link to libraries with OpenMP support.
easyblock = 'ConfigureMake'
local_crayfftw_version = '3.3.10.1'
local_craypython_version = '3.11.7'
local_Boost_version = '1.83.0' # https://www.boost.org/
local_GSL_version = '2.7.1' # https://ftp.gnu.org/gnu/gsl/
local_zlib_version = '1.3.1' # https://zlib.net/
local_PLUMED2_9_version = '2.9.2' # https://github.com/plumed/plumed2/releases
name = 'PLUMED'
version = local_PLUMED2_9_version
versionsuffix = f'-cray-python-{local_craypython_version}'
homepage = 'https://www.plumed.org'
whatis = [
'Description: PLUMED - PLUgin for MolEcular Dynamics'
]
description = """
PLUMED is an open source library for free energy calculations in molecular
systems which works together with some of the most popular molecular dynamics
engines.
Free energy calculations can be performed as a function of many order parameters
with a particular focus on biological problems, using state of the art methods
such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
The software, written in C++, can be easily interfaced with both fortran and
C/C++ codes.
NOTES:
* This module does not include the optional VMD plugins.
* This module does not include support for XDR
* The module provides the bash function plumed-completion to enable command
line completion. Note that unloading the module will not disable command
completion again.
This module is compiled with support for huge pages via the cray-hugepages modules.
Using those can significantly lower the cost of memory access. However, to benefit
from this you will have to load a suitable cray-hugepages module, e.g.,
$ module load cray-hugepages8M
However, if the size is too large, you may get out-of-memory messages due to memory
fragmentation. Hence it may require some experimenting to find the optimal page
size.
"""
toolchain = {'name': 'cpeGNU', 'version': '24.03'}
toolchainopts = {'usempi': 'True', 'openmp': True, 'strict': True}
# https://github.com/plumed/plumed2/releases/download/v2.9.2/plumed-2.9.2.tgz
source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
sources = [SOURCE_TGZ]
checksums = ['6fc23fe31074ad6b7a0eb9e2441fce5b3d92514d0d87206594c59c75e4c83d6e']
builddependencies = [
('buildtools', '%(toolchain_version)s', '', True), # For CMake and xxd
('craype-hugepages8M', EXTERNAL_MODULE),
('craype-accel-host', EXTERNAL_MODULE), # Avoid enabling OpenMP offload
]
dependencies = [
(f'cray-python/{local_craypython_version}', EXTERNAL_MODULE),
(f'cray-fftw/{local_crayfftw_version}', EXTERNAL_MODULE),
('Boost', local_Boost_version),
('zlib', local_zlib_version),
('GSL', local_GSL_version, '-OpenMP'),
]
preconfigopts = f'unset PYTHONPATH && module load cray-python/{local_craypython_version} && '
prebuildopts = f'unset PYTHONPATH && module load cray-python/{local_craypython_version} && '
preinstallopts = f'unset PYTHONPATH && module load cray-python/{local_craypython_version} && '
preconfigopts += 'module unload rocm && '
prebuildopts += 'module unload rocm && '
preinstallopts += 'module unload rocm && '
# This is a trick to avoid multiple LibSci linking problem
preconfigopts += 'export LDSHARED="CC -fopenmp -shared" && '
configopts = ' '.join([
'--enable-modules=all',
'--exec-prefix=%(installdir)s',
'--enable-boost_graph',
'--enable-boost_serialization',
'--enable-mpi',
'--enable-fftw',
'--enable-gsl',
'--enable-python',
'--enable-asmjit',
# Disable features that we do not have, avoids warnings
'--disable-xdrfile',
])
postinstallcmds = [
# Uncomment the next two lines if you want to install the regression tests with PLUMED,
# but see the bottom of this file for a better approach
#'sed -e "s|-mpirun|-srun|" -e "s| -np | -n |" -i regtest/scripts/run',
#'cp -r regtest %(installdir)s',
'mkdir -p %(installdir)s/share/licenses/%(name)s && cp COPYING.LESSER PEOPLE README.md %(installdir)s/share/licenses/%(name)s',
]
sanity_check_paths = {
'files': ['bin/%(namelower)s', 'lib/libplumedKernel.so', 'lib/libplumed.so',
'share/licenses/%(name)s/COPYING.LESSER'],
'dirs': ['lib/%(namelower)s'],
}
# Check if the requested features are indeed enabled. It turns out the the return code
# of plumed config has can actually be used for that easily. And it would also catch
# the crashes that we had when compiling with Cray BLAS.
sanity_check_commands = [
'plumed --no-mpi config has mpi',
'plumed --no-mpi config has fftw',
'plumed --no-mpi config has zlib',
'plumed --no-mpi config has gsl',
'plumed --no-mpi config has boost_graph',
'plumed --no-mpi config has boost_serialization',
'plumed --no-mpi config has asmjit',
# Tests that should be removed for a -noPython build.
'python -c "import plumed"',
'python -c "import plumed; plumed.Plumed()"', # Test still fails so something seems to be wrong.
]
modextravars = {
'PLUMED_KERNEL': '%(installdir)s/lib/libplumedKernel.so',
'PLUMED_ROOT': '%(installdir)s/lib/%(namelower)s',
'PLUMED_VIM': '%(installdir)s/lib/%(namelower)s/vim',
}
modextrapaths = {
'PYTHONPATH': 'lib/%(namelower)s/python',
}
local_bash_completion = """
[==[
_plumed() { eval "$(plumed --no-mpi completion 2>/dev/null)";} ;
complete -F _plumed -o default plumed
]==]
"""
local_csh_completion = '"echo \'Not implemented\'"'
modluafooter = """
set_shell_function( 'plumed-completion', %(bash_completion)s, %(csh_completion)s )
""" % {
'bash_completion': local_bash_completion,
'csh_completion': local_csh_completion,
}
moduleclass = 'chem'
# --------------------
# RUN REGRESSION TESTS
# --------------------
#
# tar xf $EBU_USER_PREFIX/sources/p/PLUMED/PLUMED-2.9.2.tgz
# cd plumed-2.9.2/regtest/
# sed -i 's/$mpi -np/$mpi -n/' scripts/run
# salloc -n6 -c4 -psmall -t30:00 -A <project>
# module load PLUMED/2.9.2-cpeGNU-24.03-cray-python-3.11.7
# export PLUMED_MPIRUN=srun
# make
# exit