new file: g/GROMACS/GROMACS-2021-fosscuda-2020b-PLUMED-2.7.2.eb

new file: g/GROMACS/GROMACS-2021-intel-2020b-PLUMED-2.7.2.eb new file: g/GROMACS/GROMACS-4.5.5-intel-2020b.eb new file: p/PLUMED/PLUMED-2.7.2-foss-2020b.eb new file: p/PLUMED/PLUMED-2.7.2-fosscuda-2020b.eb new file: p/Python/Python-3.8.6-GCC-10.2.0-CUDA-11.4.1-NetKet.eb
2025-04-12 09:52:12 +01:00 · 2021-11-24 10:39:39 +01:00 · 2021-11-24 10:39:39 +01:00 · e55388650f
commit e55388650f
parent f8afb4d5c6
6 changed files with 343 additions and 0 deletions
--- a/g/GROMACS/GROMACS-2021-fosscuda-2020b-PLUMED-2.7.2.eb
+++ b/g/GROMACS/GROMACS-2021-fosscuda-2020b-PLUMED-2.7.2.eb
@ -0,0 +1,78 @@
+# IT4Innovations
+# LK 2021
+
+name = 'GROMACS'
+version = '2021'
+local_plum_ver = '2.7.2'
+versionsuffix = '-PLUMED-%s' % local_plum_ver
+
+homepage = 'https://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
+Newtonian equations of motion for systems with hundreds to millions of
+particles.
+
+This is a GPU enabled build, containing both MPI and threadMPI builds.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = ['gromacs-%(version)s-plumed.tar.gz']
+patches = [
+    'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch',
+    'GROMACS-2019_increase_test_timeout_for_GPU.patch',
+    'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch',
+    'GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch',
+]
+checksums = [
+    '775fee053e128699b4ec5be659d6cbb7',  # gromacs-2021-plumed.tar.gz
+    # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch
+    '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275',
+    # GROMACS-2019_increase_test_timeout_for_GPU.patch
+    '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234',
+    # GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch
+    'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49',
+    # GROMACS-2020.5_fix_threads_gpu_Gmxapitests.patch
+    '89fbb7e2754de45573632c74f53563bb979df9758c949238a35865391d6b53fb',
+]
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+    ('scikit-build', '0.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('networkx', '2.5'),
+    ('PLUMED', local_plum_ver),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.2.0', {
+        'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ",
+        'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'
--- a/g/GROMACS/GROMACS-2021-intel-2020b-PLUMED-2.7.2.eb
+++ b/g/GROMACS/GROMACS-2021-intel-2020b-PLUMED-2.7.2.eb
@ -0,0 +1,34 @@
+# IT4Innovations 2020
+# LK
+
+name = 'GROMACS'
+version = '2021'
+local_plum_ver = '2.7.2'
+versionsuffix = '-PLUMED-%s' % local_plum_ver
+
+homepage = 'http://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics,
+ i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
+
+This is a GPU enabled build, containing both MPI and threadMPI binaries.
+"""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+]
+
+dependencies = [
+    ('PLUMED', local_plum_ver, '-Python-3.8.6'),
+]
+
+moduleclass = 'bio'
--- a/g/GROMACS/GROMACS-4.5.5-intel-2020b.eb
+++ b/g/GROMACS/GROMACS-4.5.5-intel-2020b.eb
@ -0,0 +1,46 @@
+## JK 2021
+# Based on
+##
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2013 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, Ghent University
+# Authors::   Wiktor Jurkowski <wiktor.jurkowski@uni.lu>, Fotis Georgatos <fotis.georgatos@uni.lu>, \
+#             George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Kenneth Hoste
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-93.html
+#
+# Version 5.1.4
+# Author: Adam Huffman
+# The Francis Crick Institute
+##
+easyblock = 'ConfigureMake'
+name = 'GROMACS'
+version = '4.5.5'
+
+homepage = 'http://www.gromacs.org'
+description = """GROMACS is a versatile package to perform molecular dynamics,
+ i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+import os
+if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
+   toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2'}
+else:
+    toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/', 'https://ftp.gromacs.org/pub/gromacs/']
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+    ('CMake', '3.18.4'), #'-GCCcore-10.2.0', True),
+    ('libxml2', '2.9.10'), #'-GCCcore-10.2.0', True),
+]
+
+dependencies = [('Boost', '1.74.0'), #'-GCC-10.2.0', True),
+                ('FFTW', '3.3.8', '', True),
+]
+
+moduleclass = 'bio'
--- a/p/PLUMED/PLUMED-2.7.2-foss-2020b.eb
+++ b/p/PLUMED/PLUMED-2.7.2-foss-2020b.eb
@ -0,0 +1,59 @@
+# IT4Innovations
+# LK 2021
+
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.7.2'
+
+homepage = 'https://www.plumed.org'
+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.
+"""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+toolchainopts = {'usempi': 'True'}
+
+source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
+sources = [SOURCE_TGZ]
+checksums = ['6069bc134f74cb15dd63e27e3587a15a31a9ddd9e7eebdd717da898f31512645']
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('GSL', '2.6'),
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('Boost', '1.74.0'),
+]
+
+preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
+configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
+configopts += '--enable-boost_graph --enable-boost_serialization '
+configopts += '--enable-asmjit '
+prebuildopts = 'source sourceme.sh && '
+
+# make sure that ld.gold linker is used
+# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
+# (problem with intel build but maintain consistency between easyconfigs)
+buildopts = 'LD_RO="ld.gold -r -o"'
+
+# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
+preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
+
+sanity_check_paths = {
+    'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["python -c 'import plumed'"]
+
+modextrapaths = {
+    'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
+    'PLUMED_ROOT': 'lib/plumed',
+    'PYTHONPATH': 'lib/plumed/python',
+}
+
+moduleclass = 'chem'
--- a/p/PLUMED/PLUMED-2.7.2-fosscuda-2020b.eb
+++ b/p/PLUMED/PLUMED-2.7.2-fosscuda-2020b.eb
@ -0,0 +1,59 @@
+# IT4Innovations
+# LK 2021
+
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.7.2'
+
+homepage = 'https://www.plumed.org'
+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.
+"""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+toolchainopts = {'usempi': 'True'}
+
+source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
+sources = [SOURCE_TGZ]
+checksums = ['6069bc134f74cb15dd63e27e3587a15a31a9ddd9e7eebdd717da898f31512645']
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('GSL', '2.6'),
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('Boost', '1.74.0'),
+]
+
+preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
+configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
+configopts += '--enable-boost_graph --enable-boost_serialization '
+configopts += '--enable-asmjit '
+prebuildopts = 'source sourceme.sh && '
+
+# make sure that ld.gold linker is used
+# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
+# (problem with intel build but maintain consistency between easyconfigs)
+buildopts = 'LD_RO="ld.gold -r -o"'
+
+# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
+preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
+
+sanity_check_paths = {
+    'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["python -c 'import plumed'"]
+
+modextrapaths = {
+    'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
+    'PLUMED_ROOT': 'lib/plumed',
+    'PYTHONPATH': 'lib/plumed/python',
+}
+
+moduleclass = 'chem'
--- a/p/Python/Python-3.8.6-GCC-10.2.0-CUDA-11.4.1-NetKet.eb
+++ b/p/Python/Python-3.8.6-GCC-10.2.0-CUDA-11.4.1-NetKet.eb
@ -0,0 +1,67 @@
+# IT4Innovations
+# LK 2021
+
+name = 'Python'
+version = '3.8.6'
+versionsuffix = '-NetKet'
+
+homepage = 'https://python.org/'
+description = """Python is a programming language that lets you work more quickly and integrate your systems
+ more effectively."""
+
+toolchain = {'name': 'GCC', 'version': '10.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/']
+sources = [SOURCE_TGZ]
+checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21']
+
+builddependencies = [
+    ('UnZip', '6.0'),
+]
+
+dependencies = [
+    ('binutils', '2.35'),
+    ('bzip2', '1.0.8'),  # required for bz2 package in Python stdlib
+    ('zlib', '1.2.11'),
+    ('libreadline', '8.0'),
+    ('ncurses', '6.2'),
+    ('SQLite', '3.33.0'),
+    ('XZ', '5.2.5'),
+    ('GMP', '6.2.0'),  # required for pycrypto
+    ('libffi', '3.3'),
+    ('CUDA', '11.4.1', '', True),
+    # OS dependency should be preferred if the os version is more recent then this version,
+    # it's nice to have an up to date openssl for security reasons
+    # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6)
+    # ('OpenSSL', '1.1.1h'),
+]
+
+osdependencies = [OS_PKG_OPENSSL_DEV]
+
+install_pip = True
+
+exts_default_options = {
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+}
+
+
+# order is important!
+# package versions updated 13 October 2020
+exts_list = [
+    ('setuptools', '50.3.0', {
+        'source_tmpl': '%(name)s-%(version)s.zip',
+        'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'],
+    }),
+    ('wheel', '0.35.1', {
+        'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'],
+    }),
+    ('pip', '20.2.3', {
+        'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'],
+    }),
+]
+
+moduleclass = 'lang'