From 1b1779e76c205df2a46aa8fc11b3328f1c53655c Mon Sep 17 00:00:00 2001 From: easybuild Date: Wed, 29 Sep 2021 16:10:36 +0200 Subject: [PATCH] new file: a/AOCC/AOCC-2.2.0-GCCcore-10.2.0.eb new file: a/Amber/Amber-20-foss-2020b.eb new file: a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb new file: l/LAMMPS/LAMMPS-20201029-intel-2020a.eb modified: o/ORCA/ORCA-5.0.1-OpenMPI-4.1.1.eb new file: p/phono3py/phono3py-2.0.0-conda.eb new file: p/phonopy/phonopy-2.11.0-conda.eb deleted: a/AOCC/AOCC-2.1.0-GCCcore-10.2.0.eb deleted: p/phonopy/phonopy-2.11.0-intel-2020a-Python-3.8.2.eb --- ...10.2.0.eb => AOCC-2.2.0-GCCcore-10.2.0.eb} | 11 ++-- a/Amber/Amber-20-foss-2020b.eb | 66 +++++++++++++++++++ .../Amber-20.11-foss-2020b-AmberTools-21.3.eb | 61 +++++++++++++++++ l/LAMMPS/LAMMPS-20201029-intel-2020a.eb | 52 +++++++++++++++ o/ORCA/ORCA-5.0.1-OpenMPI-4.1.1.eb | 2 +- p/phono3py/phono3py-2.0.0-conda.eb | 27 ++++++++ p/phonopy/phonopy-2.11.0-conda.eb | 27 ++++++++ ...phonopy-2.11.0-intel-2020a-Python-3.8.2.eb | 42 ------------ 8 files changed, 238 insertions(+), 50 deletions(-) rename a/AOCC/{AOCC-2.1.0-GCCcore-10.2.0.eb => AOCC-2.2.0-GCCcore-10.2.0.eb} (71%) create mode 100644 a/Amber/Amber-20-foss-2020b.eb create mode 100644 a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb create mode 100644 l/LAMMPS/LAMMPS-20201029-intel-2020a.eb create mode 100644 p/phono3py/phono3py-2.0.0-conda.eb create mode 100644 p/phonopy/phonopy-2.11.0-conda.eb delete mode 100644 p/phonopy/phonopy-2.11.0-intel-2020a-Python-3.8.2.eb diff --git a/a/AOCC/AOCC-2.1.0-GCCcore-10.2.0.eb b/a/AOCC/AOCC-2.2.0-GCCcore-10.2.0.eb similarity index 71% rename from a/AOCC/AOCC-2.1.0-GCCcore-10.2.0.eb rename to a/AOCC/AOCC-2.2.0-GCCcore-10.2.0.eb index 50dbb1b7..11817d2d 100644 --- a/a/AOCC/AOCC-2.1.0-GCCcore-10.2.0.eb +++ b/a/AOCC/AOCC-2.2.0-GCCcore-10.2.0.eb @@ -1,11 +1,8 @@ -# -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Author: Robert Mijakovic -# reciPY derived from preexisting reciPy for GCCcore-9.3.0. -# +# IT4Innovations +# LK 2021 + name = 'AOCC' -version = '2.1.0' +version = '2.2.0' homepage = 'https://developer.amd.com/amd-aocc/' description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 11.0" diff --git a/a/Amber/Amber-20-foss-2020b.eb b/a/Amber/Amber-20-foss-2020b.eb new file mode 100644 index 00000000..f8332078 --- /dev/null +++ b/a/Amber/Amber-20-foss-2020b.eb @@ -0,0 +1,66 @@ +# IT4Innovations +# LK 2021 + +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 21 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', +] +checksums = [ + 'a4c53639441c8cc85adee397933d07856cc4a723c82c6bea585cd76c197ead75', # Amber20.tar.bz2 + 'f55fa930598d5a8e9749e8a22d1f25cab7fcf911d98570e35365dd7f262aaafd', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # mpi4py required for MMPBSA + ('Perl', '5.32.0'), + ('Boost', '1.74.0'), + ('libreadline', '8.0'), + ('matplotlib', '3.3.3'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.2'), + ('Tkinter', '3.8.6'), + ('X11', '20201008'), +] + +# All tests are expected to pass or be skipped +runtest = True + +static = False + +moduleclass = 'chem' diff --git a/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb b/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb new file mode 100644 index 00000000..a50ee5a0 --- /dev/null +++ b/a/Amber/Amber-20.11-foss-2020b-AmberTools-21.3.eb @@ -0,0 +1,61 @@ +name = 'Amber' +local_amber_ver = 20 +local_ambertools_ver = 21 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 11) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', +] +checksums = [ + '559d5b7b872344c268a62ebd5d33f71d', # Amber20.tar.bz2 + '81bd97be0aa9d3e728f2db5f63987e04', # AmberTools21.tar.bz2 + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', #AmberTools-20_fix_xblas_missing_make_dependency.patch +] + +builddependencies = [ + ('Bison', '3.7.1'), + ('CMake', '3.18.4'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), # mpi4py required for MMPBSA + ('Perl', '5.32.0'), + ('Boost', '1.74.0'), + ('libreadline', '8.0'), + ('matplotlib', '3.3.3'), + ('netCDF', '4.7.4'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.2'), + ('Tkinter', '3.8.6'), + ('X11', '20201008'), +] + +# All tests are expected to pass or be skipped +runtest = True + +static = False + +moduleclass = 'chem' diff --git a/l/LAMMPS/LAMMPS-20201029-intel-2020a.eb b/l/LAMMPS/LAMMPS-20201029-intel-2020a.eb new file mode 100644 index 00000000..94e90eee --- /dev/null +++ b/l/LAMMPS/LAMMPS-20201029-intel-2020a.eb @@ -0,0 +1,52 @@ +# IT4Innovations 2021 + +easyblock = 'CmdCp' + +name = 'LAMMPS' +version = '20201029' + +homepage = 'http://lammps.sandia.gov' +description = """LAMMPS is a classical molecular dynamics code, +and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. +Has potentials for solid-state materials (metals, semiconductors) and soft +matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. +It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, +meso, or continuum scale.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/lammps/lammps/archive/refs/tags/'] +sources = ['stable_29Oct2020.tar.gz'] + +dependencies = [ + ('tbb', '2020.1'), + ('gperftools', '2.8'), +] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +# deprecated MEAM, REAX + +local_commands = "cd src && " +local_commands += "make yes-kokkos && make yes-user-meamc && " +local_commands += "make yes-user-phonon && make yes-misc && " +local_commands += "make yes-kspace && make yes-manybody && make yes-molecule && " +local_commands += "make yes-qeq && make yes-rigid && make yes-user-misc && " +local_commands += "make yes-user-reaxc && make yes-user-omp && " +local_commands += "make yes-spin && make yes-user-diffraction && " +local_commands += "make -j 16 intel_cpu_intelmpi && mv lmp_intel_cpu_intelmpi lammps" + +cmds_map = [('.*', local_commands)] + +files_to_copy = [ + (['src/lammps'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/lammps'], + 'dirs': [''], +} + +moduleclass = 'chem' diff --git a/o/ORCA/ORCA-5.0.1-OpenMPI-4.1.1.eb b/o/ORCA/ORCA-5.0.1-OpenMPI-4.1.1.eb index 05c8fab6..fe57eb51 100644 --- a/o/ORCA/ORCA-5.0.1-OpenMPI-4.1.1.eb +++ b/o/ORCA/ORCA-5.0.1-OpenMPI-4.1.1.eb @@ -19,7 +19,7 @@ toolchain = SYSTEM # Download from https://orcaforum.kofo.mpg.de sources = ['orca_5_0_1_linux_x86-64_openmpi411.tar.xz'] checksums = ['aea3885f746f35e24485384a374c1217'] -dependencies = [('OpenMPI', '4.1.1', '-GCC-10.3.0')] +dependencies = [('OpenMPI', '4.1.1', '-GCC-10.2.0')] sanity_check_paths = { 'files': ['orca_%s%s' % (x, y) for x in ['anoint', 'casscf', 'cis', 'cpscf', diff --git a/p/phono3py/phono3py-2.0.0-conda.eb b/p/phono3py/phono3py-2.0.0-conda.eb new file mode 100644 index 00000000..90dff000 --- /dev/null +++ b/p/phono3py/phono3py-2.0.0-conda.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2021 +# JK + +easyblock = "Conda" + +name = 'phono3py' +version = '2.0.0' +versionsuffix = '-conda' + +homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' +description = """This software calculates phonon-phonon interaction related properties""" + +toolchain = SYSTEM + +dependencies = [ + ('Anaconda3', '2021.05'), +] + +requirements = "%(namelower)s" +channels = ['atztogo'] + +sanity_check_paths = { + 'files': ['bin/phono3py', 'bin/phonopy'], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'phys' diff --git a/p/phonopy/phonopy-2.11.0-conda.eb b/p/phonopy/phonopy-2.11.0-conda.eb new file mode 100644 index 00000000..186b36ec --- /dev/null +++ b/p/phonopy/phonopy-2.11.0-conda.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2021 +# JK + +easyblock = "Conda" + +name = 'phonopy' +version = '2.11.0' +versionsuffix = '-conda' + +homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' +description = """This software calculates phonon-phonon interaction related properties""" + +toolchain = SYSTEM + +dependencies = [ + ('Anaconda3', '2021.05'), +] + +requirements = "%(namelower)s" +channels = ['atztogo'] + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['bin', 'lib'] +} + +moduleclass = 'phys' diff --git a/p/phonopy/phonopy-2.11.0-intel-2020a-Python-3.8.2.eb b/p/phonopy/phonopy-2.11.0-intel-2020a-Python-3.8.2.eb deleted file mode 100644 index ee6198b6..00000000 --- a/p/phonopy/phonopy-2.11.0-intel-2020a-Python-3.8.2.eb +++ /dev/null @@ -1,42 +0,0 @@ -# IT4Innovations 2021 -# JK - -easyblock = 'PythonPackage' - -name = 'phonopy' -version = '2.11.0' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://atztogo.github.io/phonopy/' -description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" - -toolchain = {'name': 'intel', 'version': '2020a'} - -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', versionsuffix), # for numpy - ('matplotlib', '3.2.1', versionsuffix), - ('PyYAML', '5.3.1', '-GCCcore-10.2.0', True), - ('h5py', '2.10.0', versionsuffix), - ('spglib-python', '1.16.0', versionsuffix), -] - -# required because we're building a Python package using Intel compilers on top of Python built with GCC -check_ldshared = True - -download_dep_fail = True -use_pip = True - -sanity_check_paths = { - 'files': ['bin/phonopy'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["phonopy --help"] - -sanity_pip_check = True - -# EasyBuilders to maji jako lib, ale ma to byt chem -moduleclass = 'chem'