From 5f3b84f8fffe0ede4d30994ee7850923da64f025 Mon Sep 17 00:00:00 2001 From: Lukas Krupcik Date: Mon, 1 Aug 2022 10:38:12 +0200 Subject: [PATCH] new file: a/ABCluster/ABCluster-3.1.eb modified: b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb new file: b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb.bak_20220801085422_29482 new file: c/CP2K/CP2K-2022.1-foss-2021a-CUDA-11.4.1.eb new file: c/CP2K/CP2K-2022.1-fosscuda-2020b.eb new file: f/fromage/fromage-1.1.0.eb modified: g/glibc/glibc-2.19.eb new file: g/glibc/glibc-2.29-GCCcore-10.2.0.eb modified: g/glibc/glibc-2.30-GCCcore-10.2.0.eb new file: i/iRODS/iRODS-0.7.3.eb modified: p/pymatgen/pymatgen-2022.0.12-foss-2020b.eb new file: s/sqsgenerator/sqsgenerator-0.2-foss-2020b-Python-3.8.6.eb deleted: i/IRODS/IRODS-0.7.3.eb --- a/ABCluster/ABCluster-3.1.eb | 36 +++++++++++++ .../Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb | 3 +- ...0-Python-3.8.6.eb.bak_20220801085422_29482 | 30 +++++++++++ c/CP2K/CP2K-2022.1-foss-2021a-CUDA-11.4.1.eb | 42 +++++++++++++++ c/CP2K/CP2K-2022.1-fosscuda-2020b.eb | 39 ++++++++++++++ f/fromage/fromage-1.1.0.eb | 54 +++++++++++++++++++ g/glibc/glibc-2.19.eb | 3 +- g/glibc/glibc-2.29-GCCcore-10.2.0.eb | 37 +++++++++++++ g/glibc/glibc-2.30-GCCcore-10.2.0.eb | 4 +- i/IRODS/IRODS-0.7.3.eb | 20 ------- i/iRODS/iRODS-0.7.3.eb | 26 +++++++++ p/pymatgen/pymatgen-2022.0.12-foss-2020b.eb | 6 +-- ...qsgenerator-0.2-foss-2020b-Python-3.8.6.eb | 45 ++++++++++++++++ 13 files changed, 318 insertions(+), 27 deletions(-) create mode 100644 a/ABCluster/ABCluster-3.1.eb create mode 100644 b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb.bak_20220801085422_29482 create mode 100644 c/CP2K/CP2K-2022.1-foss-2021a-CUDA-11.4.1.eb create mode 100644 c/CP2K/CP2K-2022.1-fosscuda-2020b.eb create mode 100644 f/fromage/fromage-1.1.0.eb create mode 100644 g/glibc/glibc-2.29-GCCcore-10.2.0.eb delete mode 100644 i/IRODS/IRODS-0.7.3.eb create mode 100644 i/iRODS/iRODS-0.7.3.eb create mode 100644 s/sqsgenerator/sqsgenerator-0.2-foss-2020b-Python-3.8.6.eb diff --git a/a/ABCluster/ABCluster-3.1.eb b/a/ABCluster/ABCluster-3.1.eb new file mode 100644 index 00000000..c74583ca --- /dev/null +++ b/a/ABCluster/ABCluster-3.1.eb @@ -0,0 +1,36 @@ +# IT4Innovatins 2022 +# JK + +easyblock = 'Tarball' + +name = 'ABCluster' +version = '3.1' + +homepage = 'http://zhjun-sci.com/home-EN.php' +description = """ABCluster a program for the global optimization of chemical cluster structures.""" +docurls = 'http://www.zhjun-sci.com/abcluster/doc/introduction.html' + +toolchain = SYSTEM +toolchainopts = { 'openmp': True } + +# Segfaults! +# dependencies = [ ('glibc', '2.29') ] + +source_urls = ['http://www.zhjun-sci.com/docs/abcluster/'] +sources = ['%(name)s-%(version)s-Linux.tar.gz'] +checksums = ['4e4de1b354ac5965334f725523a435c2ddad9257811c73c282884625ec267fd3'] + +sanity_check_paths = { + 'files': [ + 'abcinp', 'atom', 'bee', 'gaussian2xyz', 'geom', 'isomer', 'libiomp5.so', + 'rigidmol', 'topgen', 'xyz2gaussian' +], + 'dirs': ['misc', 'testfiles'] +} + +modextrapaths = { + 'PATH': '.', + 'LD_LIBRARY_PATH': '.' + } + +moduleclass = 'chem' diff --git a/b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb b/b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb index 8f6d0fb1..35c09864 100644 --- a/b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb +++ b/b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb @@ -12,8 +12,9 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] - sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['5347464af5b14ac54bb945dc68f1dd7c56f0dad7262816b956138fc53bcc0131'] + #patches = ['Boost-1.65.1_fix-Python3.patch'] dependencies = [ diff --git a/b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb.bak_20220801085422_29482 b/b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb.bak_20220801085422_29482 new file mode 100644 index 00000000..8f6d0fb1 --- /dev/null +++ b/b/Boost/Boost-1.77.0-GCC-10.2.0-Python-3.8.6.eb.bak_20220801085422_29482 @@ -0,0 +1,30 @@ +# IT4Innovations +# LK 2022 + +name = 'Boost' +version = '1.77.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] + +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +#patches = ['Boost-1.65.1_fix-Python3.patch'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('Python', '3.8.6') +] + +configopts = '--with-python=$EBROOTPYTHON/bin/python' + +# also build boost_mpi +boost_mpi = False + +moduleclass = 'devel' diff --git a/c/CP2K/CP2K-2022.1-foss-2021a-CUDA-11.4.1.eb b/c/CP2K/CP2K-2022.1-foss-2021a-CUDA-11.4.1.eb new file mode 100644 index 00000000..c9c5dbaa --- /dev/null +++ b/c/CP2K/CP2K-2022.1-foss-2021a-CUDA-11.4.1.eb @@ -0,0 +1,42 @@ +# IT4Innovations 2022 +# JK +# uses special easyblock for CUDA support! + +name = 'CP2K' +version = '2022.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2c34f1a7972973c62d471cd35856f444f11ab22f2ff930f6ead20f3454fd228b'] + +dependencies = [ + ('CUDA', '11.4.1', '', True), + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '5.1.5'), + ('libxsmm', '1.16.2'), + ('FFTW', '3.3.9'), + ('PLUMED', '2.7.2'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/c/CP2K/CP2K-2022.1-fosscuda-2020b.eb b/c/CP2K/CP2K-2022.1-fosscuda-2020b.eb new file mode 100644 index 00000000..6464c970 --- /dev/null +++ b/c/CP2K/CP2K-2022.1-fosscuda-2020b.eb @@ -0,0 +1,39 @@ +# IT4Innovations 2022 +# LK JK + +name = 'CP2K' +version = '8.2' + +homepage = 'https://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'fosscuda', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s.0/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['2e24768720efed1a5a4a58e83e2aca502cd8b95544c21695eb0de71ed652f20a'] + +dependencies = [ + ('Libint', '2.6.0', '-lmax-6-cp2k'), + ('libxc', '5.1.3'), + ('libxsmm', '1.16.1'), + ('FFTW', '3.3.8'), + ('PLUMED', '2.8.0'), +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.1'), +] + +type = 'psmp' + +# regression test reports handful of failures, +# we're assuming those are OK to ignore... +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/f/fromage/fromage-1.1.0.eb b/f/fromage/fromage-1.1.0.eb new file mode 100644 index 00000000..7245cd40 --- /dev/null +++ b/f/fromage/fromage-1.1.0.eb @@ -0,0 +1,54 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'PythonBundle' + +name = 'fromage' +version = '1.1.0' +docurls = 'https://fromage.readthedocs.io/' + +homepage = 'https://github.com/Crespo-Otero-group/fromage' +description = """ +fromage (FRamewOrk for Molecular AGgregate Excitations) is a Python framework designed to facilitate +the study of molecular aggregates in the excited state. It contains utilities for geometry manipulation going from +periodic to finite models, exciton analysis and ONIOM calculations. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +import os +if os.environ.get("CLUSTERNAME") in ["KAROLINA"]: + toolchainopts = {'optarch': 'march=core-avx2'} + +dependencies = [ + ('SciPy-bundle', '2021.10'), + ('SWIG', '4.0.2'), +] + +#use_pip = True +skipsteps = ['sanitycheck'] +sanity_pip_check = False + +# stahnout zdrojak z githubu +exts_list = [ + (name, version, { + 'sources': 'v%(version)s.tar.gz', + 'checksums': ['88e5108a0081d3c306d34d5abb7b6e10a5b4dc0e886e28a27c5f56c9a79002ee'], + }), +] + +sanity_check_paths = { + 'files': [ + 'bin/fro_assign_charges.py', 'bin/fro_coupling.py', 'bin/fro_dimer_tools.py', + 'bin/fro_exciton_classification.py', 'bin/fro_pick_mol.py', 'bin/fro_pop_stat.py', + 'bin/fro_prep_run.py', 'bin/fro_run.py', 'bin/fro_uc_tools.py', 'bin/fro_volumetrics.py' +], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +postinstallcmds = [ + 'git clone https://github.com/Crespo-Otero-group/Ewald.git', + 'cc -o Ewald-bin Ewald/Ewald.c Ewald/randome.c -lscalapack -lflexiblas -lgfortran -lm -Wno-error', + 'mv Ewald-bin %(installdir)s/bin/Ewald' +] + +moduleclass = 'python' diff --git a/g/glibc/glibc-2.19.eb b/g/glibc/glibc-2.19.eb index 71dfe133..d39c7e6d 100644 --- a/g/glibc/glibc-2.19.eb +++ b/g/glibc/glibc-2.19.eb @@ -10,8 +10,9 @@ description = """The Glibc package contains the main C library. This library pro toolchain = SYSTEM -sources = ['%(name)s-%(version)s.tar.gz'] source_urls = ['http://ftp.gnu.org/gnu/glibc/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['18ad6db70724699d264add80b1f813630d0141cf3a3558b4e1a7c15f6beac796'] preconfigopts = 'mkdir build && ' preconfigopts += 'cd build && ' diff --git a/g/glibc/glibc-2.29-GCCcore-10.2.0.eb b/g/glibc/glibc-2.29-GCCcore-10.2.0.eb new file mode 100644 index 00000000..6451a7d6 --- /dev/null +++ b/g/glibc/glibc-2.29-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +# IT4Innovations +# LK 2021 + +easyblock = 'ConfigureMake' + +name = 'glibc' +version = '2.29' + +homepage = 'https://www.gnu.org/software/libc/' +description = """The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, + as well as many other systems that use Linux as the kernel.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/glibc/'] +sources = ['glibc-%(version)s.tar.xz'] +checksums = ['f3eeb8d57e25ca9fc13c2af3dae97754f9f643bc69229546828e3a240e2af04b'] + +builddependencies = [ + ('binutils', '2.35'), + ('make', '4.2.1'), + ('texinfo', '6.7'), + ('Bison', '3.7.1'), + ('Python', '3.8.6'), +] + +preconfigopts = 'mkdir obj && cd obj && CC="$CC -fuse-ld=bfd -w" ' # --disable-werror" ' +configure_cmd_prefix = '../' +prebuildopts = "cd obj && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/ldd', 'lib/libc.a', 'lib/libc.%s' % SHLIB_EXT], + 'dirs': ['etc', 'libexec', 'include', 'sbin', 'share'], +} + +moduleclass = 'lib' diff --git a/g/glibc/glibc-2.30-GCCcore-10.2.0.eb b/g/glibc/glibc-2.30-GCCcore-10.2.0.eb index 2f351588..8ab630f4 100644 --- a/g/glibc/glibc-2.30-GCCcore-10.2.0.eb +++ b/g/glibc/glibc-2.30-GCCcore-10.2.0.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'glibc' version = '2.30' -homepags = 'https://www.gnu.org/software/libc/' +homepage = 'https://www.gnu.org/software/libc/' description = """The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, as well as many other systems that use Linux as the kernel.""" @@ -24,7 +24,7 @@ builddependencies = [ ('Python', '3.8.6'), ] -preconfigopts = 'mkdir obj && cd obj && CC="$CC -fuse-ld=bfd --disable-werror" ' +preconfigopts = 'mkdir obj && cd obj && CC="$CC -fuse-ld=bfd -w" ' # --disable-werror" ' configure_cmd_prefix = '../' prebuildopts = "cd obj && " preinstallopts = prebuildopts diff --git a/i/IRODS/IRODS-0.7.3.eb b/i/IRODS/IRODS-0.7.3.eb deleted file mode 100644 index fdf64b62..00000000 --- a/i/IRODS/IRODS-0.7.3.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'IRODS' -version = '0.7.3' - -homepage = 'http://www.example.com' -description = """TEMPLATE DESCRIPTION""" - -toolchain = SYSTEM - -source_urls = ['https://github.com/cyverse/irodsfs/releases/download/v%(version)s/'] -sources = ['irodsfs_amd64_linux_v%(version)s.tar'] -checksums = ['0c973134e7646309a9292d3b2f3df8b62f27c686c9a04de49f71ea9f9b15a038'] - -sanity_check_paths = { - 'files': ['irodsfs'], - 'dirs': [] -} - -moduleclass = 'lib' diff --git a/i/iRODS/iRODS-0.7.3.eb b/i/iRODS/iRODS-0.7.3.eb new file mode 100644 index 00000000..e68c1fd7 --- /dev/null +++ b/i/iRODS/iRODS-0.7.3.eb @@ -0,0 +1,26 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'PackedBinary' + +name = 'iRODS' +version = '0.7.3' + +homepage = 'https://github.com/cyverse/irodsfs/' +description = """iRODS FUSE Lite FUSE implementation of iRODS Client written in Golang.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cyverse/irodsfs/releases/download/v%(version)s/'] +sources = ['irodsfs_amd64_linux_v%(version)s.tar'] +checksums = ['0c973134e7646309a9292d3b2f3df8b62f27c686c9a04de49f71ea9f9b15a038'] + +sanity_check_paths = { + 'files': ['irodsfs'], + 'dirs': [] +} + +postinstallcmds = ['cp /mnt/proj3/easybuild/scripts/irods-startup.sh %(installdir)s/'] +modluafooter = 'execute{cmd="bash $EBROOTIRODS/irods-startup.sh", modeA={"load"}}' + +moduleclass = 'tools' diff --git a/p/pymatgen/pymatgen-2022.0.12-foss-2020b.eb b/p/pymatgen/pymatgen-2022.0.12-foss-2020b.eb index 63fa2e8e..f8cda0b7 100644 --- a/p/pymatgen/pymatgen-2022.0.12-foss-2020b.eb +++ b/p/pymatgen/pymatgen-2022.0.12-foss-2020b.eb @@ -1,8 +1,8 @@ -<<<<<<< HEAD +#<<<<<<< HEAD # taken from develop and updated from 2022.0.4 to 2022.0.12 -======= +#======= # taken from develop and updated to 2022.0.12 from 2022.0.4 ->>>>>>> 828ac88762b4c4479e53485570fcede5d2b35c47 +#>>>>>>> 828ac88762b4c4479e53485570fcede5d2b35c47 # JK easyblock = 'PythonBundle' diff --git a/s/sqsgenerator/sqsgenerator-0.2-foss-2020b-Python-3.8.6.eb b/s/sqsgenerator/sqsgenerator-0.2-foss-2020b-Python-3.8.6.eb new file mode 100644 index 00000000..7ec7314a --- /dev/null +++ b/s/sqsgenerator/sqsgenerator-0.2-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,45 @@ +# IT4Innovations 2022 +# JK + +easyblock = 'PythonPackage' + +name = 'sqsgenerator' +version = '0.2' +versionsuffix = '-Python-3.8.6' + +homepage = 'https://github.com/dnoeger/sqsgenerator' +description = """This package is a Special Quasirandom Structure generator written in Python3/Cython. +Please note that the programm currently only works with Python 3.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/dgehringer/sqsgenerator/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['983e20a97203b37dc4d21850e1a9693023cb1516bf543f645cbbac198a84f23c'] + +builddependencies = [ + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('GMP', '6.2.0'), + ('Boost', '1.77.0', '-Python-3.8.6', ('GCC', '10.2.0')), + ('SciPy-bundle', '2020.11'), + ('pymatgen', '2022.0.12'), +] + +use_pip = True +preinstallopts = 'pip install --prefix=%(installdir)s --no-deps --no-build-isolation -r docs/requirements.txt && ' +preinstallopts += 'SQS_BOOST_ROOT=$EBROOTBOOST ' +preinstallopts += 'SQS_USE_MPI=ON ' + +sanity_check_paths = { + 'files': [ + 'bin/sqsgen'], + 'dirs': [ + 'bin', + 'lib']} + +moduleclass = 'lang'