From d748f3b8540094581a9ce1c14ce93713f266c9b4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Fri, 21 Aug 2020 13:44:21 +0200 Subject: [PATCH] modified: c/CheMPS2/CheMPS2-1.8.9-intel-2020a.eb new file: d/deepdiff/deepdiff-4.0.6-GCCcore-9.3.0-Python-3.8.2.eb modified: h/HDF5/HDF5-1.10.6-intel-2020a-parallel.eb new file: h/h5py/h5py-2.10.0-intel-2020a.eb new file: i/iccifort/iccifort-2020.1.217.eb new file: i/iimpi/iimpi-2020a.eb.old new file: i/intel/intel-2020a.eb.old modified: l/libxc/libxc-4.3.4-intel-2020a.eb modified: m/METIS/METIS-5.1.0-intel-2020a.eb modified: m/Molden/Molden-6.3-intel-2020a.eb modified: n/netCDF/netCDF-4.7.3-intel-2020a.eb new file: n/networkx/networkx-2.4-intel-2020a-Python-3.8.2.eb new file: o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb modified: p/PETSc/PETSc-3.12.4-intel-2020a.eb new file: p/PSI4/PSI4-1.3.2-intel-2020a-Py-3.8.2.eb new file: p/pytest/pytest-6.0.1-Python-3.7.8.eb new file: p/pytest/pytest-6.0.1-Python-3.8.2.eb modified: q/QMCPACK/QMCPACK-3.9.1-intel-2020a.eb modified: r/RELION/RELION-3.1.0-intel-2020a.eb modified: s/SCOTCH/SCOTCH-6.0.9-foss-2020a.eb new file: s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.7.8.eb modified: s/Score-P/Score-P-6.0-intel-2020a.eb modified: s/SuiteSparse/SuiteSparse-5.6.0-intel-2020a-METIS-5.1.0.eb new file: u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb new file: v/VTK/VTK-8.2.0-intel-2020a-Python-3.7.8.eb deleted: i/iimpi/iimpi-2020a.eb deleted: i/intel/intel-2020a.eb deleted: u/UCX/UCX-1.8.1-GCC-9.3.0.eb deleted: u/UCX/UCX-1.8.1-GCCcore-8.3.0.eb deleted: v/VTK/VTK-8.2.0-intel-2020a-Py-3.7.eb --- c/CheMPS2/CheMPS2-1.8.9-intel-2020a.eb | 2 +- ...epdiff-4.0.6-GCCcore-9.3.0-Python-3.8.2.eb | 33 +++++++++++ h/HDF5/HDF5-1.10.6-intel-2020a-parallel.eb | 4 +- h/h5py/h5py-2.10.0-intel-2020a.eb | 41 +++++++++++++ i/iccifort/iccifort-2020.1.217.eb | 40 +++++++++++++ .../{iimpi-2020a.eb => iimpi-2020a.eb.old} | 0 .../{intel-2020a.eb => intel-2020a.eb.old} | 0 l/libxc/libxc-4.3.4-intel-2020a.eb | 4 +- m/METIS/METIS-5.1.0-intel-2020a.eb | 4 +- m/Molden/Molden-6.3-intel-2020a.eb | 4 +- n/netCDF/netCDF-4.7.3-intel-2020a.eb | 2 +- .../networkx-2.4-intel-2020a-Python-3.8.2.eb | 28 +++++++++ o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb | 42 ++++++++++++++ p/PETSc/PETSc-3.12.4-intel-2020a.eb | 2 +- p/PSI4/PSI4-1.3.2-intel-2020a-Py-3.8.2.eb | 57 +++++++++++++++++++ p/pytest/pytest-6.0.1-Python-3.7.8.eb | 29 ++++++++++ p/pytest/pytest-6.0.1-Python-3.8.2.eb | 29 ++++++++++ q/QMCPACK/QMCPACK-3.9.1-intel-2020a.eb | 10 ++-- r/RELION/RELION-3.1.0-intel-2020a.eb | 4 +- s/SCOTCH/SCOTCH-6.0.9-foss-2020a.eb | 3 + ...bundle-2020.03-intel-2020a-Python-3.7.8.eb | 54 ++++++++++++++++++ s/Score-P/Score-P-6.0-intel-2020a.eb | 4 +- ...iteSparse-5.6.0-intel-2020a-METIS-5.1.0.eb | 4 +- ...CC-9.3.0.eb => UCX-1.8.0-GCCcore-9.3.0.eb} | 26 ++++++--- u/UCX/UCX-1.8.1-GCCcore-8.3.0.eb | 48 ---------------- ... => VTK-8.2.0-intel-2020a-Python-3.7.8.eb} | 16 +++--- 26 files changed, 407 insertions(+), 83 deletions(-) create mode 100644 d/deepdiff/deepdiff-4.0.6-GCCcore-9.3.0-Python-3.8.2.eb create mode 100644 h/h5py/h5py-2.10.0-intel-2020a.eb create mode 100644 i/iccifort/iccifort-2020.1.217.eb rename i/iimpi/{iimpi-2020a.eb => iimpi-2020a.eb.old} (100%) rename i/intel/{intel-2020a.eb => intel-2020a.eb.old} (100%) create mode 100644 n/networkx/networkx-2.4-intel-2020a-Python-3.8.2.eb create mode 100644 o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb create mode 100644 p/PSI4/PSI4-1.3.2-intel-2020a-Py-3.8.2.eb create mode 100644 p/pytest/pytest-6.0.1-Python-3.7.8.eb create mode 100644 p/pytest/pytest-6.0.1-Python-3.8.2.eb create mode 100644 s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.7.8.eb rename u/UCX/{UCX-1.8.1-GCC-9.3.0.eb => UCX-1.8.0-GCCcore-9.3.0.eb} (59%) delete mode 100644 u/UCX/UCX-1.8.1-GCCcore-8.3.0.eb rename v/VTK/{VTK-8.2.0-intel-2020a-Py-3.7.eb => VTK-8.2.0-intel-2020a-Python-3.7.8.eb} (91%) diff --git a/c/CheMPS2/CheMPS2-1.8.9-intel-2020a.eb b/c/CheMPS2/CheMPS2-1.8.9-intel-2020a.eb index 4ce2671d..c6b39cad 100644 --- a/c/CheMPS2/CheMPS2-1.8.9-intel-2020a.eb +++ b/c/CheMPS2/CheMPS2-1.8.9-intel-2020a.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] sources = ['v%(version)s.tar.gz'] builddependencies = [ - ('CMake', '3.16.2', '', True) + ('CMake', '3.16.4') ] dependencies = [ diff --git a/d/deepdiff/deepdiff-4.0.6-GCCcore-9.3.0-Python-3.8.2.eb b/d/deepdiff/deepdiff-4.0.6-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000..dbcdb466 --- /dev/null +++ b/d/deepdiff/deepdiff-4.0.6-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,33 @@ +# JH 2020 + +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '4.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://deepdiff.readthedocs.io/en/latest/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [('binutils', '2.34')] +dependencies = [('Python', '3.8.2')] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('jsonpickle', '1.1', { + 'checksums': ['625098cc8e5854b8c23b587aec33bc8e33e0e597636bfaca76152249c78fe5c1'], + }), + ('ordered-set', '3.1.1', { + 'checksums': ['a7bfa858748c73b096e43db14eb23e2bc714a503f990c89fac8fab9b0ee79724'], + }), + (name, version, { + 'checksums': ['55e461f56dcae3dc540746b84434562fb7201e5c27ecf28800e4cfdd17f61e56'], + }), +] + +moduleclass = 'tools' diff --git a/h/HDF5/HDF5-1.10.6-intel-2020a-parallel.eb b/h/HDF5/HDF5-1.10.6-intel-2020a-parallel.eb index 9cafd43a..c08aa328 100644 --- a/h/HDF5/HDF5-1.10.6-intel-2020a-parallel.eb +++ b/h/HDF5/HDF5-1.10.6-intel-2020a-parallel.eb @@ -18,8 +18,8 @@ sources = [SOURCELOWER_TAR_GZ] configopts = '--enable-fortran --enable-fortran 2003 --enable-cxx' dependencies = [ - ('zlib', '1.2.11', '', True), - ('Szip', '2.1', '', True), + ('zlib', '1.2.11'), + ('Szip', '2.1.1'), ] moduleclass = 'data' diff --git a/h/h5py/h5py-2.10.0-intel-2020a.eb b/h/h5py/h5py-2.10.0-intel-2020a.eb new file mode 100644 index 00000000..8f7cb782 --- /dev/null +++ b/h/h5py/h5py-2.10.0-intel-2020a.eb @@ -0,0 +1,41 @@ +# JH 2020 + +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.10.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d'] + +builddependencies = [('pkgconfig', '1.5.1', '-Python-3.8.2')] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), + ('HDF5', '1.10.6', '', ('iimpi', '2020a')), +] + +use_pip = False +download_dep_fail = True + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# to really use mpi enabled hdf5 we now seem to need a configure step, which is the reason we can't use pip +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +# skip regular 'import h5py', and run it via mpirun (since 'import h5py' results in an MPI_Init call) +options = {'modulename': False} +sanity_check_commands = ["%(mpi_cmd_prefix)s python -c 'import %(name)s'"] + +moduleclass = 'data' diff --git a/i/iccifort/iccifort-2020.1.217.eb b/i/iccifort/iccifort-2020.1.217.eb new file mode 100644 index 00000000..da714d80 --- /dev/null +++ b/i/iccifort/iccifort-2020.1.217.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'iccifort' +version = '2020.1.217' + +homepage = 'https://software.intel.com/en-us/intel-compilers/' +description = "Intel C, C++ & Fortran compilers" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16530/'] +sources = ['parallel_studio_xe_%(version_major)s_update%(version_minor)s_composer_edition.tgz'] +patches = ['iccifort-%(version)s_no_mpi_rt_dependency.patch'] +checksums = [ + # parallel_studio_xe_2020_update1_composer_edition.tgz + '26c7e7da87b8a83adfd408b2a354d872be97736abed837364c1bf10f4469b01e', + # iccifort-2020.1.217_no_mpi_rt_dependency.patch + '61b558089d3d9253fad2139a16dc0899b9f839f34303e094efd70b281fc41a96', +] + +local_gccver = '9.3.0' + +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.34', '', ('GCCcore', local_gccver)), +] + +# list of regex for components to install +# full list of components can be obtained from pset/mediaconfig.xml in unpacked sources +# cfr. https://software.intel.com/en-us/articles/intel-composer-xe-2015-silent-installation-guide +components = [ + 'intel-comp', 'intel-ccomp', 'intel-fcomp', 'intel-icc', 'intel-ifort', + 'intel-openmp', 'intel-ipsc?_', 'intel-gdb(?!.*mic)' +] + +dontcreateinstalldir = True + +license_file = '/apps/licenses/intel/license.lic' + +moduleclass = 'compiler' diff --git a/i/iimpi/iimpi-2020a.eb b/i/iimpi/iimpi-2020a.eb.old similarity index 100% rename from i/iimpi/iimpi-2020a.eb rename to i/iimpi/iimpi-2020a.eb.old diff --git a/i/intel/intel-2020a.eb b/i/intel/intel-2020a.eb.old similarity index 100% rename from i/intel/intel-2020a.eb rename to i/intel/intel-2020a.eb.old diff --git a/l/libxc/libxc-4.3.4-intel-2020a.eb b/l/libxc/libxc-4.3.4-intel-2020a.eb index 3b03ab37..a2513d85 100644 --- a/l/libxc/libxc-4.3.4-intel-2020a.eb +++ b/l/libxc/libxc-4.3.4-intel-2020a.eb @@ -19,8 +19,8 @@ patches = [ ] builddependencies = [ - ('CMake', '3.16.2', '', True), - ('Perl', '5.30.0', '', ('GCCcore', '8.3.0')), + ('CMake', '3.16.4'), + ('Perl', '5.30.2'), ] separate_build_dir = True diff --git a/m/METIS/METIS-5.1.0-intel-2020a.eb b/m/METIS/METIS-5.1.0-intel-2020a.eb index 652f8210..0b3b6709 100644 --- a/m/METIS/METIS-5.1.0-intel-2020a.eb +++ b/m/METIS/METIS-5.1.0-intel-2020a.eb @@ -1,3 +1,5 @@ +# IT41 + name = 'METIS' version = '5.1.0' @@ -18,7 +20,7 @@ source_urls = [ # We use 32bit for indices and 64bit for content patches = ['METIS-5.1.0-use-doubles.patch'] -builddependencies = [('CMake', '3.16.2', '', True)] +builddependencies = [('CMake', '3.16.4')] configopts = ['', 'shared=1'] diff --git a/m/Molden/Molden-6.3-intel-2020a.eb b/m/Molden/Molden-6.3-intel-2020a.eb index 4065d382..8fe84c03 100644 --- a/m/Molden/Molden-6.3-intel-2020a.eb +++ b/m/Molden/Molden-6.3-intel-2020a.eb @@ -1,5 +1,5 @@ # IT4Innovations 2020 -# LK +# LK / JH 2020 easyblock = 'MakeCp' @@ -17,7 +17,7 @@ source_urls = ['ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/'] sources = ['%(namelower)s%(version)s.tar.gz'] dependencies = [ - ('X11', '20190717', '', ('GCCcore', '8.3.0')), + ('X11', '20200222'), ] buildopts = 'CC="$CC" FC="$F90" molden' diff --git a/n/netCDF/netCDF-4.7.3-intel-2020a.eb b/n/netCDF/netCDF-4.7.3-intel-2020a.eb index d2ca532c..9dbc298d 100644 --- a/n/netCDF/netCDF-4.7.3-intel-2020a.eb +++ b/n/netCDF/netCDF-4.7.3-intel-2020a.eb @@ -18,7 +18,7 @@ source_urls = [ dependencies = [ ('HDF5', '1.10.6'), - ('cURL', '7.65.3', '', True), + ('cURL', '7.69.1'), ('Szip', '2.1.1'), ] diff --git a/n/networkx/networkx-2.4-intel-2020a-Python-3.8.2.eb b/n/networkx/networkx-2.4-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000..37e0bbb3 --- /dev/null +++ b/n/networkx/networkx-2.4-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,28 @@ +# JH 2020 + +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb b/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb new file mode 100644 index 00000000..94b93713 --- /dev/null +++ b/o/OpenFOAM/OpenFOAM-v2006-intel-2020a.eb @@ -0,0 +1,42 @@ +# JH 2020 WIP + + +name = 'OpenFOAM' +version = 'v2006' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + 'OpenFOAM-%(version)s-cleanup.patch', +] +checksums = [ + '30c6376d6f403985fc2ab381d364522d1420dd58a42cb270d2ad86f8af227edc', # OpenFOAM-v2006.tgz + 'cb3c6d26569cf11d22941963acb9741238fe829f21b452506a51a71b5c42ae84', # OpenFOAM-v2006-cleanup.patch +] + +dependencies = [ + ('libreadline', '8.0'), + ('ncurses', '6.1'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.0.9'), + ('CGAL', '4.14.3', '-Python-3.8.2'), + ('ParaView', '5.8.0', '-Python-3.8.2-mpi'), +] + +builddependencies = [ + ('Bison', '3.5.3'), + ('CMake', '3.16.4'), + ('flex', '2.6.4'), +] + +moduleclass = 'cae' diff --git a/p/PETSc/PETSc-3.12.4-intel-2020a.eb b/p/PETSc/PETSc-3.12.4-intel-2020a.eb index 778b2808..64865e02 100644 --- a/p/PETSc/PETSc-3.12.4-intel-2020a.eb +++ b/p/PETSc/PETSc-3.12.4-intel-2020a.eb @@ -24,7 +24,7 @@ checksums = [ '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch ] -builddependencies = [('CMake', '3.16.2', '', True)] +builddependencies = [('CMake', '3.16.4')] dependencies = [ ('Boost', '1.72.0'), diff --git a/p/PSI4/PSI4-1.3.2-intel-2020a-Py-3.8.2.eb b/p/PSI4/PSI4-1.3.2-intel-2020a-Py-3.8.2.eb new file mode 100644 index 00000000..4dfac5af --- /dev/null +++ b/p/PSI4/PSI4-1.3.2-intel-2020a-Py-3.8.2.eb @@ -0,0 +1,57 @@ +# JH 2020 + +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + local_computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/psi4/psi4/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['PSI4-1.3.2_fix_cmake_release.patch'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + # PCMSolver recent versions fail with recent intel local_compilers. + # Tried with intel/201{7,8}b, and versions 1.1.12, and 1.2.1 + # See in more details: https://github.com/PCMSolver/pcmsolver/issues/159 + # ('PCMSolver', '1.2.1'), + ('CheMPS2', '1.8.9'), + ('HDF5', '1.10.6', '', ('iimpi', '2020a')), + # Tests are failing with pytest 3.9.2 + ('pytest', '6.0.1', versionsuffix), + ('networkx', '2.4', versionsuffix), + ('deepdiff', '4.0.6', versionsuffix), +] + +builddependencies = [ + ('CMake', '3.16.4'), + # Perl needed for the ctest test suite during the installation, not for the pytest test suite after the installation + # ('Perl', '5.28.0'), +] + +configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' +# Install python mudule to the standard location instead of lib +configopts += '-DPYMOD_INSTALL_LIBDIR=/python3.7/site-packages ' +# Add bundled (downloaded) packages +# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore +configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON -DENABLE_CheMPS2=ON ' + +# runtest uses ctest, and some of the thests have to be manually local_compared +# to the reference output (those tests are marked failed) +# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) +# runtest = '-L smoke' +runtest = False + +modextrapaths = {'PYTHONPATH': 'lib/python3.7/site-packages'} + +moduleclass = 'chem' diff --git a/p/pytest/pytest-6.0.1-Python-3.7.8.eb b/p/pytest/pytest-6.0.1-Python-3.7.8.eb new file mode 100644 index 00000000..99c07663 --- /dev/null +++ b/p/pytest/pytest-6.0.1-Python-3.7.8.eb @@ -0,0 +1,29 @@ +# JH 2020 + +easyblock = 'PythonPackage' + +name = 'pytest' +version = '6.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = 'Simple powerful testing with Python' + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +#download_dep_fail = True +use_pip = False + +dependencies = [ + ('Python', '3.7.8'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.7/site-packages/%(name)s-%(version)s-py3.7.egg'], +} + +moduleclass = 'python' diff --git a/p/pytest/pytest-6.0.1-Python-3.8.2.eb b/p/pytest/pytest-6.0.1-Python-3.8.2.eb new file mode 100644 index 00000000..42a2f1a1 --- /dev/null +++ b/p/pytest/pytest-6.0.1-Python-3.8.2.eb @@ -0,0 +1,29 @@ +# JH 2020 + +easyblock = 'PythonPackage' + +name = 'pytest' +version = '6.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = 'Simple powerful testing with Python' + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +#download_dep_fail = True +use_pip = False + +dependencies = [ + ('Python', '3.8.2'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.8/site-packages/%(name)s-%(version)s-py3.8.egg'], +} + +moduleclass = 'python' diff --git a/q/QMCPACK/QMCPACK-3.9.1-intel-2020a.eb b/q/QMCPACK/QMCPACK-3.9.1-intel-2020a.eb index eb2a6ad3..8297517f 100644 --- a/q/QMCPACK/QMCPACK-3.9.1-intel-2020a.eb +++ b/q/QMCPACK/QMCPACK-3.9.1-intel-2020a.eb @@ -1,4 +1,5 @@ # IT4Innovations 2020 +# JH 2020 easyblock = 'CMakeMake' @@ -16,11 +17,12 @@ source_urls = ['https://github.com/QMCPACK/qmcpack/archive/'] sources = ['v%(version)s.tar.gz'] dependencies = [ - ('CMake', '3.16.2', '', True), - ('libxml2', '2.9.9', '', True), + ('CMake', '3.16.4'), + ('libxml2', '2.9.10'), ('Boost', '1.72.0'), - ('HDF5', '1.10.6'), - ('h5py', '2.10.0', '-Py-3.7'), + ('HDF5', '1.10.6', '', ('iimpi', '2020a')), + ('Python', '3.8.2'), + ('h5py', '2.10.0'), ] separate_build_dir = True diff --git a/r/RELION/RELION-3.1.0-intel-2020a.eb b/r/RELION/RELION-3.1.0-intel-2020a.eb index 4a77ead2..fb26146f 100644 --- a/r/RELION/RELION-3.1.0-intel-2020a.eb +++ b/r/RELION/RELION-3.1.0-intel-2020a.eb @@ -18,11 +18,11 @@ sources = ['%(version)s.tar.gz'] patches = ['fltk-ftp.patch'] builddependencies = [ - ('CMake', '3.16.2'), + ('CMake', '3.16.4'), ] dependencies = [ - ('LibTIFF', '4.1.0', '', ('GCCcore', '8.3.0')), + ('LibTIFF', '4.1.0'), ] configopts = "-DMKLFFT=ON -DFORCE_OWN_FLTK=ON " diff --git a/s/SCOTCH/SCOTCH-6.0.9-foss-2020a.eb b/s/SCOTCH/SCOTCH-6.0.9-foss-2020a.eb index ae3ce4c2..b3fea7e8 100644 --- a/s/SCOTCH/SCOTCH-6.0.9-foss-2020a.eb +++ b/s/SCOTCH/SCOTCH-6.0.9-foss-2020a.eb @@ -17,4 +17,7 @@ dependencies = [ ('zlib', '1.2.11'), ] +# https://support.it4i.cz/rt/Ticket/Display.html?id=23817 +threadedmpi = False + moduleclass = 'math' diff --git a/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.7.8.eb b/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.7.8.eb new file mode 100644 index 00000000..03910775 --- /dev/null +++ b/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020a-Python-3.7.8.eb @@ -0,0 +1,54 @@ +# JH 2020 + +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2020.03' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.7.8'), + ('pybind11', '2.4.3', versionsuffix), # required by scipy +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# order is important! +exts_list = [ + ('numpy', '1.18.3', { + 'patches': ['numpy-1.18.2-mkl.patch'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['e46e2384209c91996d5ec16744234d1c906ab79a701ce1a26155c9ec890b8dc8'], + }), + ('scipy', '1.4.1', { + 'patches': ['scipy-1.4.1-fix-pthread.patch'], + 'checksums': [ + 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz + '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch + ], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('pandas', '1.0.3', { + 'checksums': ['32f42e322fb903d0e189a4c10b75ba70d90958cc4f66a1781ed027f1a1d14586'], + }), + ('mpmath', '1.1.0', { + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' diff --git a/s/Score-P/Score-P-6.0-intel-2020a.eb b/s/Score-P/Score-P-6.0-intel-2020a.eb index 0d6a1815..474ed4b2 100644 --- a/s/Score-P/Score-P-6.0-intel-2020a.eb +++ b/s/Score-P/Score-P-6.0-intel-2020a.eb @@ -23,8 +23,8 @@ dependencies = [ # ('Cube', '4.4.4'), # internal build ('OPARI2', '2.0.5'), ('OTF2', '2.2'), - ('PAPI', '5.7.0'), - ('PDT', '3.25'), + ('PAPI', '6.0.0'), + ('PDT', '3.25.1'), ] configopts = '--enable-shared' diff --git a/s/SuiteSparse/SuiteSparse-5.6.0-intel-2020a-METIS-5.1.0.eb b/s/SuiteSparse/SuiteSparse-5.6.0-intel-2020a-METIS-5.1.0.eb index c59aa840..edf95c30 100644 --- a/s/SuiteSparse/SuiteSparse-5.6.0-intel-2020a-METIS-5.1.0.eb +++ b/s/SuiteSparse/SuiteSparse-5.6.0-intel-2020a-METIS-5.1.0.eb @@ -1,4 +1,4 @@ -# IT4Innovations 2020 +# JH 2020 name = 'SuiteSparse' version = '5.6.0' @@ -15,7 +15,7 @@ source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] sources = ['v%(version)s.tar.gz'] checksums = ['76d34d9f6dafc592b69af14f58c1dc59e24853dcd7c2e8f4c98ffa223f6a1adb'] -builddependencies = [('CMake', '3.16.2', '', True)] +builddependencies = [('CMake', '3.16.4')] dependencies = [('METIS', local_metis_ver)] diff --git a/u/UCX/UCX-1.8.1-GCC-9.3.0.eb b/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb similarity index 59% rename from u/UCX/UCX-1.8.1-GCC-9.3.0.eb rename to u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb index 1e6a089a..3370594c 100644 --- a/u/UCX/UCX-1.8.1-GCC-9.3.0.eb +++ b/u/UCX/UCX-1.8.0-GCCcore-9.3.0.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' name = 'UCX' -version = '1.8.1' +version = '1.8.0' homepage = 'http://www.openucx.org/' description = """Unified Communication X @@ -12,36 +12,48 @@ An open-source production grade communication framework for data centric and high-performance applications """ -toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] sources = ['%(namelower)s-%(version)s.tar.gz'] - patches = [ + 'UCX-1.7.0_binutils_2.34_api_fix.patch', 'UCX-1.8.0_fix-undefined-symbol.patch', ] +checksums = [ + 'e400f7aa5354971c8f5ac6b881dc2846143851df868088c37d432c076445628d', # ucx-1.8.0.tar.gz + 'c09ebe4d734d520ae23f56d95ba0b91e464a42ccbaf435675424515ebd3fa3a9', # UCX-1.7.0_binutils_2.34_api_fix.patch + 'eb757242ab3eecd8a851f329cb4baf3c64d46788ab61675f29ab4cc6a0274a45', # UCX-1.8.0_fix-undefined-symbol.patch +] builddependencies = [ - ('pkg-config', '0.29.2', '', True), + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), ] osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] dependencies = [ - ('numactl', '2.0.12'), + ('numactl', '2.0.13'), ] +preconfigopts = 'autoreconf && ' configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' configopts += '--without-java --disable-doxygen-doc ' buildopts = 'V=1' -sanity_check_commands = ["ucx_info -d"] - sanity_check_paths = { 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], 'dirs': ['include', 'lib', 'share'] } +sanity_check_commands = ["ucx_info -d"] + +modextravars = { + 'UCX_TLS': 'rc,ud,sm,self', +} + moduleclass = 'lib' diff --git a/u/UCX/UCX-1.8.1-GCCcore-8.3.0.eb b/u/UCX/UCX-1.8.1-GCCcore-8.3.0.eb deleted file mode 100644 index d4e4dc7b..00000000 --- a/u/UCX/UCX-1.8.1-GCCcore-8.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -# IT4Innovations 2020 -# LK - -easyblock = 'ConfigureMake' - -name = 'UCX' -version = '1.8.1' - -homepage = 'http://www.openucx.org/' -description = """Unified Communication X -An open-source production grade communication framework for data centric -and high-performance applications -""" - -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] - -patches = [ - 'UCX-1.8.0_fix-undefined-symbol.patch', -] - -builddependencies = [ - ('pkg-config', '0.29.2', '', True), - ('binutils', '2.32'), -] - -osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] - -dependencies = [ - ('numactl', '2.0.12'), -] - -configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' -configopts += '--without-java --disable-doxygen-doc ' - -buildopts = 'V=1' - -sanity_check_commands = ["ucx_info -d"] - -sanity_check_paths = { - 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], - 'dirs': ['include', 'lib', 'share'] -} - -moduleclass = 'lib' diff --git a/v/VTK/VTK-8.2.0-intel-2020a-Py-3.7.eb b/v/VTK/VTK-8.2.0-intel-2020a-Python-3.7.8.eb similarity index 91% rename from v/VTK/VTK-8.2.0-intel-2020a-Py-3.7.eb rename to v/VTK/VTK-8.2.0-intel-2020a-Python-3.7.8.eb index 35c1bc80..73f56235 100644 --- a/v/VTK/VTK-8.2.0-intel-2020a-Py-3.7.eb +++ b/v/VTK/VTK-8.2.0-intel-2020a-Python-3.7.8.eb @@ -4,7 +4,7 @@ easyblock = 'CMakeMake' name = 'VTK' version = '8.2.0' -versionsuffix = '-Py-3.7' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.vtk.org' description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for @@ -28,17 +28,17 @@ checksums = [ '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b', # vtk-version.egg-info ] -builddependencies = [('CMake', '3.16.2', '', True)] +builddependencies = [('CMake', '3.16.4')] dependencies = [ - ('Py', '3.7', '', True), - ('XZ', '5.2.4'), + ('Python', '3.7.8'), + ('XZ', '5.2.5'), ('HDF5', '1.10.6'), ('netCDF', '4.7.3'), - ('libGLU', '9.0.1', '-Mesa-19.2.1'), - ('X11', '20190717'), - ('numpy', '1.18.1', versionsuffix, True), - ('mpi4py', '3.0.1', versionsuffix), + ('libGLU', '9.0.1'), + ('Mesa', '20.0.2'), + ('X11', '20200222'), + ('SciPy-bundle', '2020.03', versionsuffix), ] separate_build_dir = True