new file: a/arpack-ng/arpack-ng-3.8.0-intel-2020b.eb

new file: b/BerkeleyGW/BerkeleyGW-2.1.0-intel-2020b-Python-3.8.6.eb new file: b/BerkeleyGW/BerkeleyGW-2.1.0_missing_file.patch new file: b/BerkeleyGW/BerkeleyGW-2.1.0_tests.patch new file: d/DFTB+/DFTB+-21.1-intel-2020b-Python-3.8.6.eb new file: d/DFTB+/config.cmake-MANUAL-INSTALATION.patch new file: d/dftd3-lib/dftd3-lib-0.9.2-GCC-10.2.0.eb new file: d/dftd3-lib/dftd3-lib-0.9.2_fix-extras-syntax.patch new file: e/ELPA/ELPA-2019.11.001-intel-2020b.eb new file: h/HDF5/HDF5-1.10.6-iimpi-2020b.eb new file: h/h5py/h5py-2.10.0-intel-2020b-Python-3.8.6.eb new file: h/hypothesis/hypothesis-6.13.1-GCC-10.2.0.eb new file: i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb new file: i/intel-compilers/intel-compilers-2021.2.0.eb new file: n/Newton-X/Newton-X-2.2-B09-intel-2020b.eb new file: n/Newton-X/newton-x-2.2.patch new file: p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb new file: p/pybind11/pybind11-2.4.3-GCC-10.2.0-Python-3.8.6.eb new file: p/pybind11/pybind11-2.6.0-GCC-10.2.0-Python-3.8.6.eb new file: s/Schrodinger/Schrodinger_2021-2_Linux-x86_64.eb new file: s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020b-Python-3.8.6.eb new file: s/SciPy-bundle/SciPy-bundle-2021.05-intel-2020b.eb
2025-04-07 23:42:12 +01:00 · 2021-06-16 07:42:30 +02:00 · 2021-06-16 07:42:30 +02:00 · 747221f326
commit 747221f326
parent 0c4c927907
22 changed files with 942 additions and 0 deletions
--- a/a/arpack-ng/arpack-ng-3.8.0-intel-2020b.eb
+++ b/a/arpack-ng/arpack-ng-3.8.0-intel-2020b.eb
@ -0,0 +1,38 @@
+# IT$Innovations 2021
+# LK
+
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = "3.8.0"
+
+homepage = 'https://github.com/opencollab/arpack-ng'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+github_account = 'opencollab'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+checksums = ['ada5aeb3878874383307239c9235b716a8a170c6d096a6625bfd529844df003d']
+
+builddependencies = [
+    ('Autotools', '20200321'),
+    ('pkg-config', '0.29.2'),
+]
+
+dependencies = [
+    ('Eigen', '3.3.8')
+]
+
+preconfigopts = "sh bootstrap && "
+configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib64/libarpack.la", "lib64/libarpack.%s" % SHLIB_EXT,
+              "lib64/libparpack.la", "lib64/libparpack.%s" % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'numlib'
--- a/b/BerkeleyGW/BerkeleyGW-2.1.0-intel-2020b-Python-3.8.6.eb
+++ b/b/BerkeleyGW/BerkeleyGW-2.1.0-intel-2020b-Python-3.8.6.eb
@ -0,0 +1,37 @@
+# IT4Innovations 2021
+# LK
+
+name = 'BerkeleyGW'
+version = '2.1.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://www.berkeleygw.org'
+description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle
+ properties and the optical responses of a large variety of materials from bulk periodic crystals to
+ nanostructures such as slabs, wires and molecules."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'usempi': True, 'openmp': True, 'precise': True}
+
+source_urls = ['https://berkeley.box.com/shared/static/']
+sources = [{'download_filename': 'ze3azi5vlyw7hpwvl9i5f82kaiid6g0x.gz', 'filename': SOURCE_TAR_GZ}]
+patches = [
+    'BerkeleyGW-2.1.0_missing_file.patch',
+    'BerkeleyGW-2.1.0_tests.patch',
+]
+checksums = [
+    '31f3b643dd937350c3866338321d675d4a1b1f54c730b43ad74ae67e75a9e6f2',  # BerkeleyGW-2.1.0.tar.gz
+    '3689262976b873d65ffce4c89a5dc8ef5731914a5b71eadacba244750fc6b7ae',  # BerkeleyGW-2.1.0_missing_file.patch
+    '340bb854ae78cf5a1ce7b277f1c16dc3140ef9dbc39715082097b632858ef633',  # BerkeleyGW-2.1.0_tests.patch
+]
+
+dependencies = [
+    ('ELPA', '2019.11.001'),
+    ('Python', '3.8.6'),
+    ('h5py', '2.10.0', versionsuffix),
+]
+
+# two tests failing (Si-EPM_subspace_cplx) with the intel toolchain, a few more if on skylake
+runtest = False
+
+moduleclass = 'phys'
--- a/b/BerkeleyGW/BerkeleyGW-2.1.0_missing_file.patch
+++ b/b/BerkeleyGW/BerkeleyGW-2.1.0_missing_file.patch
@ -0,0 +1,13 @@
+* manual.html is missing from the distribution
+author: Miguel Dias Costa (National University of Singapore)
+--- Makefile.orig	2018-06-18 12:12:48.081168468 +0800
+++ Makefile	2018-06-18 12:13:02.795191541 +0800
+@@ -124,7 +124,7 @@
+ # install cannot work on a whole directory
+ 	cp -rf examples  $(INSTDIR)/share/BerkeleyGW/
+ 	cp -rf testsuite $(INSTDIR)/share/BerkeleyGW/
+-	install manual.html $(INSTDIR)/share/BerkeleyGW/
+	#install manual.html $(INSTDIR)/share/BerkeleyGW/
+ else
+ 	$(error Error: Please define installation prefix INSTDIR via 'make install INSTDIR='.)
+ endif
--- a/b/BerkeleyGW/BerkeleyGW-2.1.0_tests.patch
+++ b/b/BerkeleyGW/BerkeleyGW-2.1.0_tests.patch
@ -0,0 +1,42 @@
+* enable parallel tests
+* allow test scripts to inherit environment
+* slightly raise tolerance in one test
+author: Miguel Dias Costa (National University of Singapore)
+--- Makefile.orig	2019-07-23 17:40:16.489733901 +0800
+++ Makefile	2019-07-23 17:40:33.656497133 +0800
+@@ -157,7 +157,7 @@
+ endif
+ 
+ check: all
+-	cd testsuite && $(MAKE) check
+	cd testsuite && $(MAKE) check && $(MAKE) check-parallel
+ 
+ check-save: all
+ 	cd testsuite && $(MAKE) check-save
+--- testsuite/run_testsuite.sh.orig	2019-07-25 14:48:12.000000000 +0800
+++ testsuite/run_testsuite.sh	2019-07-25 14:47:50.000000000 +0800
+@@ -1,4 +1,4 @@
+-#!/bin/bash -l
+#!/bin/bash
+ #
+ # Copyright (C) 2005-2009 Heiko Appel, David Strubbe
+ #
+--- MeanField/Utilities/mf_convert_wrapper.sh.orig	2019-07-26 09:52:27.648341000 +0800
+++ MeanField/Utilities/mf_convert_wrapper.sh	2019-07-26 09:52:39.922114228 +0800
+@@ -1,4 +1,4 @@
+-#!/bin/bash -l
+#!/bin/bash
+ 
+ # David Strubbe, October 2010
+ # Wrapper for mf_convert.x
+--- testsuite/GaAs-EPM/GaAs.test.orig	2019-07-26 10:45:19.798520000 +0800
+++ testsuite/GaAs-EPM/GaAs.test	2019-07-26 10:45:37.753775275 +0800
+@@ -32,7 +32,7 @@
+ Output : WFN.out
+ Input  : WFN.in PIPE
+ 
+-Precision : 8e-15
+Precision : 9e-15
+ match ; Eigenvalue  1 at k-pt 1   ; GREP(WFN.out,   "kpoint          1", 2,  1); -0.2710614199849328
+ match ; Eigenvalue 10 at k-pt 1   ; GREP(WFN.out,   "kpoint          1", 2, 10);  1.2565373697755460
+ match ; Eigenvalue 18 at k-pt 2   ; GREP(WFN.out,   "kpoint          2", 2, 18);  2.1322637363008994
--- a/d/DFTB+/DFTB+-21.1-intel-2020b-Python-3.8.6.eb
+++ b/d/DFTB+/DFTB+-21.1-intel-2020b-Python-3.8.6.eb
@ -0,0 +1,74 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'CMakeMake'
+
+name = 'DFTB+'
+version = '21.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://www.dftb-plus.info'
+description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package.
+It is based on the Density Functional Tight Binding (DFTB) method, containing
+almost all of the useful extensions which have been developed for the DFTB
+framework so far.  Using DFTB+ you can carry out quantum mechanical simulations
+like with ab-initio density functional theory based packages, but in an
+approximate way gaining typically around two order of magnitude in speed."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'lowopt': True, 'optarch': False}
+
+local_external_dir = '%%(builddir)s/dftbplus-%%(version)s/external/%s/origin/'
+local_external_extract = 'mkdir -p %s && tar -C %s' % (local_external_dir, local_external_dir)
+local_external_extract += ' --strip-components=1 -xzf %%s'
+
+sources = [
+    {
+        # DFTB+ source code
+        'source_urls': ['https://github.com/dftbplus/dftbplus/archive'],
+        'download_filename': '%(version)s.tar.gz',
+        'filename': SOURCE_TAR_GZ,
+    },
+    {
+        # Slater-Koster (slakos) data for testing
+        'source_urls': ['https://github.com/dftbplus/testparams/archive'],
+        'download_filename': 'd0ea16df2b56d14c7c3dc9329a8d3bac9fea50a0.tar.gz',
+        'filename': 'slakos-data-%(version)s.tar.gz',
+        'extract_cmd': local_external_extract % ('slakos', 'slakos'),
+    },
+]
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.03', versionsuffix),
+    ('arpack-ng', '3.8.0'),
+    ('dftd3-lib', '0.9.2', '', ('GCC', '10.2.0')),
+]
+
+# Link to Arpack
+local_makeopts = ' WITH_ARPACK=1 ARPACK_LIBS="-L$EBROOTARPACKMINNG/lib -larpack" ARPACK_NEEDS_LAPACK=1'
+# Use DFTD3 from EB
+local_makeopts += ' WITH_DFTD3=1 COMPILE_DFTD3=0 DFTD3_INCS="-I$EBROOTDFTD3MINLIB/include"'
+local_makeopts += ' DFTD3_LIBS="-L$EBROOTDFTD3MINLIB/lib -ldftd3"'
+
+buildopts = local_makeopts
+
+#runtest = 'test' + local_makeopts
+
+installopts = 'INSTALLDIR="%(installdir)s"'
+
+sanity_check_paths = {
+    'files': ['bin/' + x for x in ['dftb+', 'dp_bands', 'dp_dos', 'gen2cif', 'gen2xyz', 'makecube',
+                                   'modes', 'repeatgen', 'straingen', 'waveplot', 'xyz2gen']],
+    'dirs': ['lib/python%(pyshortver)s/site-packages']
+}
+
+sanity_check_commands = [('python', '-c "import dptools"')]
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+moduleclass = 'phys'
--- a/d/DFTB+/config.cmake-MANUAL-INSTALATION.patch
+++ b/d/DFTB+/config.cmake-MANUAL-INSTALATION.patch
@ -0,0 +1,133 @@
+#
+# Global architecture independent build settings
+#
+
+#set(CMAKE_BUILD_TYPE "Debug" CACHE STRING "Build type (Release|RelWithDebInfo|Debug|MinSizeRel)")
+# CMAKE_BUILD_TYPE is commented out in order to allow for multi-configuration builds. It will
+# automatically default to RelWithDebInfo if used in a single configuration build. Uncomment or
+# override it only if you want a non-default single configuration build.
+
+option(WITH_OMP "Whether OpenMP thread parallisation should be enabled" TRUE)
+
+option(WITH_MPI "Whether DFTB+ should support MPI-parallelism" FALSE)
+# If you build an MPI-parallised binary, consider to set WITH_OMP (OpenMP thread parallelisaton) to
+# FALSE unless you want hybrid parallelisation (for experts only).
+
+option(WITH_ELSI "Whether DFTB+ with MPI-parallelism should use the ELSI libraries" FALSE)
+# Works only with MPI-parallel build.
+
+option(WITH_GPU "Whether DFTB+ should support GPU-acceleration via the MAGMA-library" FALSE)
+
+option(WITH_TRANSPORT "Whether transport via libNEGF should be included." TRUE)
+# Works only when building static libraries (see option BUILD_SHARED_LIBS)
+
+option(WITH_POISSON "Whether the Poisson-solver should be included" ${WITH_TRANSPORT})
+# The Poisson-solver is mostly used in transport calculations only. Enable this option
+# if you want to use it in a non-transport build. Note, the Poisson-solver is not
+# multi-instance safe and is therefore not allowed, if WITH_API (see below) is on.
+
+option(WITH_SOCKETS "Whether socket communication should be allowed for" FALSE)
+
+option(WITH_ARPACK "Whether the ARPACK library should be included (needed for TD-DFTB)" TRUE)
+# Works only with non-MPI (serial) build, needed for Casida linear response
+
+option(WITH_DFTD3 "Whether the DFTD3 library should be included" TRUE)
+# NOTE: Due to the license of the DFTD3 library, the combined code must be distributed under the
+# GPLv3 license (as opposed to the LGPLv3 license of the DFTB+ package)
+
+option(WITH_MBD "Whether DFTB+ should be built with many-body-dispersion support" FALSE)
+
+option(WITH_PLUMED "Whether metadynamics via the PLUMED2 library should be allowed for" FALSE)
+
+option(WITH_API "Whether public API should be included and the DFTB+ library installed" FALSE)
+# Turn this on, if you want to use the DFTB+ library to integrate DFTB+ into other software
+# packages. (Otherwise only a stripped down version of the library without the public API is built.)
+# This will also install necessary include and module files and further libraries needed to link the
+# DFTB+ library.
+
+option(INSTANCE_SAFE_BUILD "Whether build should support concurrent DFTB+ instances" FALSE)
+# Turn this on, if you want to create multiple concurrent DFTB+ instances **within one process** via
+# the API. This option will ensure that only components without writable global variables are
+# included in the build, so that multiple instances can safely coexist. There are components
+# (e.g. Poisson, DFTD-D3, ARPACK) which can not be included if this option is on. Note, this option
+# is not relevant for the standalone DFTB+ binary, only for the API (if WITH_API had been turned
+# on).
+
+option(WITH_PYTHON "Whether the Python components of DFTB+ should be tested and installed" TRUE)
+
+option(BUILD_SHARED_LIBS "Whether the libraries built should be shared" FALSE)
+# Turn this on, if the DFTB+ library (and other compiled libraries) should be shared libraries and
+# dynamically linked to their applications. This results in smaller applications, but the libraries
+# must be present at run-time (and the correct LD_LIBRARY_PATH environment variable must be set, so
+# that they can be found by the operating system). If you want use the DFTB+ library from other
+# software packages (see WITH_API option above), they may also require a shared library (e.g.
+# calling DFTB+ functions from Python or Julia).
+
+
+#
+# Test environment settings
+#
+set(TEST_MPI_PROCS "1" CACHE STRING "Nr. of MPI processes used for testing")
+
+set(TEST_OMP_THREADS "1" CACHE STRING "Nr. of OpenMP-threads used for testing")
+
+# Command line used to launch the test code.
+# The escaped variables (\${VARIABLE}) will be substituted by the corresponding CMake variables.
+if(WITH_MPI)
+  set(TEST_RUNNER_TEMPLATE "env OMP_NUM_THREADS=\${TEST_OMP_THREADS} mpiexec -n \${TEST_MPI_PROCS}"
+    CACHE STRING "How to run the tests")
+else()
+  set(TEST_RUNNER_TEMPLATE "env OMP_NUM_THREADS=\${TEST_OMP_THREADS}" CACHE STRING
+    "How to run the tests")
+  set(MODES_RUNNER_TEMPLATE "env OMP_NUM_THREADS=\${TEST_OMP_THREADS}" CACHE STRING
+    "How to run the modes code for tests")
+endif()
+
+# Turn it on to include the unit tests (needes FyTest)
+option(WITH_UNIT_TESTS "Whether the unit tests should be built" FALSE)
+
+
+#
+# Installation options
+#
+set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}/_install" CACHE STRING
+  "Directory to install the compiled code into")
+
+set(INSTALL_INCLUDEDIR "dftbplus" CACHE PATH
+  "Name of the project specific sub-folder within the install folder for include files")
+
+set(INSTALL_MODULEDIR "${INSTALL_INCLUDEDIR}/modfiles" CACHE PATH
+  "Installation directory for Fortran module files (within the install folder for include files)")
+
+set(PKGCONFIG_LANGUAGE "Fortran" CACHE STRING
+  "Compiler and Linker language to assume when creating the pkg-config export file (C or Fortran)")
+# The pkg-config export file (lib/pkgconfig/dftbplus.pc) contains the compiler and linker options
+# needed to link the DFTB+ library to an application. (It can be queried with the pkg-config tool.)
+# Depending on the language setting ("C" or "Fortran") you would get the flags for the case of using
+# that compiler for the linking.
+
+
+#
+# Advanced options (e.g. for developers and packagers)
+#
+
+#set(TOOLCHAIN "gnu" CACHE STRING "Prefix of the toolchain file to be read from the sys/ folder")
+# Uncomment and set it if you want to override the automatic, compiler based toolchain file
+# selection.
+
+
+set(HYBRID_CONFIG_METHODS "Submodule;Find;Fetch" CACHE STRING
+  "Configuration methods to try in order to satisfy hybrid dependencies")
+#
+# This list can be used to control how hybrid dependencies (external dependencies which can
+# optionally be built during the build process) are configured. The listed methods are applied in
+# the specified order. Following methods are available:
+#
+# Submodule: Use the source in external/*/origin and build the dependency as part of the build
+#     process. If the source is not present, try to retrieve it via the 'git submodule' command
+#     (provided the source tree is a git repository and git is available)
+#
+# Find: Find the dependency as an already installed package in the system.
+#
+# Fetch: Fetch the source into the build folder and build the dependency as part of the build
+#     process (works also in cases where the source tree is not a Git repository)
--- a/d/dftd3-lib/dftd3-lib-0.9.2-GCC-10.2.0.eb
+++ b/d/dftd3-lib/dftd3-lib-0.9.2-GCC-10.2.0.eb
@ -0,0 +1,38 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'MakeCp'
+
+name = 'dftd3-lib'
+version = '0.9.2'
+
+homepage = 'https://github.com/dftbplus/dftd3-lib'
+description = """This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers.
+The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been
+converted to free format and encapsulated into modules."""
+
+toolchain = {'name': 'GCC', 'version': '10.2.0'}
+toolchainopts = {'pic': True}
+
+github_account = 'dftbplus'
+source_urls = [GITHUB_SOURCE]
+sources = ['%(version)s.tar.gz']
+patches = ['dftd3-lib-%(version)s_fix-extras-syntax.patch']
+
+parallel = 1
+
+buildopts = 'FC="$FC" FCFLAGS="$FCFLAGS" LNFLAGS="$LDFLAGS"'
+
+files_to_copy = [
+    (['prg/dftd3', 'test/testapi'], 'bin'),
+    (['lib/libdftd3.a'], 'lib'),
+    (['lib/*.mod', 'prg/*.mod'], 'include'),
+    (['doc/man.pdf', 'CHANGELOG.rst', 'LICENSE', 'README.rst'], 'share'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/dftd3', 'bin/testapi', 'lib/libdftd3.a'],
+    'dirs': ['include', 'share'],
+}
+
+moduleclass = 'chem'
--- a/d/dftd3-lib/dftd3-lib-0.9.2_fix-extras-syntax.patch
+++ b/d/dftd3-lib/dftd3-lib-0.9.2_fix-extras-syntax.patch
@ -0,0 +1,22 @@
+Fix syntax of extras.f90
+Author: Alex Domingo (Vrije Universiteit Brussel)
+--- prg/extras.f90.orig	2020-04-07 15:53:37.579346000 +0200
+++ prg/extras.f90	2020-04-07 15:53:47.270025090 +0200
+@@ -285,7 +285,7 @@
+     close(11)
+ 
+     write(*,*) 'checksum (Edisp) ',check
+-    if (abs(check-etot).gt.1.d-3)stop'something is weired in adisp'
+    if (abs(check-etot).gt.1.d-3) stop 'something is weired in adisp'
+ 
+     inquire(file='fragment',exist=ex)
+     if (.not.ex) return
+@@ -1746,7 +1746,7 @@
+     close(11)
+ 
+     write(*,*) 'checksum (Edisp) ',check
+-    if (abs(check-etot).gt.1.d-3)stop'something is weired in adisp'
+    if (abs(check-etot).gt.1.d-3) stop 'something is weired in adisp'
+ 
+     deallocate(dist,li)
+     return
--- a/e/ELPA/ELPA-2019.11.001-intel-2020b.eb
+++ b/e/ELPA/ELPA-2019.11.001-intel-2020b.eb
@ -0,0 +1,28 @@
+# IT4Innovations 2021
+# LK
+
+name = 'ELPA'
+version = '2019.11.001'
+
+homepage = 'http://elpa.rzg.mpg.de'
+description = """Eigenvalue SoLvers for Petaflop-Applications ."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['http://elpa.mpcdf.mpg.de/html/Releases/%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+
+preconfigopts = "export FC='mpiifort' && "
+preconfigopts += "export CC='mpicc' && "
+preconfigopts += 'export FCFLAGS="-O3 -xAVX2" && '
+preconfigopts += 'export CFLAGS="-O3 -march=native -mavx2 -mfma -funsafe-loop-optimizations -funsafe-math-optimizations -ftree-vect-loop-version -ftree-vectorize" && '
+preconfigopts += 'export SCALAPACK_LDFLAG=S"-L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread " && '
+preconfigopts += 'export SCALAPACK_FCFLAGS="-I$MKL_HOME/include/intel64/lp64" && '
+configopts = '--enable-option-checking=fatal'
+
+builddependencies = [
+    ('Autotools', '20200321'),
+]
+
+moduleclass = 'math'
--- a/h/HDF5/HDF5-1.10.6-iimpi-2020b.eb
+++ b/h/HDF5/HDF5-1.10.6-iimpi-2020b.eb
@ -0,0 +1,24 @@
+# IT4Innovations 2021
+# LK
+
+name = 'HDF5'
+version = '1.10.6'
+
+homepage = 'https://portal.hdfgroup.org/display/support'
+description = """HDF5 is a data model, library, and file format for storing and managing data.
+ It supports an unlimited variety of datatypes, and is designed for flexible
+ and efficient I/O and for high volume and complex data."""
+
+toolchain = {'name': 'iimpi', 'version': '2020b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5f9a3ee85db4ea1d3b1fa9159352aebc2af72732fc2f58c96a3f0768dba0e9aa']
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('Szip', '2.1.1'),
+]
+
+moduleclass = 'data'
--- a/h/h5py/h5py-2.10.0-intel-2020b-Python-3.8.6.eb
+++ b/h/h5py/h5py-2.10.0-intel-2020b-Python-3.8.6.eb
@ -0,0 +1,40 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'PythonPackage'
+
+name = 'h5py'
+version = '2.10.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://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': '2020b'}
+toolchainopts = {'usempi': True}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+#patches = ['h5py-%(version)s_avoid-mpi-init.patch']
+#checksums = [
+#    '84412798925dc870ffd7107f045d7659e60f5d46d1c70c700375248bf6bf512d',  # h5py-2.10.0.tar.gz
+#    '6bacb71f5d9fbd7bd9a01018d7fe21b067a2317f33c4a7c21fde9cd404c1603f',  # h5py-2.10.0_avoid-mpi-init.patch
+#]
+
+builddependencies = [('pkgconfig', '1.5.1', versionsuffix)]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.03', versionsuffix),
+    ('HDF5', '1.10.6', '', ('iimpi', '2020b')),
+]
+
+use_pip = False
+download_dep_fail = 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 && '
+
+moduleclass = 'data'
--- a/h/hypothesis/hypothesis-6.13.1-GCC-10.2.0.eb
+++ b/h/hypothesis/hypothesis-6.13.1-GCC-10.2.0.eb
@ -0,0 +1,25 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'PythonPackage'
+
+name = 'hypothesis'
+version = '6.13.1'
+
+homepage = "https://github.com/HypothesisWorks/hypothesis"
+description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized
+ by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets
+ you find more bugs in your code with less work."""
+
+toolchain = {'name': 'GCC', 'version': '10.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['074e27e514b305ba0b0c6bc0037faad1abbe2ea641ab4a8ec90e12a5e3238009']
+
+dependencies = [('Python', '3.8.6')]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'tools'
--- a/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb
+++ b/i/impi/impi-2021.2.0-intel-compilers-2021.2.0.eb
@ -0,0 +1,29 @@
+# IT4Innovatios 2021
+# LK
+
+name = 'impi'
+version = '2021.2.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html'
+description = "Intel MPI Library, compatible with MPICH ABI"
+
+toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'}
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17729/']
+sources = ['l_mpi_oneapi_p_%(version)s.215_offline.sh']
+checksums = ['d0d4cdd11edaff2e7285e38f537defccff38e37a3067c02f4af43a3629ad4aa3']
+
+dependencies = [('UCX', '1.10.0')]
+
+modextravars = {
+    'I_MPI_OFI_PROVIDER': 'MLX',
+    'FI_PROVIDER': 'verbs',
+    'I_MPI_CC' : 'icc',
+    'I_MPI_CXX': 'icpc',
+    'I_MPI_F77': 'ifort',
+    'I_MPI_F90': 'ifort',
+    'I_MPI_FC': 'ifort',
+}
+
+moduleclass = 'mpi'
--- a/i/intel-compilers/intel-compilers-2021.2.0.eb
+++ b/i/intel-compilers/intel-compilers-2021.2.0.eb
@ -0,0 +1,45 @@
+# IT4Innovatios 2021
+# LK
+
+name = 'intel-compilers'
+version = '2021.2.0'
+
+homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html'
+description = "Intel C, C++ & Fortran compilers (classic and oneAPI)"
+
+toolchain = SYSTEM
+
+# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html
+sources = [
+    {
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17749/'],
+        'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.118_offline.sh',
+    },
+    {
+        'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/17756/'],
+        'filename': 'l_fortran-compiler_p_%(version)s.136_offline.sh',
+    },
+]
+checksums = [
+    # l_dpcpp-cpp-compiler_p_2021.2.0.118_offline.sh
+    '5d01cbff1a574c3775510cd97ffddd27fdf56d06a6b0c89a826fb23da4336d59',
+    'a62e04a80f6d2f05e67cd5acb03fa58857ee22c6bd581ec0651c0ccd5bdec5a1',  # l_fortran-compiler_p_2021.2.0.136_offline.sh
+]
+
+local_gccver = '10.3.0'
+dependencies = [
+    ('GCCcore', local_gccver),
+    ('binutils', '2.36.1', '', ('GCCcore', local_gccver)),
+]
+
+modextravars = {
+    'CC': 'icc',
+    'CXX': 'icpc',
+    'F90': 'ifort',
+    'F77': 'ifort',
+    'FC': 'ifort',
+    'OPTFLAGS': '-O3 -xHost -ip',
+    'DEBUGFLAGS': '-O0 -g'
+}
+
+moduleclass = 'compiler'
--- a/n/Newton-X/Newton-X-2.2-B09-intel-2020b.eb
+++ b/n/Newton-X/Newton-X-2.2-B09-intel-2020b.eb
@ -0,0 +1,35 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'PackedBinary'
+
+name = 'Newton-X'
+version = '2.2-B09'
+
+homepage = 'https://sourceforge.net/projects/actc'
+description = "ACTC converts independent triangles into triangle strips or fans."
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+
+#source_urls = [https://amubox.univ-amu.fr/s/aBMnEq7dXeZPm2H/download]
+sources = ['nx-2.2-b09.tgz']
+patches = ['newton-x-2.2.patch']
+
+dependencies = [
+   ['GSL', '2.6'],
+]
+
+install_cmd = 'NX-2.2-B09/install/installnx.pl ifort $EBROOTGSL %(installdir)s 0'
+
+sanity_check_paths = {
+    'files': [ 'bin/tplot', 'bin/moldyn.pl', 'bin/plot', 'source/lib/nx_la.pm'],
+    'dirs': ['bin', 'batch', 'docs', 'install', 'source', 'test-nx'],
+}
+
+modextrapaths = {
+   'NX': 'bin',
+   'LIBRARY_PATH': 'source/lib',
+   'LD_LIBRARY_PATH': 'source/lib'
+}
+
+moduleclass = 'chem'
--- a/n/Newton-X/newton-x-2.2.patch
+++ b/n/Newton-X/newton-x-2.2.patch
@ -0,0 +1,70 @@
+--- NX-2.2-B09/install/installnx.pl.orig	2020-03-06 12:35:13.000000000 +0100
+++ NX-2.2-B09/install/installnx.pl	2021-06-08 07:41:44.615480573 +0200
+@@ -22,7 +22,7 @@
+ 
+ # 1) Select compiler
+   #$comp = "ifort"; 
+-  $comp = "gfortran"; 
+  $comp = "$ARGV[0]"; 
+ 
+ # 2) Choose the BLAS/LAPACK variables (_OD will be used for cioverlap_od only)
+   if($comp eq "ifort"){
+@@ -44,8 +44,8 @@
+   }
+ 
+ # 3) Choose GSL paths:
+-  $idgsl="/usr/include/gsl";              # Headers
+-  $ldgsl="/usr/lib";                      # Libraries
+  $idgsl="$ARGV[1]/include/gsl";              # Headers
+  $ldgsl="$ARGV[1]/lib";                      # Libraries
+ 
+ # 4) If necessary (usually it isn't), change the flags for the selected compiler (_OD will be used for cioverlap_od only) 
+   if ($comp eq "ifort"){
+@@ -98,13 +98,14 @@
+ #================================================================
+ #
+ sub create_dir{
+-  print STDOUT "\n Please enter directory for the NEWTON-X installation \n ";
+-  $_ = <STDIN>;
+-  chomp;$_ =~ s/^\s*//;$_ =~ s/\s*$//;
+-  $instd = $_;
+  #print STDOUT "\n Please enter directory for the NEWTON-X installation \n ";
+  #$_ = <STDIN>;
+  #chomp;$_ =~ s/^\s*//;$_ =~ s/\s*$//;
+  $instd = $ARGV[2];
+ 
+   if  (!-s $instd){
+-    $create_d=simple_question("\n This directory seems not to exist - create it? (y/n) ","y");
+    #$create_d=simple_question("\n This directory seems not to exist - create it? (y/n) ","y");
+    $create_d = "y";
+     if ($create_d eq "y"){
+       system("mkdir -p $instd");
+       if  (-s $instd){
+@@ -140,7 +141,7 @@
+   print STDOUT "    [4] Time-dependent overlaps I (CIOVERLAP)\n";
+   print STDOUT "    [5] Time-dependent overlaps II (CIOVERLAP_OD)\n";
+   print STDOUT " Enter comma separated list or dash separated range (<ENTER> for default): ";
+-  $_=<STDIN>;
+  $_=$ARGV[3];
+   chomp;$_ =~ s/^\s*//;$_ =~ s/\s*$//;
+   @list=make_num_sequence($_);
+   if (($_ eq "") or ($_ eq "0")){
+@@ -358,12 +359,12 @@
+ #
+ sub copy_nx{
+   print_STDOUT(" Copying files  ");
+-  copyfiles("$original_dir/../","source",$instd,1);
+-  copyfiles("$original_dir/../","docs",$instd,1);
+-  copyfiles("$original_dir/../","test-nx",$instd,1);
+-  copyfiles("$original_dir/../","batch",$instd,1);
+-  copyfiles("$original_dir/../","install",$instd,1);
+-  copyfiles("$original_dir/../","README.install",$instd,1);
+  copyfiles("$original_dir/NX-2.2-B09/","source",$instd,1);
+  copyfiles("$original_dir/NX-2.2-B09/","docs",$instd,1);
+  copyfiles("$original_dir/NX-2.2-B09/","test-nx",$instd,1);
+  copyfiles("$original_dir/NX-2.2-B09/","batch",$instd,1);
+  copyfiles("$original_dir/NX-2.2-B09/","install",$instd,1);
+  copyfiles("$original_dir/NX-2.2-B09/","README.install",$instd,1);
+ # Create bin directory
+   if (!-e $bin){
+     system("mkdir $bin");
--- a/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb
+++ b/p/pkgconfig/pkgconfig-1.5.1-GCCcore-10.2.0-python.eb
@ -0,0 +1,30 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'PythonPackage'
+
+name = 'pkgconfig'
+version = '1.5.1'
+versionsuffix = '-Python-3.8.6'
+
+homepage = 'https://github.com/matze/pkgconfig'
+description = """pkgconfig is a Python module to interface with the pkg-config command line tool"""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+checksums = ['97bfe3d981bab675d5ea3ef259045d7919c93897db7d3b59d4e8593cba8d354f']
+
+builddependencies = [('binutils', '2.35')]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('pkg-config', '0.29.2'),
+]
+
+use_pip = True
+download_dep_fail = True
+sanity_pip_check = True
+
+moduleclass = 'devel'
--- a/p/pybind11/pybind11-2.4.3-GCC-10.2.0-Python-3.8.6.eb
+++ b/p/pybind11/pybind11-2.4.3-GCC-10.2.0-Python-3.8.6.eb
@ -0,0 +1,30 @@
+# IT4Innovations 2021
+# LK
+
+name = 'pybind11'
+version = '2.4.3'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://pybind11.readthedocs.io'
+description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
+ mainly to create Python bindings of existing C++ code."""
+
+toolchain = {'name': 'GCC', 'version': '10.2.0'}
+
+source_urls = ['https://github.com/pybind/pybind11/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['%(name)s-%(version)s-fix-get-include.patch']
+checksums = [
+    '1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d',  # v2.4.3.tar.gz
+    'b03550f05dcff97eeb3d7f4cd393b0584341ac7a310c89ee120f95e54fdc3125',  # pybind11-2.4.3-fix-get-include.patch
+]
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+    ('Eigen', '3.3.8'),
+]
+dependencies = [('Python', '3.8.6')]
+
+configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python"
+
+moduleclass = 'lib'
--- a/p/pybind11/pybind11-2.6.0-GCC-10.2.0-Python-3.8.6.eb
+++ b/p/pybind11/pybind11-2.6.0-GCC-10.2.0-Python-3.8.6.eb
@ -0,0 +1,26 @@
+# IT4Innovations 2021
+# LK
+
+name = 'pybind11'
+version = '2.6.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://pybind11.readthedocs.io'
+description = """pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa,
+ mainly to create Python bindings of existing C++ code."""
+
+toolchain = {'name': 'GCC', 'version': '10.2.0'}
+
+source_urls = ['https://github.com/pybind/pybind11/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571']
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+    ('Eigen', '3.3.8'),
+]
+dependencies = [('Python', '3.8.6')]
+
+configopts = "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python"
+
+moduleclass = 'lib'
--- a/s/Schrodinger/Schrodinger_2021-2_Linux-x86_64.eb
+++ b/s/Schrodinger/Schrodinger_2021-2_Linux-x86_64.eb
@ -0,0 +1,40 @@
+# IT4Innovations 2021
+# LK
+
+easyblock='Binary'
+
+name = "Schrodinger"
+version = "2021-2"
+versionsuffix = "_Linux-x86_64"
+
+homepage = 'http://www.schrodinger.com/'
+description = """ Schrödinger aims to provide integrated software solutions and services
+ that truly meet its customers’ needs. We want to empower researchers around the world to
+ achieve their goals of improving human health and quality of life through advanced local_computational
+ techniques that transform the way chemists design local_compounds and materials. """
+
+toolchain = SYSTEM
+
+#Schrodinger_Suites_2021-2_Linux-x86_64.tar
+sources = ['%(name)s_Suites_%(version)s%(versionsuffix)s.tar']
+
+#  -d <distribution-dir>... directory containing the install files
+#  -m ..................... manual mode (no automatically included modules)
+#  -b ..................... batch install
+#  -s <SCHRODINGER> ....... installation directory
+#  -k <tmpdir> ............ scratch directory
+#  -t <thirdparty-dir> .... install directory for third-party modules
+install_cmd = 'tar xfv Schrodinger_Suites_%(version)s%(versionsuffix)s.tar && '
+install_cmd += 'cd Schrodinger_Suites_%(version)s%(versionsuffix)s && '
+install_cmd += './INSTALL -d . -s %(installdir)s -k %(builddir)s -t %(installdir)s/thirdparty -b *'
+
+modextrapaths = {'SCHRODINGER': ''}
+
+modextravars = {'SCHROD_LICENSE_FILE': '/apps/licenses/Schrodinger/license.dat'}
+
+sanity_check_paths = {
+    'files': ["maestro", "desmond" ],
+    'dirs': ["thirdparty"]
+}
+
+moduleclass = 'chem'
--- a/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020b-Python-3.8.6.eb
+++ b/s/SciPy-bundle/SciPy-bundle-2020.03-intel-2020b-Python-3.8.6.eb
@ -0,0 +1,58 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2020.03'
+versionsuffix = '-Python-3.8.6'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('pybind11', '2.6.0', '-GCC-10.2.0-Python-3.8.6', True),  # 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',  # numpy-1.18.2.zip
+            'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf',  # numpy-1.18.2-mkl.patch
+        ],
+    }),
+    ('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'
--- a/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2020b.eb
+++ b/s/SciPy-bundle/SciPy-bundle-2021.05-intel-2020b.eb
@ -0,0 +1,65 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2021.05'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [('hypothesis', '6.13.1', '', ('GCC', '10.2.0'))]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('pybind11', '2.6.0'),  # required by scipy
+]
+
+use_pip = True
+
+# order is important!
+exts_list = [
+    ('numpy', '1.20.3', {
+        'sources': [SOURCE_ZIP],
+        'patches': [
+            'numpy-1.20.3_skip-ppc-long-complex-test.patch',
+            'numpy-1.20.3_xfail-test-nan.patch',
+        ],
+        'checksums': [
+            'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69',  # numpy-1.20.3.zip
+            # numpy-1.20.3_skip-ppc-long-complex-test.patch
+            '2f9a12e3a352b39076db84a7622fc8f4796abd3cb7f97f71958a495e864659a4',
+            'f0ce961f7d79551598e23050d92f46e827e300f6a7e5a6112e58efcc10385d4d',  # numpy-1.20.3_xfail-test-nan.patch
+        ],
+    }),
+    ('scipy', '1.6.3', {
+        'checksums': ['a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707'],
+    }),
+    ('mpi4py', '3.0.3', {
+        'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'],
+    }),
+    ('numexpr', '2.7.3', {
+        'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'],
+    }),
+    ('Bottleneck', '1.3.2', {
+        'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'],
+    }),
+    ('pandas', '1.2.4', {
+        'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """,
+        'checksums': ['649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279'],
+    }),
+    ('mpmath', '1.2.1', {
+        'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'],
+    }),
+    ('deap', '1.3.1', {
+        'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'