Merge branch 'master' of code.it4i.cz:sccs/easyconfigs-it4i

b/Blender/Blender-3.1.0-GCC-10.3.0.eb

@@ -14,11 +14,7 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'}
 
 source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender3.1/']
 sources = ['blender-%(version)s-linux-x64.tar.xz']
-<<<<<<< HEAD
-checksums = ['8cf60d0c2cbda2ad26d8ff65e54cce45']
-=======
 checksums = ['ced2aaabc75731c2ae0e29493d0d2db7803d2bbb70a11cd0e7f50546d465bd8c']
->>>>>>> f9b20a6876de43df220c97513f83ee10c203bb30
 
 postinstallcmds = [
 	'ml CUDAcore;"nvcc" -arch=sm_80 --cubin "%(installdir)s/3.1/scripts/addons/cycles/source/kernel/device/cuda/kernel.cu" -o "%(installdir)s/3.1/scripts/addons/cycles/lib/kernel_sm_80.cubin" -m64 --ptxas-options="-v" --use_fast_math -DNVCC -I"%(installdir)s/3.1/scripts/addons/cycles/source" -DWITH_NANOVDB',

b/Blender/Blender-3.2.2-GCC-10.3.0.eb

@@ -0,0 +1,31 @@
+# IT4Innovations 2021
+
+easyblock = 'Tarball'
+
+name = 'Blender'
+version = '3.2.2'
+
+homepage = 'https://www.blender.org/'
+description = """Blender is the free and open source 3D creation suite. It supports
+ the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering,
+ compositing and motion tracking, even video editing and game creation."""
+
+toolchain = {'name': 'GCC', 'version': '10.3.0'}
+
+source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender3.2/']
+sources = ['blender-%(version)s-linux-x64.tar.xz']
+checksums = ['1726560157d90cf2aaaeb6d25ded1783d66bff043814cd95b90fc0af1d9e018b']
+
+postinstallcmds = [
+	'ml CUDAcore;"nvcc" -arch=sm_80 --cubin "%(installdir)s/3.2/scripts/addons/cycles/source/kernel/device/cuda/kernel.cu" -o "%(installdir)s/3.2/scripts/addons/cycles/lib/kernel_sm_80.cubin" -m64 --ptxas-options="-v" --use_fast_math -DNVCC -I"%(installdir)s/3.2/scripts/addons/cycles/source" -DWITH_NANOVDB',
+	'find %(installdir)s -executable -exec chmod +x {} \;',
+]
+
+modextrapaths = {'PATH': ''}
+
+sanity_check_paths = {
+    'files': ["blender"],
+    'dirs': []
+}
+
+moduleclass = 'vis'

b/bwidget/bwidget-1.9.15-GCCcore-11.3.0.eb

@@ -0,0 +1,26 @@
+easyblock = 'Tarball'
+
+name = 'bwidget'
+version = '1.9.15'
+
+homepage = 'https://core.tcl-lang.org/bwidget/home'
+description = 'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.'
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://downloads.sourceforge.net/project/tcllib/BWidget/%(version)s/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['9c4dd648fdfd31de7cb5af44b392a1916f949dd195820684d940edcd8485ac13']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [('Tk', '8.6.12')]
+
+modextrapaths = {'TCLLIBPATH': '.'}
+
+sanity_check_paths = {
+    'files': ['button.tcl'],
+    'dirs': ['BWman', 'demo', 'images', 'lang', 'tests'],
+}
+
+moduleclass = 'vis'

c/CP2K/CP2K-2022.1-foss-2022a.eb

@@ -0,0 +1,44 @@
+# IT4Innovations 2022
+# JK
+#16007
+
+##
+# Author:    Robert Mijakovic <robert.mijakovic@lxp.lu>
+##
+name = 'CP2K'
+version = '2022.1'
+
+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': '2022a'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+source_urls = ['https://github.com/cp2k/cp2k/releases/download/v%(version)s/']
+sources = [SOURCELOWER_TAR_BZ2]
+checksums = ['2c34f1a7972973c62d471cd35856f444f11ab22f2ff930f6ead20f3454fd228b']
+
+#                https://github.com/cp2k/cp2k/releases/download/v2022.1/cp2k-2022.1.tar.bz2
+dependencies = [
+    ('Libint', '2.7.2', '-lmax-6-cp2k'),
+    ('libxc', '5.2.3'),
+    ('libxsmm', '1.17'),
+    ('FFTW', '3.3.10'),
+    ('PLUMED', '2.8.0'),
+]
+
+builddependencies = [
+    ('flex', '2.6.4'),
+    ('Bison', '3.8.2'),
+]
+
+type = 'psmp'
+
+# regression test reports handful of failures,
+# we're assuming those are OK to ignore...
+ignore_regtest_fails = True
+
+moduleclass = 'chem'

c/Cordax/Cordax-1.0-Python-2.7.18.eb

@@ -1,26 +0,0 @@
-easyblock = 'Binary'
-
-name = 'Cordax'
-version = '1.0'
-versionsuffix = '-Python-%(pyver)s'
-
-homepage = 'N/A'
-description = """CORDAX is an aggregation propensity predictor based on predicted packing energies."""
-
-toolchain = {'name': 'foss', 'version': '2020b'}
-
-sources = ['%(namelower)s-%(version)s.tar.gz']
-
-dependencies = [
-    ('Python', '2.7.18'),
-    ('matplotlib', '2.2.5', '-Python-%(pyver)s'),
-    ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'),
-    ('scikit-learn', '0.20.4', '-Python-%(pyver)s'),
-    ('Biopython', '1.72', '-Python-%(pyver)s'),
-    ('FoldX', '5.0', '', True),
-]
-
-extract_sources = True
-skipsteps = ['sanitycheck']
-
-moduleclass = 'bio'

c/Cordax/Cordax-20220830-foss-2020b.eb

@@ -0,0 +1,40 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'Tarball'
+
+name = 'Cordax'
+version = '20220830'
+
+homepage = 'https://cordax.switchlab.org/'
+description = """CORDAX is an aggregation propensity predictor based on predicted packing energies."""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+
+sources = ['%(namelower)s-%(version)s.tar.gz']
+patches = ['Cordax-20220830-set-proper-paths.patch']
+checksums = [
+    'bc2b2e84f3df84c1ecabc774fed247998d1aeb38bade04127e47cd585130160d',  # cordax-20220830.tar.gz
+    'df8261e08da5d4e698f8621284d22bab99a0064f27d7735933c0d15c9ed730ff',  # Cordax-20220830-set-proper-paths.patch
+]
+
+dependencies = [
+    ('Python', '2.7.18'),
+    ('matplotlib', '2.2.5', '-Python-%(pyver)s'),
+    ('SciPy-bundle', '2020.11', '-Python-%(pyver)s'),
+    ('scikit-learn', '0.20.4', '-Python-%(pyver)s'),
+    ('Biopython', '1.72', '-Python-%(pyver)s'),
+    ('FoldX', '5.0', '', True),
+]
+
+sanity_check_paths = {
+    'files': ['parser.py', 'precomputed_dg.py', 'predictor.py', 'propensity.py', 'run_foldx.py',
+    'standalone.py', 'utils.py'],
+    'dirs': ['dataset', 'foldx', 'test', 'DATADIR'],
+}
+
+modextrapaths = {'PATH': ''}
+
+modloadmsg = "Precalculated models are available at $EBROOTCORDAX/DATADIR"
+
+moduleclass = 'bio'

c/ctffind/ctffind-4.1.14-foss-2021a.eb

@@ -0,0 +1,48 @@
+# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics
+#
+# Author: Ake Sandgren, HPC2N, Umea University
+
+easyblock = 'ConfigureMake'
+
+name = 'ctffind'
+version = '4.1.14'
+
+homepage = 'https://grigoriefflab.umassmed.edu/ctffind4'
+description = """Program for finding CTFs of electron micrographs."""
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    '%(name)s-%(version)s_asm-fix.patch',
+    '%(name)s-%(version)s_void-functions.patch'
+]
+checksums = [
+    'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5',  # ctffind-4.1.14.tar.gz
+    'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28',  # ctffind-4.1.14_asm-fix.patch
+    '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10',  # ctffind-4.1.14_void-functions.patch
+]
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('libjpeg-turbo', '2.0.6'),
+    ('LibTIFF', '4.2.0'),
+    ('GSL', '2.7'),
+    ('wxWidgets', '3.1.5'),
+]
+
+configopts = '--enable-openmp '
+
+parallel = 1
+
+sanity_check_paths = {
+    'files': ['bin/ctffind'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

f/FFTW.MPI/FFTW.MPI-3.3.8-NVHPC-22.2.eb

@@ -0,0 +1,25 @@
+# IT4Innovations 2022
+# JK
+
+name = 'FFTW.MPI'
+version = '3.3.8'
+
+homepage = 'https://www.fftw.org'
+description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data."""
+
+toolchain = {'name': 'NVHPC', 'version': '22.2'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = ['fftw-%(version)s.tar.gz']
+checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303']
+
+dependencies = [
+    ('FFTW', '3.3.8'),
+    ('OpenMPI', '4.1.2', '-CUDA-11.6.0'),
+]
+
+runtest = 'check'
+
+moduleclass = 'numlib'

f/FFTW/FFTW-3.3.10-NVHPC-22.2-amd.eb

@@ -0,0 +1,30 @@
+# IT4Innovations 2022
+# JK
+
+name = 'FFTW'
+version = '3.3.10'
+local_amd_fftw_ver = '3.2'
+versionsuffix = '-amd'
+
+homepage = 'https://developer.amd.com/amd-aocl/fftw/'
+description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data.
+AMD FFTW includes selective kernels and routines optimized for the AMD EPYC™ processor family."""
+
+toolchain = {'name': 'NVHPC', 'version': '22.2'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/amd/amd-fftw/archive/refs/tags/']
+sources = [{
+    'download_filename': '%s.tar.gz' % local_amd_fftw_ver,
+    'filename': 'amd-fftw-%s.tar.gz' % local_amd_fftw_ver,
+}]
+checksums = ['31cab17a93e03b5b606e88dd6116a1055b8f49542d7d0890dbfcca057087b8d0']
+
+builddependencies = [('binutils', '2.35')]
+
+configopts = '--enable-amd-opt'
+
+#runtest = 'check'
+
+moduleclass = 'numlib'

f/FFTW/FFTW-3.3.8-NVHPC-22.2-amd.eb

@@ -0,0 +1,30 @@
+# IT4Innovations 2022
+# JK
+
+name = 'FFTW'
+version = '3.3.8'
+local_amd_fftw_ver = '2.2'
+versionsuffix = '-amd'
+
+homepage = 'https://developer.amd.com/amd-aocl/fftw/'
+description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT)
+in one or more dimensions, of arbitrary input size, and of both real and complex data.
+AMD FFTW includes selective kernels and routines optimized for the AMD EPYC™ processor family."""
+
+toolchain = {'name': 'NVHPC', 'version': '22.2'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/amd/amd-fftw/archive/']
+sources = [{
+    'download_filename': '%s.tar.gz' % local_amd_fftw_ver,
+    'filename': 'amd-fftw-%s.tar.gz' % local_amd_fftw_ver,
+}]
+checksums = ['de9d777236fb290c335860b458131678f75aa0799c641490c644c843f0e246f8']
+
+builddependencies = [('binutils', '2.35')]
+
+configopts = '--enable-amd-opt'
+
+#runtest = 'check'
+
+moduleclass = 'numlib'

f/FFTW/FFTW-3.3.8-NVHPC-22.2.eb

@@ -0,0 +1,28 @@
+# IT4Innovations 2022
+# JK
+
+name = 'FFTW'
+version = '3.3.8'
+
+homepage = 'http://www.fftw.org'
+description = """FFTW is a C subroutine library for local_computing the discrete Fourier transform (DFT)
+ in one or more dimensions, of arbitrary input size, and of both real and local_complex data."""
+
+toolchain = {'name': 'NVHPC', 'version': '22.2'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303']
+
+# no quad precision, requires GCC v4.6 or higher
+# see also
+# http://www.fftw.org/doc/Extended-and-quadruple-precision-in-Fortran.html
+with_quad_prec = False
+
+# local_compilation fails when configuring with --enable-avx-128-fma, Intel local_compilers do not support FMA4 instructions
+use_fma4 = False
+
+runtest = 'check'
+
+moduleclass = 'numlib'

f/FoldX/FoldX-5.0.eb

@@ -6,7 +6,7 @@ easyblock = 'Binary'
 name = 'FoldX'
 version = '5.0'
 
-homepage = 'http://http://foldxsuite.crg.eu/'
+homepage = 'https://foldxsuite.crg.eu/'
 description = """FoldX is used to provide a fast and quantitative estimation of the importance of the interactions
  contributing to the stability of proteins and protein complexes."""
 

f/fio/fio-3.32-GCCcore-11.3.0.eb

@@ -0,0 +1,31 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'ConfigureMake'
+
+name = 'fio'
+version = '3.32'
+
+homepage = 'https://github.com/axboe/fio'
+
+description = 'Flexible I/O tester'
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+github_account = 'axboe'
+source_urls = [GITHUB_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['409e459840912e68be487dbbda9a7a1b3f6ddf1478e3f456f278f957ce4f7b66']
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/fio'],
+    'dirs': ['bin', 'man', 'share'],
+}
+
+sanity_check_commands = ['fio -h']
+
+moduleclass = 'tools'

g/gh/gh-2.14.7.eb

@@ -0,0 +1,24 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'GoPackage'
+
+name = 'gh'
+version = '2.14.7'
+
+homepage = 'https://github.com/cli/cli'
+description = """gh is GitHub on the command line."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/cli/cli/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['a1a048714d7c7b237ea05f1fb51b3f3f4cdf90a16c60fa46f1df2eb5d96ce28d']
+
+builddependencies = [
+    ('Go', '1.18.1'),
+]
+
+installopts = './cmd/%(namelower)s'
+
+moduleclass = 'tools'

g/gpu_burn/gpu_burn-1.1-NVHPC-22.2-CUDA-11.6.0.eb

@@ -0,0 +1,43 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'MakeCp'
+
+name = 'gpu_burn'
+version = '1.1'
+local_cudaversion = '11.6.0'
+local_commit = 'c535b67'
+versionsuffix = "-CUDA-%s" % local_cudaversion
+
+homepage = 'http://wili.cc/blog/gpu-burn.html'
+description = """Multi-GPU CUDA stress test"""
+
+toolchain = {'name': 'NVHPC', 'version': '22.2'}
+toolchainopts = {'opt': False}
+
+source_urls = ['https://github.com/wilicc/gpu-burn/archive']
+sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}]
+checksums = [
+    '2dec738c935642395e15bd6ce71a14f8307c86661b3c8bc3826ff0272abf8f20',  # gpu_burn-1.1.tar.gz
+]
+
+dependencies = [('OpenMPI', '4.1.2', versionsuffix)]
+
+build_cmd = 'unset CFLAGS; make COMPUTE=8.0 CUDAPATH=${EBROOTCUDACORE}'
+
+files_to_copy = ['gpu_burn', 'gpu_burn-drv.o', 'compare.ptx', 'gpu_burn-drv.cpp', 'compare.cu']
+
+sanity_check_paths = {
+    'files': ['gpu_burn'],
+    'dirs': []
+}
+
+modluafooter = """
+add_property('arch', 'gpu')
+"""
+
+modextrapaths = {'PATH': '.'}
+
+parallel = 1 
+
+moduleclass = 'tools'

h/HDF5/HDF5-1.12.1-NVHPC-22.2.eb

@@ -0,0 +1,27 @@
+# IT4Innovations 2022
+# LK JK
+
+name = 'HDF5'
+version = '1.12.1'
+
+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': 'NVHPC', 'version': '22.2'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['79c66ff67e666665369396e9c90b32e238e501f345afd2234186bfb8331081ca']
+
+configopts = '--enable-fortran --enable-fortran 2003 --enable-cxx --enable-parallel --enable-unsupported --enable-shared'
+
+dependencies = [
+    ('OpenMPI', '4.1.2', '-CUDA-11.6.0'),
+    ('zlib', '1.2.11'),
+    ('Szip', '2.1.1'),
+]
+
+moduleclass = 'data'

h/HDF5/HDF5-1.12.2-gompi-2022a.eb

@@ -2,7 +2,7 @@
 # JK
 
 name = 'HDF5'
-version = '1.13.1'
+version = '1.12.2'
 
 homepage = 'https://portal.hdfgroup.org/display/support'
 description = """HDF5 is a data model, library, and file format for storing and managing data.
@@ -14,7 +14,7 @@ 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 = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53']
+checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14']
 
 import os
 if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:

h/HDF5/HDF5-1.12.2-iimpi-2022a.eb

@@ -2,7 +2,7 @@
 # JK
 
 name = 'HDF5'
-version = '1.13.1'
+version = '1.12.2'
 
 homepage = 'https://portal.hdfgroup.org/display/support'
 description = """HDF5 is a data model, library, and file format for storing and managing data.
@@ -14,9 +14,10 @@ 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 = ['051655873105112f7aeccd5f59ab21f35f7f4907f06921ae61aaf1ef1c71fd53']
+checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14']
 
 import os
+# core-avx2 is required due to a but in fortran compiler
 if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
     toolchainopts = {'pic': True, 'usempi': True, 'optarch': 'march=core-avx2'}
 else:

h/HyperQueue/HyperQueue-0.12.0.eb

@@ -0,0 +1,27 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'PackedBinary'
+
+name = 'HyperQueue'
+version = '0.12.0'
+
+homepage = 'https://it4innovations.github.io/hyperqueue/'
+description = """HyperQueue lets you build a computation plan consisting of a large amount of tasks
+ and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs
+ and distributes them to fully utilize allocated notes.
+ You thus do not have to manually aggregate your tasks into SLURM/PBS jobs."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://github.com/It4innovations/hyperqueue/releases/download/v%(version)s/']
+sources = ['hq-v%(version)s-linux-x64.tar.gz']
+checksums = ['43de90b23dae2ba1534f98e9aaed439fcf32cf3c5728790445894b487b49f7ec']
+
+sanity_check_paths = {
+    'files': ['hq'],
+    'dirs': [],
+}
+
+
+moduleclass = 'devel'

i/IMOD/IMOD-4.11.1-fosscuda-2020b.eb

@@ -0,0 +1,111 @@
+# IT4Innovations 2022
+# JK
+# Had to fix some arch-specifying files in the source code!
+
+# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04
+easyblock = 'ConfigureMake'
+
+name = 'IMOD'
+version = '4.11.1'
+
+homepage = 'https://bio3d.colorado.edu/imod/'
+description = """IMOD is a set of image processing, modeling and display
+programs used for tomographic reconstruction and for 3D reconstruction of EM
+serial sections and optical sections. The package contains tools for assembling
+and aligning data within multiple types and sizes of image stacks, viewing 3-D
+data from any orientation, and modeling and display of the image files. IMOD
+was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim
+Kremer, Quanren Xiong, and John Heumann at the University of Colorado."""
+
+toolchain = {'name': 'fosscuda', 'version': '2020b'}
+toolchainopts = {'pic': True, 'openmp': True}
+
+# download manually from mercurial repository and create source tarball:
+# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
+# get lunch ????? co to je
+# cd IMOD
+# hg update -r IMOD_4-11-1
+# cd ..
+# tar czf IMOD-4.11.1.tar.gz IMOD
+sources = [SOURCE_TAR_GZ]
+patches = ['IMOD-4.11.5_fix-csvtohtml-py3.patch']
+checksums = [
+    '4a2a51641a3169d1066faa8011caa90196fa1aef71da5d93cfafcf0703f8bcc6',  # IMOD-4.11.1.tar.gz
+    '8ba0c3cbe30d755ab3fb918688982e818795b9f7f41218bd6bf231c85bea4971',  # IMOD-4.11.5_fix-csvtohtml-py3.patch
+]
+
+# can't include a valid checksum, since tarball has to be created manually
+dependencies = [
+    ('LibTIFF', '4.1.0'),
+    ('Qt5', '5.14.2'),
+    ('Java', '11', '', True),
+    ('HDF5', '1.10.7'),
+    ('Python', '3.8.6'),
+]
+
+# parallel build sometimes fails
+parallel = 1
+
+# replace hardcoded CUDA compute capabilitites in machines/rhlinux. 
+local_cuda_replace = 'echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|'
+local_cuda_replace += '   awk \'{'
+local_cuda_replace += '          printf "-arch sm_"$1; '
+local_cuda_replace += '          for (i=1;i<=NF; i++){printf(" -gencode=arch=compute_%s,code=sm_%s",$i,$i) } '
+local_cuda_replace += '   }\''
+local_cudaarch_sed = 'sed -i "s/-arch sm_35/`' + local_cuda_replace + '`/g" machines/rhlinux &&'
+
+# modify all qmake pro files in order to pass CFLAGS
+local_qmake_pass_cflags = "find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&"
+
+# exports required for configure and build
+local_exports = 'export QTDIR=$EBROOTQT5 &&'
+local_exports += 'export HDF5_DIR=$EBROOTHDF5 &&'
+local_exports += 'export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&'
+local_exports += 'export CUDA_DIR=$CUDA_HOME &&'
+#  readw_or_imod.f and others with gfortran10: 
+#     Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2))
+#     => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0.
+local_exports += 'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&'  # required for gfortran10
+
+preconfigopts = local_exports
+preconfigopts += local_cudaarch_sed
+preconfigopts += local_qmake_pass_cflags
+
+preconfigopts += "mv pysrc/pip.py pysrc/imodpip.py &&"
+preconfigopts += "sed -i 's/pip.py/imodpip.py/' pysrc/Makefile &&"
+preconfigopts += "sed -i 's/from pip/from imodpip/' pysrc/* &&"
+
+# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. 
+# CFLAGs are passed with -flags.
+configure_cmd = './setup '
+configure_cmd += '-flags "$CFLAGS" '    # inject CFLAGS
+configure_cmd += '-i %(installdir)s '  # set installdir
+configure_cmd += ' #'  # avoid passing unknown arg --prefix
+
+prebuildopts = local_exports
+
+# create some missing directories required for installation process:
+preinstallopts = 'mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&'
+
+# patch hardcoded /usr/bin/python to use Python included as dependency
+preinstallopts += "find pysrc -name '*.py' | xargs sed -i 's@^#!/usr/bin/python@#!/usr/bin/env python@g' && "
+preinstallopts += "ls manpages/{csvtohtml,adocdefaults} | xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' && "
+preinstallopts += "xargs sed -i 's@^#!.*/python -u@#!/usr/bin/env python@g' html/makeqhp && "
+
+modextravars = {
+    'IMOD_DIR': "%(installdir)s",
+    'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug',
+    'IMOD_JAVADIR': '$JAVA_HOME',
+    'FOR_DISABLE_STACK_TRACE': '1',
+}
+modloadmsg = 'Please set the environment variable $IMOD_CALIB_DIR if appropriate.'
+# Observed problems with alias on a tcl based module system. Use bin/subm python script instead.
+# modaliases = {
+#     'subm': 'submfg $* &'
+# }
+sanity_check_paths = {
+    'files': ['VERSION', 'bin/subm'],
+    'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
+}
+
+moduleclass = 'vis'

i/IMOD/IMOD-4.11.1_RHEL7-64_CUDA8.0.eb

@@ -0,0 +1,28 @@
+# IT4Innovations 2022
+# JK
+# --include-easyblock /apps/easybuild/it4i-easyblocks/easyblocks/i/imod.py !!!
+
+name = 'IMOD'
+version = '4.11.1'
+versionsuffix = '_RHEL7-64_CUDA8.0'
+
+homepage = 'http://bio3d.colorado.edu/imod/'
+description = """IMOD is a set of image processing, modeling and display
+programs used for tomographic reconstruction and for 3D reconstruction of EM
+serial sections and optical sections. The package contains tools for assembling
+and aligning data within multiple types and sizes of image stacks, viewing 3-D
+data from any orientation, and modeling and display of the image files.
+"""
+
+toolchain = SYSTEM
+
+source_urls = ['https://bio3d.colorado.edu/imod/AMD64-RHEL5/']
+sources = ['%(namelower)s_%(version)s%(versionsuffix)s.sh']
+checksums = ['8fefab2c85c85d8343005b2ac352c6b7de22e00847dc0975766b0312e44be0b8']
+
+dependencies = [
+    ('CUDA', '11.4.1'),
+    ('Java', '13.0.2'),
+]
+
+moduleclass = 'vis'

i/irodsfs/irodsfs-0.7.6.eb

@@ -23,7 +23,8 @@ sanity_check_paths = {
 
 postinstallcmds = [
     'cp /mnt/proj3/easybuild/scripts/irods-startup.sh %(installdir)s/',
-    'curl -L https://docs.it4i.cz/irods1.it4i.cz.crt -o %(installdir)s/irods1.it4i.cz.crt',
+    'cp /mnt/proj3/easybuild/scripts/irods.it4i.cz.crt %(installdir)s/',
+#    'curl -L https://docs.it4i.cz/irods1.it4i.cz.crt -o %(installdir)s/irods1.it4i.cz.crt',
 ]
 
 modluafooter = 'execute{cmd="bash $EBROOTIRODSFS/irods-startup.sh", modeA={"load"}}'

l/libmad/libmad-0.15.1b-GCCcore-11.3.0-remove-depreciated-gcc-options.patch

@@ -1,22 +0,0 @@
-diff -Nru libmad-0.15.1b.orig/configure libmad-0.15.1b/configure
---- libmad-0.15.1b.orig/configure	2022-08-19 11:44:53.156998000 +0200
-+++ libmad-0.15.1b/configure	2022-08-19 11:45:31.855629909 +0200
-@@ -19099,7 +19099,6 @@
-     case "$optimize" in
- 	-O|"-O "*)
- 	    optimize="-O"
--	    optimize="$optimize -fforce-mem"
- 	    optimize="$optimize -fforce-addr"
- 	    : #x optimize="$optimize -finline-functions"
- 	    : #- optimize="$optimize -fstrength-reduce"
-diff -Nru libmad-0.15.1b.orig/configure.ac libmad-0.15.1b/configure.ac
---- libmad-0.15.1b.orig/configure.ac	2022-08-19 11:44:53.172288000 +0200
-+++ libmad-0.15.1b/configure.ac	2022-08-19 11:45:43.617447388 +0200
-@@ -140,7 +140,6 @@
-     case "$optimize" in
- 	-O|"-O "*)
- 	    optimize="-O"
--	    optimize="$optimize -fforce-mem"
- 	    optimize="$optimize -fforce-addr"
- 	    : #x optimize="$optimize -finline-functions"
- 	    : #- optimize="$optimize -fstrength-reduce"

l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb

@@ -1,5 +1,7 @@
-# IT4Innovations 2022
-# JK
+# Institution: IT4Innovations National Supercomputing Center, Czech Republic
+# Author: Jakub Kropacek
+# License: GPLv3
+# Year: 2022
 
 easyblock = 'ConfigureMake'
 
@@ -7,24 +9,24 @@ name = 'libmad'
 version = '0.15.1b'
 
 homepage = 'https://www.underbit.com/products/mad/'
-description = """MAD is a high-quality MPEG audio decoder. It currently supports MPEG-1 and the MPEG-2 extension to lower sampling frequencies, as well as the de facto MPEG 2.5 format. All three audio layers — Layer I, Layer II, and Layer III (i.e. MP3) — are fully implemented."""
+description = """MAD is a high-quality MPEG audio decoder."""
 
 toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-source_urls = ['https://sourceforge.net/projects/mad/files/libmad/%(version)s']
+source_urls = ['https://sourceforge.net/projects/mad/files/%(name)s/%(version)s/']
 sources = [SOURCELOWER_TAR_GZ]
-patches = ['libmad-0.15.1b-GCCcore-11.3.0-remove-depreciated-gcc-options.patch']
+patches = ['libmad-0.15.1b-remove-depreciated-gcc-option.patch']
 checksums = [
     'bbfac3ed6bfbc2823d3775ebb931087371e142bb0e9bb1bee51a76a6e0078690',  # libmad-0.15.1b.tar.gz
-    # libmad-0.15.1b-GCCcore-11.3.0-remove-depreciated-gcc-options.patch
-    'c7dc07f0d502e31a09ddb82b30827a71d8dfacd39053ee2107d4fc4b0470d2c3',
+    # libmad-0.15.1b-remove-depreciated-gcc-option.patch
+    '8f96a23a22ba66e62f32e20064d01f4c7f6a18ba0aab85d3be9ce63794b2c678',
 ]
 
 builddependencies = [('binutils', '2.38')]
 
 sanity_check_paths = {
-    'files': [],
-    'dirs': ["."]
+    'files': ['include/mad.h', 'lib/libmad.a', 'lib/libmad.la', 'lib/libmad.%s' % SHLIB_EXT],
+    'dirs': ['include', 'lib', 'lib64']
 }
 
 moduleclass = 'lib'

l/libxsmm/libxsmm-1.17-GCC-11.3.0.eb

@@ -0,0 +1,31 @@
+# IT4Innovations 2022
+# JK
+#16007
+
+easyblock = 'ConfigureMake'
+
+name = 'libxsmm'
+version = '1.17'
+
+homepage = 'https://github.com/hfp/libxsmm'
+description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications
+targeting Intel Architecture (x86)."""
+
+toolchain = {'name': 'GCC', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/hfp/libxsmm/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['8b642127880e92e8a75400125307724635ecdf4020ca4481e5efe7640451bb92']
+
+# install both static and dynamic version
+installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0']
+
+skipsteps = ['configure']
+maxparallel = 1
+
+sanity_check_paths = {
+    'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT],
+    'dirs': ['share']
+}
+
+moduleclass = 'math'

m/matplotlib/matplotlib-3.5.2-intel-2022a.eb

@@ -0,0 +1,69 @@
+easyblock = 'PythonBundle'
+
+name = 'matplotlib'
+version = '3.5.2'
+
+homepage = 'https://matplotlib.org'
+description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of
+ hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python
+ and ipython shell, web application servers, and six graphical user interface toolkits."""
+
+toolchain = {'name': 'intel', 'version': '2022a'}
+
+builddependencies = [
+    ('pkgconf', '1.8.0'),
+    ('cppy', '1.2.1')
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('libpng', '1.6.37'),
+    ('freetype', '2.12.1'),
+    ('Tkinter', '%(pyver)s'),
+    ('Pillow', '9.1.1'),
+    ('Qhull', '2020.2')
+]
+
+use_pip = True
+sanity_pip_check = True
+
+# avoid that matplotlib downloads and builds its own copies of freetype and qhull
+_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' "
+_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >setup.cfg && "
+
+_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && "
+
+exts_list = [
+    ('fonttools', '4.34.0', {
+        'modulename': 'fontTools',
+        'source_tmpl': SOURCE_ZIP,
+        'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'],
+    }),
+    ('Cycler', '0.11.0', {
+        'modulename': 'cycler',
+        'source_tmpl': 'cycler-%(version)s.tar.gz',
+        'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'],
+        'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'],
+    }),
+    ('kiwisolver', '1.4.3', {
+        'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'],
+        'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'],
+    }),
+    (name, version, {
+        'preinstallopts': _fix_setup + _include_path,
+        'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'],
+        'checksums': ['48cf850ce14fa18067f2d9e0d646763681948487a8080ec0af2686468b4607a2'],
+    }),
+]
+
+sanity_check_commands = [
+    """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """,
+    "python -c 'from mpl_toolkits.mplot3d import Axes3D'",
+]
+
+# use non-interactive plotting backend as default
+# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend
+modextravars = {'MPLBACKEND': 'Agg'}
+
+moduleclass = 'vis'

n/nano/nano-6.3.eb

@@ -1,25 +0,0 @@
-# IT4Innovations 2022
-# JK LK
-
-easyblock = 'ConfigureMake'
-
-name = 'nano'
-version = '6.3'
-
-homepage = 'http://www.nano-editor.org/'
-description = """Small and friendly text editor"""
-
-toolchain = SYSTEM
-
-source_urls = ['https://www.nano-editor.org/dist/v6/']
-sources = [SOURCE_TAR_GZ]
-checksums = ['24c51bb2bddc682f95ae745c743cbceebd836549de66bdfd6af80a40333cc6a7']
-
-dependencies = [('ncurses', '6.2')]
-
-sanity_check_paths = {
-    'files': ['bin/nano'],
-    'dirs': [],
-}
-
-moduleclass = 'tools'

n/nano/nano-6.4-GCCcore-11.3.0.eb

@@ -0,0 +1,30 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'ConfigureMake'
+
+name = 'nano'
+version = '6.4'
+
+homepage = 'https://www.nano-editor.org/'
+docurls = 'https://www.nano-editor.org/docs.php'
+description = """a simple editor, inspired by Pico"""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://www.nano-editor.org/dist/v6/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['85ebd9b4dba49839821d529bea16ac1acae0c9b9db2157531e40c9dffeb1b656']
+
+builddependencies = [('binutils', '2.38')]
+
+dependencies = [('ncurses', '6.3')]
+
+sanity_check_paths = {
+    'files': ['bin/nano'],
+    'dirs': ['bin', 'share'],
+}
+
+sanity_check_commands = ['nano --version']
+
+moduleclass = 'tools'

p/PLUMED/PLUMED-2.8.0-foss-2022a.eb

@@ -0,0 +1,64 @@
+# IT4Innovations 2022
+# JK
+#16007
+
+easyblock = 'ConfigureMake'
+
+name = 'PLUMED'
+version = '2.8.0'
+
+homepage = 'https://www.plumed.org'
+description = """PLUMED is an open source library for free energy calculations in molecular systems which
+ works together with some of the most popular molecular dynamics engines. Free energy calculations can be
+ performed as a function of many order parameters with a particular  focus on biological problems, using
+ state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD.
+ The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'usempi': 'True'}
+
+source_urls = ['https://github.com/plumed/plumed2/releases/download/v%(version)s/']
+sources = [SOURCE_TGZ]
+checksums = ['24b243c531fa83752be5e54f5f0b677164855da539bc2b2c5b00dcc9f192aa82']
+
+builddependencies = [
+    ('xxd', '8.2.4220'),
+]
+
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('GSL', '2.7'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('Boost', '1.79.0'),
+]
+
+preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" '
+configopts = '--exec-prefix=%(installdir)s --enable-gsl --enable-modules=all --enable-python '
+configopts += '--enable-boost_graph --enable-boost_serialization '
+configopts += '--enable-asmjit '
+prebuildopts = 'source sourceme.sh && '
+
+# make sure that ld.gold linker is used
+# required to work around problems like "ld: BFD (GNU Binutils) 2.30 assertion fail elf.c:3564"
+# (problem with intel build but maintain consistency between easyconfigs)
+buildopts = 'LD_RO="ld.gold -r -o"'
+
+# install path for PLUMED libraries must be included in $LD_LIBRARY_PATH when Python bindings get built/installed
+preinstallopts = 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" '
+
+sanity_check_paths = {
+    'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+sanity_check_commands = ["python -c 'import plumed'"]
+
+modextrapaths = {
+    'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT,
+    'PLUMED_ROOT': 'lib/plumed',
+    'PYTHONPATH': 'lib/plumed/python',
+}
+
+moduleclass = 'chem'

q/QD/QD-2.3.17-NVHPC-22.2.eb

@@ -0,0 +1,24 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'ConfigureMake'
+
+name = 'QD'
+version = '2.3.17'
+local_gitcommit = 'a5dbb61'
+
+homepage = 'https://github.com/scibuilder/QD'
+description = "Quad Double computation package"
+
+toolchain = {'name': 'NVHPC', 'version': '22.2'}
+
+source_urls = ['https://github.com/scibuilder/QD/archive/']
+sources = [{'download_filename': '%s.tar.gz' % local_gitcommit, 'filename': SOURCE_TAR_GZ}]
+checksums = ['1e5949b7d20434193d496c28070d8f2fb6406a7688a86080dfdac57fbe730624']
+
+sanity_check_paths = {
+    'files': ['lib/lib%s.a' % x for x in ['qdmod', 'qd']],
+    'dirs': []
+}
+
+moduleclass = 'math'

q/QuantumESPRESSO/QuantumESPRESSO-7.1-foss-2022a.eb

@@ -40,7 +40,7 @@ checksums = [
 builddependencies = [('M4', '1.4.19')]
 
 dependencies = [
-    ('HDF5', '1.13.1'),
+    ('HDF5', '1.12.2'),
     ('ELPA', '2021.11.001'),
     ('libxc', '5.2.3'),
 ]

q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a.eb

@@ -15,7 +15,6 @@ toolchain = {'name': 'intel', 'version': '2022a'}
 import os
 if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
     toolchainopts = {'usempi': True, 'openmp': True,  'optarch': 'march=core-avx2', 'opt': 'O3'}
-#    prebuildopts = "echo %(builddir)s && while read i; do echo $i; sed 's|-xHost|-march=core-avx2|g' -i $i; done < <(grep xHost %(builddir)s -R | cut -d ':' -f 1 | sort -u) && "
 else:
     toolchainopts = {'usempi': True, 'openmp': True, 'opt': 'O3'}
 
@@ -41,7 +40,7 @@ checksums = [
 builddependencies = [('M4', '1.4.19')]
 
 dependencies = [
-    ('HDF5', '1.13.1'),
+    ('HDF5', '1.12.2'),
     ('ELPA', '2021.11.001'),
     ('libxc', '5.2.3'),
 ]

r/RELION/RELION-4.0-beta-foss-2021a.eb

@@ -0,0 +1,52 @@
+easyblock = 'CMakeMake'
+
+name = 'RELION'
+version = '4.0_beta.2022.04.20'
+_commit = '9b23e50'
+
+homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page'
+description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer
+ program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class
+ averages in electron cryo-microscopy (cryo-EM).
+ """
+
+toolchain = {'name': 'foss', 'version': '2021a'}
+toolchainopts = {'opt': True}
+
+sources = [{
+    'download_filename': '%(version)s.tar.gz',
+    'filename': SOURCELOWER_TAR_GZ,
+    'git_config': {
+        'url': 'https://github.com/3dem',
+        'repo_name': '%(namelower)s',
+        'commit': _commit,
+        'keep_git_dir': True,
+    },
+}]
+checksums = ['98b053a11c9ccdd144bcee5296e29cc08a05094094b27ad34536175b5a8405c2']
+
+# Note: no checksum(s), due to use of `git_config`
+
+builddependencies = [('CMake', '3.20.1')]
+
+dependencies = [
+    ('ctffind', '4.1.14'),   # required for most workloads
+    ('tbb', '2020.3'),
+    # optional graphics libraries:
+    ('Ghostscript', '9.54.0'),
+    ('libpng', '1.6.37'),
+    ('LibTIFF', '4.2.0'),
+    # GUI-specific dependencies:
+    ('FLTK', '1.3.6'),
+    ('X11', '20210518'),
+]
+
+local_disable_gui = False
+
+# Useful information for non-release builds
+_version_maj = version.split('_')[0]
+modloadmsg = "Current version pulled from commit %s from https://github.com/3dem/relion ver%s branch" % (_commit, _version_maj)
+
+skipsteps = ['sanitycheck']
+
+moduleclass = 'bio'

s/ScaLAPACK/ScaLAPACK-3.0-NVHPC-22.2.eb

@@ -0,0 +1,49 @@
+# IT4Innovations 2022
+# LK JK
+
+easyblock = 'CMakeMake'
+
+name = 'ScaLAPACK'
+version = '3.0'
+
+homepage = 'https://www.netlib.org/scalapack/'
+description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines
+redesigned for distributed memory MIMD parallel computers."""
+
+toolchain = {'name': 'NVHPC', 'version': '22.2'}
+toolchainopts = {'pic': True}
+
+# https://github.com/amd/scalapack/archive/3.0.tar.gz
+source_urls = ['https://github.com/amd/scalapack/archive/']
+sources = ['%(version)s.tar.gz']
+checksums = ['6e6f3578f44a8e64518d276e7580530599ecfa8729f568303ed2590688e7096f']
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+]
+
+dependencies = [
+    ('OpenMPI', '4.1.2', '-CUDA-11.6.0'),
+    ('BLIS', '3.0.1'),
+    ('libFLAME', '5.2.0'),
+]
+
+# Config Opts based on AOCL User Guide:
+# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf
+
+configopts = '-DBUILD_SHARED_LIBS=ON '
+configopts += '-DBLAS_LIBRARIES="$EBROOTBLIS/lib/libblis-mt.a" '
+configopts += '-DLAPACK_LIBRARIES="$EBROOTLIBFLAME/lib/libflame.a" '
+configopts += '-DCMAKE_C_COMPILER=mpicc '
+configopts += '-DCMAKE_Fortran_COMPILER=mpif90 '
+configopts += '-DUSE_OPTIMIZED_LAPACK_BLAS=ON '
+configopts += '-DUSE_F2C=ON '
+configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" '
+
+sanity_check_paths = {
+    'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT],
+    'dirs': ["lib", "lib64"],
+}
+
+
+moduleclass = 'numlib'

t/Togl/Togl-2.0-GCCcore-11.3.0.eb

@@ -1,5 +1,5 @@
-# IT4Innovations 2021
-# JK, LK
+# Last contribution from IT4Innovations National Supercomputing Center, Czech Republic
+# Jakub Kropacek, 2022
 
 easyblock = 'ConfigureMake'
 
@@ -9,9 +9,9 @@ version = '2.0'
 homepage = 'https://sourceforge.net/projects/togl/'
 description = """A Tcl/Tk widget for OpenGL rendering."""
 
-toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
 
-source_urls = ['https://downloads.sourceforge.net/project/togl/Togl/2.0/']
+source_urls = ['https://downloads.sourceforge.net/project/%(namelower)s/%(name)s/%(version)s/']
 sources = ['%(name)s%(version)s-src.tar.gz']
 patches = [
     'Togl-2.0_configure.patch',
@@ -23,12 +23,12 @@ checksums = [
     '05db6b3ca5139f60616d074903883a3070fcfb1eb8c965b0938779b4f9a6ec6a',  # Togl-2.0_decl.patch
 ]
 
-builddependencies = [('binutils', '2.35')]
+builddependencies = [('binutils', '2.38')]
 
 dependencies = [
-    ('Mesa', '20.2.1'),
-    ('Tk', '8.6.11'),
-    ('Tcl', '8.6.11'),
+    ('Mesa', '22.0.3'),
+    ('Tk', '8.6.12'),
+    ('Tcl', '8.6.12'),
 ]
 
 preconfigopts = 'export CFLAGS="$CFLAGS -DTOGL_USE_FONTS=0" && '
@@ -38,12 +38,12 @@ configopts += "--with-tcl=$EBROOTTCL/lib --with-tk=$EBROOTTK/lib"
 
 sanity_check_paths = {
     'files': [],
-    'dirs': ['include', 'lib'],
+    'dirs': ['include', 'lib', 'lib/%(name)s%(version)s'],
 }
 
 modextrapaths = {
-     'LD_LIBRARY_PATH': 'lib/Togl2.0',
-     'LIBRARY_PATH': 'lib/Togl2.0',
+     'LD_LIBRARY_PATH': 'lib/%(name)s%(version)s',
+     'LIBRARY_PATH': 'lib/%(name)s%(version)s',
 }
 
 moduleclass = 'vis'

v/VASP/VASP-5.4.1-24Jun15-intel-2020b.eb

@@ -60,4 +60,4 @@ sanity_check_paths = {
     'dirs': []
 }
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF-karolina.eb

@@ -67,4 +67,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-BEEF.eb

@@ -72,4 +72,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-VASPsol-karolina.eb

@@ -66,4 +66,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-karolina.eb

@@ -68,4 +68,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential-vtst-karolina.eb

@@ -69,4 +69,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-5.4.4-intel-2020a-mkl=sequential.eb

@@ -63,4 +63,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-5.4.4-intel-2020a.eb

@@ -60,4 +60,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential-BEEF.eb

@@ -66,4 +66,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.1.1-intel-2020a-mkl=sequential.eb

@@ -59,4 +59,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential-karolina.eb

@@ -64,4 +64,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.2.0-intel-2020b-mkl=sequential.eb

@@ -59,4 +59,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.2.0-intel-2020b.eb

@@ -49,4 +49,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-VASPsol-karolina.eb

@@ -64,4 +64,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential-karolina.eb

@@ -64,4 +64,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.2.1-intel-2020b-mkl=sequential.eb

@@ -60,4 +60,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.3.0-intel-2020b-mkl=sequential-vtst-karolina.eb

@@ -68,4 +68,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential-march=znver3-karolina.eb

@@ -64,4 +64,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.3.0-intel-2021b-mkl=sequential.eb

@@ -63,4 +63,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.3.1-foss-2022a.eb

@@ -77,4 +77,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.3.1-intel-2021b.eb

@@ -75,4 +75,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0-adjust-makefile.patch

@@ -0,0 +1,65 @@
+# IT4Innovations 2022
+# JK
+#
+# Adjusts makefile.include for use within the EasyBuild environment.
+--- arch/makefile.include.nvhpc_acc.orig	2022-09-02 21:28:42.393086358 +0200
++++ arch/makefile.include.nvhpc_acc	2022-09-02 21:28:48.142969028 +0200
+@@ -16,8 +16,8 @@
+ 
+ # N.B.: you might need to change the cuda-version here
+ #       to one that comes with your NVIDIA-HPC SDK
+-FC          = mpif90 -acc -gpu=cc60,cc70,cc80,cuda11.0
+-FCL         = mpif90 -acc -gpu=cc60,cc70,cc80,cuda11.0 -c++libs
++FC          = mpif90 -acc -gpu=cc60,cc70,cc80,cuda11.6
++FCL         = mpif90 -acc -gpu=cc60,cc70,cc80,cuda11.6 -c++libs
+ 
+ FREE        = -Mfree
+ 
+@@ -60,19 +60,19 @@
+ 
+ # Specify your NV HPC-SDK installation (mandatory)
+ #... first try to set it automatically
+-NVROOT      =$(shell which nvfortran | awk -F /compilers/bin/nvfortran '{ print $$1 }')
++#NVROOT      =$(shell which nvfortran | awk -F /compilers/bin/nvfortran '{ print $$1 }')
+ 
+ # If the above fails, then NVROOT needs to be set manually
+-#NVHPC      ?= /opt/nvidia/hpc_sdk
+-#NVVERSION   = 21.11
+-#NVROOT      = $(NVHPC)/Linux_x86_64/$(NVVERSION)
++NVHPC      ?= ${EBROOTNVHPC}
++NVVERSION   = ${EBVERSIONNVHPC}
++NVROOT      = $(NVHPC)/Linux_x86_64/$(NVVERSION)
+ 
+ ## Improves performance when using NV HPC-SDK >=21.11 and CUDA >11.2
+-#OFLAG_IN   = -fast -Mwarperf
+-#SOURCE_IN  := nonlr.o
++OFLAG_IN   = -fast -Mwarperf
++SOURCE_IN  := nonlr.o
+ 
+ # Software emulation of quadruple precsion (mandatory)
+-QD         ?= $(NVROOT)/compilers/extras/qd
++QD         ?= ${EBROOTQD}
+ LLIBS      += -L$(QD)/lib -lqdmod -lqd
+ INCS       += -I$(QD)/include/qd
+ 
+@@ -88,15 +88,15 @@
+ LLIBS      += $(SCALAPACK) $(LAPACK) $(BLAS)
+ 
+ # FFTW (mandatory)
+-FFTW_ROOT  ?= /path/to/your/fftw/installation
++FFTW_ROOT  ?= ${EBROOTFFTWMPI}
+ LLIBS      += -L$(FFTW_ROOT)/lib -lfftw3
+ INCS       += -I$(FFTW_ROOT)/include
+ 
+ # HDF5-support (optional but strongly recommended)
+-#CPP_OPTIONS+= -DVASP_HDF5
+-#HDF5_ROOT  ?= /path/to/your/hdf5/installation
+-#LLIBS      += -L$(HDF5_ROOT)/lib -lhdf5_fortran
+-#INCS       += -I$(HDF5_ROOT)/include
++CPP_OPTIONS+= -DVASP_HDF5
++HDF5_ROOT  ?= ${EBROOTHDF5}
++LLIBS      += -L$(HDF5_ROOT)/lib -lhdf5_fortran
++INCS       += -I$(HDF5_ROOT)/include
+ 
+ # For the VASP-2-Wannier90 interface (optional)
+ #CPP_OPTIONS    += -DVASP2WANNIER90

v/VASP/VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0.eb

@@ -0,0 +1,72 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'MakeCp'
+
+name = 'VASP'
+version = '6.3.2'
+local_cudaversion = '11.6.0'
+versionsuffix = '-CUDA-%s' % local_cudaversion
+
+homepage = 'https://www.vasp.at'
+docurls = 'https://www.vasp.at/wiki/index.php/The_VASP_Manual'
+description = """
+The Vienna Ab initio Simulation Package (VASP) is a local computer program for atomic scale
+materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
+from first principles.
+
+This is a GPU-enabled build.
+
+To use VASP, you need an academic license from University of Vienna.
+Follow the instructions at https://www.vasp.at/index.php/faqs.
+
+Please send us the ID of your VASP license, list of authorized users for whom you require access,
+and their email which is associated with your license (use only https://support.it4i.cz/rt).
+We are responsible for verifying your licenses.
+"""
+
+toolchain = {'name': 'NVHPC', 'version': '22.2'}
+toolchainopts = {'pic': True}
+
+# Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on
+# how to get access to the code
+sources = ['%(namelower)s.%(version)s.tgz']
+patches = ['VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0-adjust-makefile.patch']
+checksums = [
+    'f7595221b0f9236a324ea8afe170637a578cdd5a837cc7679e7f7812f6edf25a',  # vasp.6.3.2.tgz
+    # VASP-6.3.2-NVHPC-22.2-CUDA-11.6.0-adjust-makefile.patch
+    'ba944e61219684af0313fc32fd64c31a0b61919b8c3829ed4651c40d60675ed3',
+]
+
+dependencies = [
+    ('OpenMPI', '4.1.2', versionsuffix),
+    ('FFTW.MPI', '3.3.8'),
+    ('imkl', '2022.1.0', '', True),
+    ('ScaLAPACK', '3.0'),
+    ('HDF5', '1.12.1'),
+    ('QD', '2.3.17'),
+]
+
+prebuildopts = 'cp arch/makefile.include.nvhpc_acc ./makefile.include && '
+
+# VASP uses LIBS as a list of folders
+prebuildopts += 'unset LIBS && '
+
+buildopts = 'std gam ncl '
+
+parallel = 1
+
+files_to_copy = [(['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'],
+    'dirs': []
+}
+
+modluafooter = """
+add_property('state','license')
+add_property('arch', 'gpu')
+"""
+
+
+moduleclass = 'chem'

v/VASP/VASP-6.3.2-intel-2021b-SCPC.eb

@@ -93,4 +93,4 @@ sanity_check_paths = {
 
 modluafooter = 'add_property("state","license")'
 
-moduleclass = 'phys'
+moduleclass = 'chem'

v/vaspkit/vaspkit-1.3.5-foss-2022a-WIP.eb

@@ -0,0 +1,30 @@
+# IT4Innovations 2022
+# JK
+
+easyblock = 'Tarball'
+
+name = 'vaspkit'
+version = '1.3.5'
+
+homepage = 'https://vaspkit.com/'
+docurls = 'https://vaspkit.com/'
+description = """VASPKIT aims at providing a powerful and user-friendly interface to perform high
+ throughput analysis of various material properties from the raw calculated data using the widely-used
+ VASP code."""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(namelower)s.%(version)s.linux.x64.tar.gz']
+patches = ['vaspkit-1.3.5-fix-install.patch']
+
+dependencies = [('matplotlib', '3.5.2')]
+
+sanity_check_paths = {
+    'files': ["bin/vaspkit", "how_to_set_environment_variables"],
+    'dirs': ["bin", "utilities", "examples"],
+}
+
+modloadmsg = "Vaspkit configuration template is available at $EBROOTVASPKIT/how_to_set_environment_variables."
+
+moduleclass = 'tools'

x/XCrySDen/XCrySDen-1.6.2-foss-2022a.eb

@@ -0,0 +1,42 @@
+# Contribution from IT4Innovations National Supercomputing Center, Czech Republic
+# Jakub Kropacek, 2022
+
+name = 'XCrySDen'
+version = '1.6.2'
+
+homepage = "http://www.xcrysden.org/"
+description = """
+XCrySDen is a crystalline and molecular structure visualisation program aiming
+at display of isosurfaces and contours, which can be superimposed on
+crystalline structures and interactively rotated and manipulated.
+"""
+docurls = "http://www.xcrysden.org/Documentation.html"
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+
+source_urls = ["http://www.xcrysden.org/download/"]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['XCrySDen-1.6.2-no-bwidget-tcl-download.patch']
+checksums = [
+    '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f',  # xcrysden-1.6.2.tar.gz
+    'e5f79c77116c6faf441d63f62bb3d22c5520163995b28e505d2168424a587bac',  # XCrySDen-1.6.2-no-bwidget-tcl-download.patch
+]
+
+dependencies = [
+    ('Togl', '2.0'),
+    ('Mesa', '22.0.3'),
+    ('libGLU', '9.0.2'),
+    ('bwidget', '1.9.15'),
+]
+
+# gcc fix by Jakob Schiotz, commit 7433b19bd05d1d511ee135a92b3ba845c89814d7
+prebuildopts = "export LDLIB='-ldl -Wl,--allow-multiple-definition' &&"
+
+sanity_check_commands = [
+    'xcrysden --help',
+    # requires DISPLAY
+    #'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \
+    # && rm output.png',
+]
+
+moduleclass = 'vis'

x/XCrySDen/XCrySDen-1.6.2-intel-2022a.eb

@@ -0,0 +1,40 @@
+# Contribution from IT4Innovations National Supercomputing Center, Czech Republic
+# Jakub Kropacek, 2022
+
+name = 'XCrySDen'
+version = '1.6.2'
+
+homepage = "http://www.xcrysden.org/"
+docurls = "http://www.xcrysden.org/Documentation.html"
+description = """
+XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces
+and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
+It also possesses some tools for analysis of properties in reciprocal space such as interactive selection
+of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces.
+"""
+
+toolchain = {'name': 'intel', 'version': '2022a'}
+
+source_urls = ["http://www.xcrysden.org/download/"]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['XCrySDen-1.6.2-no-bwidget-tcl-download.patch']
+checksums = [
+    '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f',  # xcrysden-1.6.2.tar.gz
+    'e5f79c77116c6faf441d63f62bb3d22c5520163995b28e505d2168424a587bac',  # XCrySDen-1.6.2-no-bwidget-tcl-download.patch
+]
+
+dependencies = [
+    ('Togl', '2.0'),
+    ('Mesa', '22.0.3'),
+    ('libGLU', '9.0.2'),
+    ('bwidget', '1.9.15'),
+]
+
+sanity_check_commands = [
+    'xcrysden --help',
+    # requires DISPLAY
+    #'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \
+    # && rm output.png',
+]
+
+moduleclass = 'vis'

x/xxd/xxd-8.2.4220-GCCcore-11.3.0.eb

@@ -0,0 +1,43 @@
+# IT4Innovations 2022
+# JK
+#16007
+
+# Last contribution from the NIHR Biomedical Research Centre
+# Guy's and St Thomas' NHS Foundation Trust and King's College London
+# uploaded by J. Sassmannshausen
+
+easyblock = 'MakeCp'
+
+name = 'xxd'
+version = '8.2.4220'
+
+homepage = 'https://www.vim.org'
+description = """xxd is part of the VIM package and this will only install xxd, not vim!
+xxd converts to/from hexdumps of binary files."""
+
+toolchain = {'name': 'GCCcore', 'version': '11.3.0'}
+
+source_urls = ['https://github.com/vim/vim/archive/refs/tags']
+sources = ['v%(version)s.tar.gz']
+checksums = [
+    '8b0406834b4f03af8bc6dedbf4c69977f7b9df6905182623842d7c4f3065c604',  # v8.2.4220.tar.gz
+]
+
+builddependencies = [
+    ('binutils', '2.38'),
+]
+
+start_dir = 'src/xxd'
+
+files_to_copy = [
+    (['xxd'], 'bin'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/xxd'],
+    'dirs': [],
+}
+
+sanity_check_commands = ["xxd -h 2>&1 | grep -A 4 '^Usage:'"]
+
+moduleclass = 'tools'