new file: g/GROMACS/GROMACS-2022-constantph-fix_missing_header.patch

new file:   g/GROMACS/GROMACS-2022-foss-2022a-constantph.eb
	new file:   g/git/git-2.38.1.eb
	modified:   l/libmad/libmad-0.15.1b-GCCcore-11.3.0.eb
	new file:   l/libmad/libmad-0.15.1b-GCCcore-12.2.0.eb
	new file:   l/libmad/libmad-0.15.1b-remove-depreciated-gcc-option.patch
	new file:   n/NVHPC/NVHPC-23.1.eb
	new file:   n/NVSHMEM/NVSHMEM-2.8.0-gompi-2022a-CUDA-11.7.0.eb
	modified:   o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb
	new file:   s/STAR-CCM+/STAR-CCM+-18.02.008-r8.eb
	new file:   s/SoX/SoX-14.4.2-GCCcore-12.2.0.eb
	modified:   x/XALT/XALT-2.10.45-GPU-eb.eb

g/GROMACS/GROMACS-2022-constantph-fix_missing_header.patch

@@ -0,0 +1,11 @@
+diff -ruN constantph-main.orig/gromacs-constantph/src/gromacs/applied_forces/densityfitting/densityfitting.cpp constantph-main/gromacs-constantph/src/gromacs/applied_forces/densityfitting/densityfitting.cpp
+--- constantph-main.orig/gromacs-constantph/src/gromacs/applied_forces/densityfitting/densityfitting.cpp	2023-03-21 14:25:14.929492000 +0100
++++ constantph-main/gromacs-constantph/src/gromacs/applied_forces/densityfitting/densityfitting.cpp	2023-03-21 14:25:56.962253000 +0100
+@@ -53,6 +53,7 @@
+ #include "gromacs/math/coordinatetransformation.h"
+ #include "gromacs/math/multidimarray.h"
+ #include "gromacs/mdtypes/imdmodule.h"
++#include "gromacs/selection/indexutil.h"
+ #include "gromacs/utility/classhelpers.h"
+ #include "gromacs/utility/exceptions.h"
+ #include "gromacs/utility/keyvaluetreebuilder.h"

g/GROMACS/GROMACS-2022-foss-2022a-constantph.eb

@@ -0,0 +1,78 @@
+# IT4Innovations 2023
+# JK
+# pokus o na prase instalaci devel verze, ktera by v budoucnu mela byt mergnuta do GROMACSu
+
+name = 'GROMACS'
+version = '2022'
+versionsuffix = '-constantph'
+local_commit = '9bb0cc2f'
+
+homepage = 'https://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
+Newtonian equations of motion for systems with hundreds to millions of
+particles.
+
+This is a CPU only build, containing both MPI and threadMPI builds
+for both single and double precision.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['https://gitlab.com/gromacs-constantph/constantph/-/archive/main/']
+sources = [{'download_filename': 'constantph-main.tar.gz', 'filename': 'gromacs-2022-contstantph.tar.gz', 
+'extract_cmd': "tar -xzvf %s --strip 1 constantph-main/gromacs-constantph"}]
+patches = [
+    'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch',
+    'GROMACS-2019_increase_test_timeout_for_GPU.patch',
+    'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch',
+    'GROMACS-2022-constantph-fix_missing_header.patch',
+#    'GROMACS-2021.5_fix_threads_gpu_Gmxapitests.patch',
+]
+checksums = [
+    {'gromacs-2022-contstantph.tar.gz': '58c5b4353de41996a62bbfc0288eb1487eb7ee189210388009776968f4ade9c8'},
+    {'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch':
+     '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275'},
+    {'GROMACS-2019_increase_test_timeout_for_GPU.patch':
+     '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234'},
+    {'GROMACS-2021_fix_gmxapi_gmx_allowed_cmd_name.patch':
+     'b7ffb292ec362e033db1bedd340353f0644dbaae872127750f3dda1ac7e87d49'},
+    {'GROMACS-2022-constantph-fix_missing_header.patch':
+     '1c4a9601c58e6a0c5bc4959790dc1a519c8cbca35b5ca0ac5c12e8a31198b3df'},
+]
+
+builddependencies = [
+    ('CMake', '3.23.1'),
+    ('scikit-build', '0.15.0'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('networkx', '2.8.4'),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.4.0', {
+        'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ",
+        'checksums': ['7fd58e6a4b1391043379e8ba55555ebeba255c5b394f5df9d676e6a5571d7eba'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'

g/git/git-2.38.1.eb

@@ -0,0 +1,30 @@
+# IT4Innovations 2021
+# LK
+
+easyblock = 'ConfigureMake'
+
+name = 'git'
+version = "2.38.1"
+
+homepage = 'http://git-scm.com/'
+description = """Git is a free and open source distributed version control system designed
+to handle everything from small to very large projects with speed and efficiency."""
+
+toolchain = SYSTEM
+
+source_urls = ['https://www.kernel.org/pub/software/scm/git/']
+sources = ['%(name)s-%(version)s.tar.gz']
+checksums = ['620ed3df572a34e782a2be4c7d958d443469b2665eac4ae33f27da554d88b270']
+
+builddependencies = [
+    ('Autoconf', '2.69', '', True)
+]
+
+preconfigopts = 'make configure && '
+
+sanity_check_paths = {
+    'files': ['bin/git'],
+    'dirs': [],
+}
+
+moduleclass = 'tools'

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

@@ -1,7 +1,5 @@
-# Institution: IT4Innovations National Supercomputing Center, Czech Republic
+# IT4Innovations 2023
-# Author: Jakub Kropacek
+# JK
-# License: GPLv3
-# Year: 2022
 
 easyblock = 'ConfigureMake'
 

l/libmad/libmad-0.15.1b-GCCcore-12.2.0.eb

@@ -0,0 +1,30 @@
+# IT4Innovations 2023
+# JK
+
+easyblock = 'ConfigureMake'
+
+name = 'libmad'
+version = '0.15.1b'
+
+homepage = 'https://www.underbit.com/products/mad/'
+description = """MAD is a high-quality MPEG audio decoder."""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = ['https://sourceforge.net/projects/mad/files/%(name)s/%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['libmad-0.15.1b-remove-depreciated-gcc-option.patch']
+checksums = [
+    'bbfac3ed6bfbc2823d3775ebb931087371e142bb0e9bb1bee51a76a6e0078690',  # libmad-0.15.1b.tar.gz
+    # libmad-0.15.1b-remove-depreciated-gcc-option.patch
+    '8f96a23a22ba66e62f32e20064d01f4c7f6a18ba0aab85d3be9ce63794b2c678',
+]
+
+builddependencies = [('binutils', '2.39')]
+
+sanity_check_paths = {
+    'files': ['include/mad.h', 'lib/libmad.a', 'lib/libmad.la', 'lib/libmad.%s' % SHLIB_EXT],
+    'dirs': ['include', 'lib', 'lib64']
+}
+
+moduleclass = 'lib'

l/libmad/libmad-0.15.1b-remove-depreciated-gcc-option.patch

@@ -0,0 +1,29 @@
+# Institution: IT4Innovations National Supercomputing Center, Czech Republic
+# Author: Jakub Kropacek
+# License: GPLv3
+# Year: 2022
+#
+# Option "-fforce-mem" has been removed in GCC 4.3.
+# See https://gcc.gnu.org/gcc-4.3/changes.html
+diff -Nru libmad-0.15.1b.orig/configure libmad-0.15.1b/configure
+--- libmad-0.15.1b.orig/configure	2022-08-19 14:51:49.037627000 +0200
++++ libmad-0.15.1b/configure	2022-08-19 14:52:05.758321053 +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="$optimize -fstrength-reduce"
+diff -Nru libmad-0.15.1b.orig/configure.ac libmad-0.15.1b/configure.ac
+--- libmad-0.15.1b.orig/configure.ac	2022-08-19 14:51:49.051732000 +0200
++++ libmad-0.15.1b/configure.ac	2022-08-19 14:52:10.953461180 +0200
+@@ -140,7 +140,6 @@
+     case "$optimize" in
+ 	-O|"-O "*)
+ 	    optimize="-O"
+-	    optimize="$optimize -fforce-mem"
+ 	    optimize="$optimize -fforce-addr"
+ 	    : #x optimize="$optimize -finline-functions"
+ 	    : #- optimize="$optimize -fstrength-reduce"

n/NVHPC/NVHPC-23.1.eb

@@ -0,0 +1,66 @@
+# IT4Innovations
+# LK 2022
+
+name = 'NVHPC'
+version = '23.1'
+
+homepage = 'https://developer.nvidia.com/hpc-sdk/'
+description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)"""
+
+toolchain = SYSTEM
+
+# By downloading, you accept the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html)
+accept_eula = True
+source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/']
+local_tarball_tmpl = 'nvhpc_2023_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz'
+sources = [local_tarball_tmpl % '%(arch)s']
+checksums = ['55a064415f6d4ce6a01823ee27ebd266f4fb579679871e7c1a7c054bdc18e9f5']
+
+local_gccver = '10.2.0'
+dependencies = [
+    ('GCCcore', local_gccver),
+    ('binutils', '2.35', '', ('GCCcore', local_gccver)),
+    # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails
+    ('numactl', '2.0.13', '', ('GCCcore', local_gccver))
+]
+
+# specify default CUDA version that should be used by NVHPC
+# should match one of the CUDA versions that are included with this NVHPC version
+# (see install_components/Linux_x86_64/20.7/cuda/)
+# for NVHPC 20.7, those are: 11.0, 10.2, 10.1;
+# this version can be tweaked from the EasyBuild command line with
+# --try-amend=default_cuda_version="10.2" (for example)
+default_cuda_version = '12.0'
+
+# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig.
+# The following list gives examples for the easyconfig
+#
+# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA
+# 1) Bundled CUDA
+#    If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with
+#      default_cuda_version = "11.0"
+#    in this easyconfig file; alternatively, it can be specified through the command line during installation with
+#      --try-amend=default_cuda_version="10.2"
+# 2) CUDA provided via EasyBuild
+#    Use CUDAcore as a dependency, for example
+#      dependencies = [('CUDAcore', '11.0.2')]
+#    The parameter default_cuda_version still can be set as above.
+#    If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA)
+#
+# Define a NVHPC-default Compute Capability
+#   cuda_compute_capabilities = "8.0"
+cuda_compute_capabilities = '7.0' #V100 GPU
+# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0
+# Only single values supported, not lists of values!
+#
+# Options to add/remove things to/from environment module (defaults shown)
+#   module_byo_compilers = Yes    # Remove compilers from PATH (Bring-your-own compilers)
+#   module_nvhpc_own_mpi = False  # Add NVHPC's own pre-compiled OpenMPI
+#   module_add_math_libs = Yes    # Add NVHPC's math libraries (which should be there from CUDA anyway)
+#   module_add_profilers = Yes    # Add NVHPC's NVIDIA Profilers
+#   module_add_nccl = Yes         # Add NVHPC's NCCL library
+#   module_add_nvshmem = Yes      # Add NVHPC's NVSHMEM library
+#   module_add_cuda = Yes         # Add NVHPC's bundled CUDA
+
+# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS)
+moduleclass = 'compiler'

n/NVSHMEM/NVSHMEM-2.8.0-gompi-2022a-CUDA-11.7.0.eb

@@ -0,0 +1,73 @@
+# IT4Innovations
+# LK 2023
+
+easyblock = 'ConfigureMake'
+
+name = 'NVSHMEM'
+version = '2.9.0'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://developer.nvidia.com/nvshmem'
+description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides 
+efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a 
+global address space for data that spans the memory of multiple GPUs and can be 
+accessed with fine-grained GPU-initiated operations, CPU-initiated operations, 
+and operations on CUDA streams.
+"""
+
+toolchain = {'name': 'gompi', 'version': '2022a'}
+
+download_instructions = """The sources of NVSHMEM can be downloaded at NVIDIA's webpage when you have signed up for
+their (free) developer program:
+https://developer.nvidia.com/nvshmem-downloads"""
+
+sources = ['%(namelower)s_src_%(version)s-2.tar.xz']
+checksums = ['c0e0d1a5b13f3e2f12fd79b44645dde5370e2baf7392082aee7aa0a0063d75a6']
+
+builddependencies = [
+    ('Autotools', '20220317'),
+    ('pkgconf', '1.8.0'),
+]
+
+dependencies = [
+    ('CUDA', '11.7.0', '', SYSTEM),
+    ('UCX-CUDA', '1.12.1', versionsuffix),
+    ('NCCL', '2.12.12', versionsuffix),
+]
+
+skipsteps = ['configure']
+
+prebuildopts = 'export %s &&' % ' '.join([
+    'NVSHMEM_USE_GDRCOPY=1',
+    'GDRCOPY_HOME=${EBROOTGDRCOPY}',
+
+    'MPI_HOME=${EBROOTOPENMPI}',
+    'NVSHMEM_MPI_SUPPORT=1',
+    'NVSHMEMTEST_USE_MPI_LAUNCHER=1',
+
+    'NCCL_HOME=${EBROOTNCCL}',
+    'NVSHMEM_USE_NCCL=1',
+
+    'NVSHMEM_BUILDDIR=%(builddir)s',
+    'NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj',
+    'NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj',
+    'NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj',
+    'NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj',
+
+    'NVSHMEM_PREFIX=%(installdir)s',
+    'NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples',
+    'NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest',
+    'NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest',
+    'NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test',
+])
+
+preinstallopts = prebuildopts
+
+sanity_check_paths = {
+    'files': ['lib/libnvshmem.a', 'lib/nvshmem_bootstrap_mpi.%s' % SHLIB_EXT],
+    'dirs': ['include']
+}
+
+modextravars = {'NVSHMEM_HOME': '%(installdir)s'}
+
+moduleclass = 'devel'

o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb

@@ -56,19 +56,20 @@ preconfigopts = ' && '.join([
 ])
 
 # CUDA related patches and custom configure option can be removed if CUDA support isn't wanted.
-configopts = '--with-cuda=internal '
+configopts = ' --with-cuda=internal'
 configopts += ' CC=pgcc CXX=pgc++ FC=pgfortran'
+configopts += ' CXXFLAGS="-fPIC"'
 
 # IT4I-specific settings
 
-configopts += '--enable-shared '
+#configopts += '--enable-shared '
-configopts += '--enable-mpi-thread-multiple '
+configopts += ' --enable-mpi-thread-multiple'
-configopts += '--with-verbs '
+configopts += ' --with-verbs'
-configopts += '--enable-mpirun-prefix-by-default '
+configopts += ' --enable-mpirun-prefix-by-default'
-configopts += '--with-hwloc=$EBROOTHWLOC '  # hwloc support
+configopts += ' --with-hwloc=$EBROOTHWLOC'  # hwloc support
-configopts = '--with-tm=/opt/pbs '  # Enable PBS
+configopts = ' --with-tm=/opt/pbs'  # Enable PBS
-configopts += '--enable-mpi-cxx '  # Enable building the C++ MPI bindings
+configopts += ' --enable-mpi-cxx'  # Enable building the C++ MPI bindings
-configopts += '--with-ucx=$EBROOTUCX '
+configopts += ' --with-ucx=$EBROOTUCX'
 
 osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')]
 

s/STAR-CCM+/STAR-CCM+-18.02.008-r8.eb

@@ -0,0 +1,17 @@
+# IT4Innovations 2023
+# JK
+
+name = 'STAR-CCM+'
+version = '18.02.008'
+versionsuffix = '-r8'
+
+homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus'
+description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products
+operating under real-world conditions."""
+
+toolchain = SYSTEM
+
+sources = ['%%(name)s%%(version)s_01_linux-x86_64%s.tar.gz' % versionsuffix]
+checksums = ['20b061fbf981a9e4ce1e6ebbb7d390bbc6f400f89076adf3441a3da39f98a87c']
+
+moduleclass = 'cae'

s/SoX/SoX-14.4.2-GCCcore-12.2.0.eb

@@ -0,0 +1,37 @@
+# IT4Innovations 2023
+# JK
+
+easyblock = 'ConfigureMake'
+
+name = 'SoX'
+version = '14.4.2'
+
+homepage = 'http://sox.sourceforge.net/'
+docurls = 'http://sox.sourceforge.net/Docs/Documentation'
+description = """Sound eXchange, the Swiss Army knife of audio manipulation"""
+
+toolchain = {'name': 'GCCcore', 'version': '12.2.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b45f598643ffbd8e363ff24d61166ccec4836fea6d3888881b8df53e3bb55f6c']
+
+builddependencies = [('binutils', '2.39')]
+
+dependencies = [
+    ('FLAC', '1.4.2'),
+    ('LAME', '3.100'),
+    ('libmad', '0.15.1b'),
+    ('libvorbis', '1.3.7'),
+    ('FFmpeg', '5.1.2'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/play', 'bin/rec', 'bin/sox', 'bin/soxi', 'include/sox.h',
+              'lib/libsox.la', 'lib/libsox.a', 'lib/pkgconfig/sox.pc', 'lib/libsox.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'],
+}
+
+sanity_check_commands = ['sox --help']
+
+moduleclass = 'data'

x/XALT/XALT-2.10.45-GPU-eb.eb

@@ -3,7 +3,7 @@
 
 name = 'XALT'
 version = '2.10.45'
-versionsuffix = "-GPU-eb"
+#versionsuffix = "-GPU-eb"
 
 homepage = 'https://github.com/xalt/xalt'
 description = """XALT 2 is a tool to allow a site to track user executables