Merge branch 'it4i-karolina'

c/CGAL/CGAL-5.2-gompi-2020b.eb

@@ -0,0 +1,41 @@
+# IT4Innovtions
+# LK 2021
+
+name = 'CGAL'
+version = '5.2'
+
+homepage = 'https://www.cgal.org/'
+description = """The goal of the CGAL Open Source Project is to provide easy access to efficient
+ and reliable geometric algorithms in the form of a C++ library."""
+
+toolchain = {'name': 'gompi', 'version': '2020b'}
+toolchainopts = {'strict': True}
+
+source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['744c86edb6e020ab0238f95ffeb9cf8363d98cde17ebb897d3ea93dac4145923']
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+    ('Eigen', '3.3.8'),
+]
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('Python', '3.8.6'),
+    ('Boost', '1.74.0'),
+    ('MPFR', '4.1.0'),
+    ('GMP', '6.2.0'),
+    ('Mesa', '20.2.1'),
+    ('libGLU', '9.0.1'),
+    ('Qt5', '5.14.2'),
+]
+
+configopts = "-DCGAL_HEADER_ONLY=OFF "
+configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
+configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
+configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
+configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON "
+configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON "
+
+moduleclass = 'numlib'

c/CGAL/CGAL-5.2-iimpi-2020b.eb

@@ -0,0 +1,41 @@
+# IT4Innovtions
+# LK 2021
+
+name = 'CGAL'
+version = '5.2'
+
+homepage = 'https://www.cgal.org/'
+description = """The goal of the CGAL Open Source Project is to provide easy access to efficient
+ and reliable geometric algorithms in the form of a C++ library."""
+
+toolchain = {'name': 'iimpi', 'version': '2020b'}
+toolchainopts = {'strict': True}
+
+source_urls = ['https://github.com/CGAL/cgal/releases/download/v%(version)s/']
+sources = [SOURCE_TAR_XZ]
+checksums = ['744c86edb6e020ab0238f95ffeb9cf8363d98cde17ebb897d3ea93dac4145923']
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+    ('Eigen', '3.3.8'),
+]
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('Python', '3.8.6'),
+    ('Boost', '1.74.0'),
+    ('MPFR', '4.1.0'),
+    ('GMP', '6.2.0'),
+    ('Mesa', '20.2.1'),
+    ('libGLU', '9.0.1'),
+    ('Qt5', '5.14.2'),
+]
+
+configopts = "-DCGAL_HEADER_ONLY=OFF "
+configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include "
+configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT
+configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT
+configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON "
+configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON "
+
+moduleclass = 'numlib'

g/gnuplot/gnuplot-5.4.1-GCCcore-10.2.0.eb

@@ -0,0 +1,48 @@
+# IT4Innovations
+# # LK 2021
+
+easyblock = 'ConfigureMake'
+
+name = 'gnuplot'
+version = '5.4.1'
+
+homepage = 'http://gnuplot.sourceforge.net/'
+description = """Portable interactive, function plotting utility"""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = [('https://sourceforge.net/projects/gnuplot/files/gnuplot/%(version)s', 'download')]
+sources = [SOURCE_TAR_GZ]
+checksums = ['6b690485567eaeb938c26936e5e0681cf70c856d273cc2c45fabf64d8bc6590e']
+
+builddependencies = [
+    ('binutils', '2.35'),
+    ('pkg-config', '0.29.2'),
+    ('Autotools', '20200321'),
+]
+
+dependencies = [
+    ('ncurses', '6.2'),
+    ('cairo', '1.16.0'),
+    ('libjpeg-turbo', '2.0.5'),
+    ('libpng', '1.6.37'),
+    ('libgd', '2.3.0'),
+    ('Pango', '1.47.0'),
+    ('libcerf', '1.14'),
+    ('X11', '20201008'),
+    ('Qt5', '5.14.2'),
+    ('Lua', '5.4.2'),
+]
+
+preconfigopts = 'autoreconf && '
+
+configopts = '--with-qt=qt5 --without-latex '
+
+sanity_check_paths = {
+    'files': ['bin/gnuplot'],
+    'dirs': []
+}
+# make sure that pdf terminal type is available
+sanity_check_commands = ["gnuplot -e 'set terminal pdf'"]
+
+moduleclass = 'vis'

h/HDF5/HDF5-1.10.7-iimpi-2020b.eb

@@ -0,0 +1,29 @@
+# IT4Innovations
+# LK 2021
+
+name = 'HDF5'
+version = '1.10.7'
+
+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 = ['7a1a0a54371275ce2dfc5cd093775bb025c365846512961e7e5ceaecb437ef15']
+
+# AMD/intel cpu
+import os
+if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
+  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) && "
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('Szip', '2.1.1'),
+]
+
+moduleclass = 'data'

m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb

@@ -0,0 +1,29 @@
+# IT4Innovations
+# LK 2021
+
+easyblock = 'PythonPackage'
+
+name = 'Mako'
+version = '1.1.3'
+
+homepage = 'https://www.makotemplates.org'
+description = """A super-fast templating language that borrows the best ideas from the existing templating languages"""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+sources = [SOURCE_TAR_GZ]
+checksums = ['8195c8c1400ceb53496064314c6736719c6f25e7479cd24c77be3d9361cddc27']
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+builddependencies = [('binutils', '2.35')]
+multi_deps = {'Python': ['3.8.6']}
+
+sanity_check_paths = {
+    'files': ['bin/mako-render'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'],
+}
+
+moduleclass = 'devel'

o/OpenFOAM/OpenFOAM-v2106-foss-2020b.eb

@@ -31,9 +31,9 @@ dependencies = [
     # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes)
     ('METIS', '5.1.0'),
     ('SCOTCH', '6.1.0'),
-    ('CGAL', '3.2.1'),
+    ('CGAL', '5.2'),
     ('ParaView', '5.9.1', '-mpi'),
-    ('gnuplot', '5.4.2'),
+    ('gnuplot', '5.4.1'),
 ]
 
 builddependencies = [

o/OpenFOAM/OpenFOAM-v2106-intel-2020b.eb

@@ -0,0 +1,45 @@
+# IT4Innovations
+# LK 2021
+
+name = 'OpenFOAM'
+version = 'v2106'
+
+homepage = 'https://www.openfoam.com/'
+description = """OpenFOAM is a free, open source CFD software package.
+ OpenFOAM has an extensive range of features to solve anything from complex fluid flows
+ involving chemical reactions, turbulence and heat transfer,
+ to solid dynamics and electromagnetics."""
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'cstd': 'c++11'}
+
+source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/']
+sources = [SOURCE_TGZ]
+patches = [
+    ('OpenFOAM-v2012-cleanup.patch', 1),
+    'OpenFOAM-v1906-wmake-ompi.patch',
+]
+checksums = [
+    '11e41e5b9a253ef592a8f6b79f6aded623b28308192d02cec1327078523b5a37',  # OpenFOAM-v2106.tgz
+    'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43',  # OpenFOAM-v2012-cleanup.patch
+    '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505',  # OpenFOAM-v1906-wmake-ompi.patch
+]
+
+dependencies = [
+    ('libreadline', '8.0'),
+    ('ncurses', '6.2'),
+    # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes)
+    ('METIS', '5.1.0'),
+    ('SCOTCH', '6.1.0'),
+    ('CGAL', '5.2'),
+    ('ParaView', '5.9.1', '-mpi'),
+    ('gnuplot', '5.4.1'),
+]
+
+builddependencies = [
+    ('Bison', '3.7.1'),
+    ('CMake', '3.18.4'),
+    ('flex', '2.6.4'),
+]
+
+moduleclass = 'cae'

p/ParaView/ParaView-5.9.1-intel-2020b-mpi.eb

@@ -0,0 +1,60 @@
+# IT4Innovations
+# LK 2021
+
+easyblock = 'CMakeMake'
+
+name = 'ParaView'
+version = '5.9.1'
+versionsuffix = '-mpi'
+
+homepage = "https://www.paraview.org"
+description = "ParaView is a scientific parallel visualizer."
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile='
+source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix]
+sources = ["%(name)s-v%(version)s.tar.gz"]
+checksums = ['efbcba00ba38c23d0ada1bde7144a8745caa308d9e1f94a4a71d8af63732266f']
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('XZ', '5.2.5'),
+    ('HDF5', '1.10.7'),
+    ('netCDF', '4.7.4'),
+    ('libGLU', '9.0.1'),
+    ('X11', '20201008'),
+    ('Mesa', '20.2.1'),
+    ('Qt5', '5.14.2'),
+    ('zlib', '1.2.11'),
+    ('FFmpeg', '4.3.1'),
+    ('Szip', '2.1.1'),
+]
+
+builddependencies = [('CMake', '3.18.4')]
+
+separate_build_dir = True
+
+# Paraview
+configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON '
+configopts += '-DPARAVIEW_USE_MPI=ON '
+configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON '
+configopts += '-DPARAVIEW_USE_PYTHON=ON '
+configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON '
+
+# OpenGL & Mesa
+configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT
+configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include '
+
+sanity_check_paths = {
+    'files': ['bin/paraview', 'bin/pvpython'],
+    'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ['python -c "import paraview"']
+
+modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'vis'

q/Qt5/Qt5-5.14.2-GCCcore-10.2.0.eb

@@ -0,0 +1,84 @@
+# IT4Innovatins
+# LK 2021
+
+easyblock = 'EB_Qt'
+
+name = 'Qt5'
+version = '5.14.2'
+
+homepage = 'https://qt.io/'
+description = "Qt is a comprehensive cross-platform C++ application framework."
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X)
+toolchainopts = {'vectorize': False}
+
+source_urls = [
+    'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/',
+    'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/',
+    'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/',
+]
+sources = ['qt-everywhere-src-%(version)s.tar.xz']
+patches = [
+    'Qt5-5.13.1_fix-avx2.patch',
+    'Qt5-5.13.1_fix-qmake-libdir.patch',
+    'Qt5-5.14.1_fix-OF-Gentoo.patch',
+    'Qt5-5.14.2_fix-missing-stdint.patch',
+    'Qt5-5.14.2_fix-webengine-bison.patch',
+    'Qt5-5.14.2_fix-std-runtime_error.patch',
+    'Qt5-5.14.2_fix-include-math.patch',
+]
+checksums = [
+    'c6fcd53c744df89e7d3223c02838a33309bd1c291fcb6f9341505fe99f7f19fa',  # qt-everywhere-src-5.14.2.tar.xz
+    '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc',  # Qt5-5.13.1_fix-avx2.patch
+    '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63',  # Qt5-5.13.1_fix-qmake-libdir.patch
+    '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa',  # Qt5-5.14.1_fix-OF-Gentoo.patch
+    '648e2a92d5ea139543db5d01a80aa33d4721e52bb59c785490b64497b0ede4ab',  # Qt5-5.14.2_fix-missing-stdint.patch
+    '6ace4735e35dee95d6b6c7eea3a7c46c264589a319d745310282ee724f632861',  # Qt5-5.14.2_fix-webengine-bison.patch
+    '290d91efe8fc7c6daedf01f4a055ff30123c987d41b1832a34920ef521579f5c',  # Qt5-5.14.2_fix-std-runtime_error.patch
+    '32c975b4ad12150f872554f1960c7108bc9c994e318988bab27e762a6c666fa2',  # Qt5-5.14.2_fix-include-math.patch
+]
+
+builddependencies = [
+    ('binutils', '2.35'),
+    ('pkg-config', '0.29.2'),
+    # deps for QtWebEngine
+    ('Bison', '3.7.1'),
+    ('flex', '2.6.4'),
+    ('gperf', '3.1'),
+    ('Ninja', '1.10.1'),
+#    ('Python', '2.7.18'),
+    ('re2c', '2.0.3')
+]
+
+dependencies = [
+    ('double-conversion', '3.1.5'),
+    ('GLib', '2.66.1'),
+    ('PCRE2', '10.35'),
+    ('libpng', '1.6.37'),
+    # deps for QtWebEngine
+    ('X11', '20201008'),
+    ('fontconfig', '2.13.92'),
+    ('DBus', '1.13.18'),
+    ('libevent', '2.1.12'),
+    ('libGLU', '9.0.1'),
+    ('libjpeg-turbo', '2.0.5'),
+    ('NSS', '3.57'),
+    ('snappy', '1.1.8'),
+    ('JasPer', '2.0.24'),
+    ('bzip2', '1.0.8'),
+    # OS dependency should be preferred if the os version is more recent then this version,
+    # it is nice to have an up to date openssl for security reasons
+    # ('OpenSSL', '1.1.1h'),  # Qt5 > 5.15.0 requires OpenSSL 1.1.1
+]
+
+osdependencies = [OS_PKG_OPENSSL_DEV]
+
+# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x)
+# qtwayland fails to build on (some) Centos 7 systems
+configopts = '-skip qtgamepad  -skip qtwayland'
+
+# make sure QtWebEngine component is being built & installed
+check_qtwebengine = True
+
+moduleclass = 'devel'

s/SciPy-bundle/SciPy-bundle-2020.11-intel-2020b.eb

@@ -0,0 +1,70 @@
+# IT4Innovations
+# LK 2021
+
+easyblock = 'PythonBundle'
+
+name = 'SciPy-bundle'
+version = '2020.11'
+
+homepage = 'https://python.org/'
+description = "Bundle of Python packages for scientific software"
+
+toolchain = {'name': 'intel', 'version': '2020b'}
+toolchainopts = {'pic': True, 'lowopt': True}
+
+builddependencies = [('hypothesis', '5.41.2')]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('pybind11', '2.6.0'),  # required by scipy
+]
+
+use_pip = True
+
+preconfigopts = [ 'export MKL_DEBUG_CPU_TYPE=5 && ']
+
+exts_default_options = {'source_urls': [PYPI_SOURCE]}
+
+# order is important!
+exts_list = [
+    ('numpy', '1.19.4', {
+        'source_tmpl': '%(name)s-%(version)s.zip',
+        'patches': [
+            'numpy-1.18.2-mkl.patch',
+            'numpy-1.19.4_disable-broken-test.patch',
+        ],
+        'checksums': [
+            '141ec3a3300ab89c7f2b0775289954d193cc8edb621ea05f99db9cb181530512',  # numpy-1.19.4.zip
+            'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf',  # numpy-1.18.2-mkl.patch
+             #numpy-1.19.4_disable-broken-test.patch
+            '9cc8bbd106ecba603254536101f53fdc200e81d43ca4800b5a84be9b645e9320',
+        ],
+    }),
+    ('scipy', '1.5.4', {
+        'checksums': ['4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b'],
+    }),
+    ('mpi4py', '3.0.3', {
+        'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'],
+    }),
+    ('numexpr', '2.7.1', {
+        'checksums': ['b0d239d9827e1bcee08344fd05835823bc60aff97232e35a928214d03ff802b1'],
+    }),
+    ('Bottleneck', '1.3.2', {
+        'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'],
+    }),
+    ('pandas', '1.1.4', {
+        'checksums': ['a979d0404b135c63954dea79e6246c45dd45371a88631cdbb4877d844e6de3b6'],
+        # strip out use of -Werror to avoid failing compilation due to Intel compiler warning
+        'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """,
+    }),
+    ('mpmath', '1.1.0', {
+        'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'],
+    }),
+    ('deap', '1.3.1', {
+        'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'],
+    }),
+]
+
+sanity_pip_check = True
+
+moduleclass = 'lang'

s/SciPy-bundle/SciPy-bundle-2021.05-intel-2020b.eb

@@ -28,6 +28,7 @@ exts_list = [
         'patches': [
             'numpy-1.20.3_skip-ppc-long-complex-test.patch',
             'numpy-1.20.3_xfail-test-nan.patch',
+            'numpy-1.18.2-mkl.patch',
         ],
         'checksums': [
             'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69',  # numpy-1.20.3.zip