Fix and new cgfs 2020b

foss-2020b/ANTLR-2.7.7-GCCcore-10.2.0-Java-11.eb

@@ -0,0 +1,33 @@
+easyblock = 'ConfigureMake'
+
+name = 'ANTLR'
+version = '2.7.7'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://www.antlr2.org/'
+description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS)
+ is a language tool that provides a framework for constructing recognizers,
+ compilers, and translators from grammatical descriptions containing
+ Java, C#, C++, or Python actions."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = ['https://www.antlr2.org/download/']
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['%(name)s-%(version)s_includes.patch']
+checksums = [
+    '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9',  # antlr-2.7.7.tar.gz
+    'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66',  # ANTLR-2.7.7_includes.patch
+]
+
+builddependencies = [('binutils', '2.35')]
+dependencies = [('Java', '11', '', True)]
+
+configopts = '--disable-examples --disable-csharp --disable-python'
+
+sanity_check_paths = {
+    'files': ['bin/antlr', 'bin/antlr-config'],
+    'dirs': ['include'],
+}
+
+moduleclass = 'tools'

foss-2020b/CDO-1.9.9-gompi-2020b.eb

@@ -9,15 +9,16 @@ description = """CDO is a collection of command line Operators to manipulate and
 toolchain = {'name': 'gompi', 'version': '2020b'}
 toolchainopts = {'pic': True, 'usempi': True}
 
-source_urls = ['https://code.mpimet.mpg.de/attachments/download/20826/']
+source_urls = ['https://code.mpimet.mpg.de/attachments/download/23323/']
 sources = [SOURCELOWER_TAR_GZ]
 
 dependencies = [
+    ('Python', '3.8.6'),
     ('HDF5', '1.10.7'),
     ('netCDF', '4.7.4'),
     ('YAXT', '0.6.2'),
-    ('ecCodes', '2.15.0'),
-    ('PROJ', '6.2.1'),
+    ('ecCodes', '2.19.1'),
+    ('PROJ', '7.2.0'),
 ]
 
 configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF --with-eccodes=$EBROOTECCODES --with-proj=$EBROOTPROJ"

foss-2020b/ELIC_Python-1-foss-2020b-Python-3.8.6.eb

@@ -16,14 +16,14 @@ builddependencies = [
 dependencies = [
     ('Python', '3.8.6'),
     ('SciPy-bundle', '2020.11'),
-    #('matplotlib', '3.1.1', versionsuffix),
+    ('matplotlib', '3.3.3', versionsuffix),
     ('GDAL', '3.2.0', versionsuffix),
-    ('NCL', '6.6.2'),
-    #('CDO', '1.9.9'),
-    #('NCO', '4.9.5'),
+    #('NCL', '6.6.2'),
+    ('CDO', '1.9.9'),
+    ('NCO', '4.9.5'),
     ('ncview', '2.1.7'),
     ('libmo_unpack', '3.1.2'),
-    #('orca', '1.3.0'),
+    ('orca', '3.4.3'),
 ]
 
 exts_defaultclass = 'PythonPackage'
@@ -70,7 +70,7 @@ modextrapaths = {
 postinstallcmds = [
     "cd %(installdir)s && " +
     'pip install setuptools --upgrade && ' +
-    'pip install olefile Pillow pyproj pyshp chardet urllib3 --install-option "--prefix=%(installdir)s" && ' +
+    'pip install olefile pyproj pyshp chardet urllib3 --install-option "--prefix=%(installdir)s" && ' +
     'pip install OWSLib ' +
                 'netCDF4 ' +
                 'dask ' +

foss-2020b/ESMF-8.0.1-foss-2020b.eb

@@ -22,8 +22,9 @@ dependencies = [
     ('netCDF-C++4', '4.3.1'),
 ]
 
-buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include '
-buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"'
+buildopts = 'ESMF_F90COMPILEOPTS="-O -fPIC  -m64 -mcmodel=small -pthread -ffree-line-length-none -fopenmp -fallow-argument-mismatch" '
+buildopts += 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include '
+buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`" '
 
 # too parallel causes the build to become really slow
 maxparallel = 8

foss-2020b/HDF-4.2.15-GCCcore-10.2.0.eb

@@ -33,6 +33,7 @@ dependencies = [
 preconfigopts = "LIBS='-ltirpc' "
 configopts = '--with-szlib=$EBROOTSZIP '
 configopts += '--includedir=%(installdir)s/include/%(namelower)s '
+buildopts = 'FFLAGS="$FFLAGS -fallow-argument-mismatch -I../src" '
 
 modextrapaths = {'CPATH': 'include/hdf'}
 

foss-2020b/NCO-4.9.5-gompi-2020b.eb

@@ -18,7 +18,7 @@ builddependencies = [
 
 dependencies = [
     ('UDUNITS', '2.2.26'),
-    ('expat', '2.2.7'),
+    ('expat', '2.2.9'),
     ('ANTLR', '2.7.7', '-Java-11'),
     ('libdap', '3.20.6'),
     ('GSL', '2.6'),

foss-2020b/Pillow-8.0.1-GCCcore-10.2.0-Python-3.8.6.eb

@@ -0,0 +1,33 @@
+easyblock = 'PythonPackage'
+
+name = 'Pillow'
+version = '8.0.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'https://pillow.readthedocs.org/'
+description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors.
+ PIL is the Python Imaging Library by Fredrik Lundh and Contributors."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+builddependencies = [('binutils', '2.35')]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('libjpeg-turbo', '2.0.5'),
+    ('libpng', '1.6.37'),
+    ('zlib', '1.2.11'),
+    ('LibTIFF', '4.1.0'),
+    ('freetype', '2.10.3')
+]
+
+download_dep_fail = True
+use_pip = True
+sanity_pip_check = True
+
+options = {'modulename': 'PIL'}
+
+moduleclass = 'vis'

foss-2020b/YAXT-0.6.2-gompi-2020b.eb

@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'YAXT'
+version = '0.6.2'
+
+homepage = 'https://www.dkrz.de/redmine/projects/yaxt'
+description = "Yet Another eXchange Tool"
+
+toolchain = {'name': 'gompi', 'version': '2020b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://www.dkrz.de/redmine/attachments/download/492/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['7fc9b3e5dd2e0d3d5846f389a01c935aa40528eb09d82162b76c061b496a3c5b']
+
+configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"'
+
+sanity_check_paths = {
+    'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT],
+    'dirs': ['include/xt'],
+}
+
+moduleclass = 'tools'

foss-2020b/ecCodes-2.19.1-foss-2020b-Python-3.8.6.eb

@@ -19,7 +19,7 @@ dependencies = [
     ('netCDF', '4.7.4'),
     ('JasPer', '2.0.14'),
     ('Python', '3.8.6'),
-    ('SciPy-bundle', '2020.11', '-Python-3.8.6')
+    ('SciPy-bundle', '2020.11'),
 ]
 
 separate_build_dir = True

foss-2020b/libdap-3.20.6-GCCcore-10.2.0.eb

@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'libdap'
+version = '3.20.6'
+
+homepage = 'https://www.opendap.org/software/libdap'
+description = """A C++ SDK which contains an implementation of DAP 2.0 and
+ DAP4.0. This includes both Client- and Server-side support classes."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+source_urls = ['https://www.opendap.org/pub/source/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['35cc7f952d72de4936103e8a95c67ac8f9b855c9211fae73ad065331515cc54a']
+
+builddependencies = [
+    ('binutils', '2.35'),
+    ('Bison', '3.7.1'),
+    ('flex', '2.6.4'),
+]
+
+dependencies = [
+    ('cURL', '7.72.0'),
+    ('libxml2', '2.9.10'),
+    ('libtirpc', '1.2.6'),
+    ('PCRE', '8.44'),
+    ('util-linux', '2.36'),
+]
+
+configopts = 'TIRPC_LIBS="-ltirpc"'
+
+sanity_check_paths = {
+    'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT],
+    'dirs': ['include'],
+}
+
+moduleclass = 'lib'

foss-2020b/matplotlib-3.3.3-foss-2020b-Python-3.8.6.eb

@@ -0,0 +1,63 @@
+easyblock = 'PythonBundle'
+
+name = 'matplotlib'
+version = '3.3.3'
+versionsuffix = '-Python-%(pyver)s'
+
+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': 'foss', 'version': '2020b'}
+
+builddependencies = [
+    ('pkg-config', '0.29.2'),
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('libjpeg-turbo', '2.0.5'),
+    ('SciPy-bundle', '2020.11'),
+    ('libpng', '1.6.37'),
+    ('zlib', '1.2.11'),
+    ('LibTIFF', '4.1.0'),
+    ('freetype', '2.10.3'),
+    ('Tkinter', '%(pyver)s'),
+    ('Pillow', '8.0.1', versionsuffix),
+]
+
+use_pip = True
+sanity_pip_check = True
+
+exts_list = [
+    ('Cycler', '0.10.0', {
+        'modulename': 'cycler',
+        'source_tmpl': 'cycler-%(version)s.tar.gz',
+        'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'],
+    }),
+    ('kiwisolver', '1.1.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'],
+    }),
+    (name, version, {
+        'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'],
+    }),
+]
+
+postinstallcmds = [
+    "cd %(installdir)s && " +
+    'python3 -m pip install --upgrade Pillow '
+]
+
+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'

foss-2020b/netCDF-4.7.4-gompi-2020b.eb

@@ -12,6 +12,10 @@ toolchainopts = {'pic': True, 'usempi': True}
 source_urls = ['https://github.com/Unidata/netcdf-c/archive/']
 sources = ['v%(version)s.tar.gz']
 patches = ['netCDF-%(version)s_fix-ocdebug.patch']
+checksums = [
+    '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b',  # v4.7.4.tar.gz
+    '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9',  # netCDF-4.7.4_fix-ocdebug.patch
+]
 
 builddependencies = [
     ('Autotools', '20200321'),

foss-2020b/orca-3.4.3-GCCcore-10.2.0.eb

@@ -0,0 +1,34 @@
+# Author: Pavel Grochal (INUITS)
+# License: GPLv2
+
+easyblock = 'Binary'
+
+name = 'orca'
+version = '3.4.3'
+
+homepage = 'https://github.com/plotly/orca'
+description = """Orca is an Electron app that generates images and reports of Plotly things like 
+plotly.js graphs, dash apps, dashboards from the command line."""
+
+toolchain = {'name': 'GCCcore', 'version': '10.2.0'}
+
+# https://github.com/plotly/orca/
+github_account = 'plotly'
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [('binutils', '2.35')]
+
+dependencies = [
+    ('nodejs', '12.19.0'),
+]
+
+install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s electron@6.1.4 v%(version)s.tar.gz'
+
+sanity_check_paths = {
+    'files': ['bin/%(namelower)s'],
+    'dirs': ['lib/node_modules/%(namelower)s'],
+}
+sanity_check_commands = ['%(namelower)s --help']
+
+moduleclass = 'vis'

intel-2020b/FFTW-3.3.8-intel-2020b.eb

@@ -0,0 +1,30 @@
+name = 'FFTW'
+version = '3.3.8'
+
+homepage = 'http://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': 'intel', 'version': '2020b'}
+toolchainopts = {'pic': True}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+patches = ['FFTW-%(version)s_fix-icc-no-gcc.patch']
+checksums = [
+    '6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303',  # fftw-3.3.8.tar.gz
+    '1b3319b98a2ca4ead68290b3229385c0573e22749a5a2ffb49486a0bbb37dc1e',  # FFTW-3.3.8_fix-icc-no-gcc.patch
+]
+
+# 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
+
+# compilation fails on AMD systems when configuring with --enable-avx-128-fma,
+# because Intel compilers do not support FMA4 instructions
+use_fma4 = False
+
+runtest = 'check'
+
+moduleclass = 'numlib'

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

@@ -0,0 +1,21 @@
+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']
+
+dependencies = [
+    ('zlib', '1.2.11'),
+    ('Szip', '2.1.1'),
+]
+
+moduleclass = 'data'

intel-2020b/netCDF-4.7.4-iimpi-2020b.eb

@@ -0,0 +1,38 @@
+name = 'netCDF'
+version = '4.7.4'
+
+homepage = 'https://www.unidata.ucar.edu/software/netcdf/'
+description = """NetCDF (network Common Data Form) is a set of software libraries
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented
+ scientific data."""
+
+toolchain = {'name': 'iimpi', 'version': '2020b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/Unidata/netcdf-c/archive/']
+sources = ['v%(version)s.tar.gz']
+patches = ['netCDF-%(version)s_fix-ocdebug.patch']
+checksums = [
+    '99930ad7b3c4c1a8e8831fb061cb02b2170fc8e5ccaeda733bd99c3b9d31666b',  # v4.7.4.tar.gz
+    '94c9883005f189a4551947e04191a68199cf4cdcada4b2d313115720fb4690e9',  # netCDF-4.7.4_fix-ocdebug.patch
+]
+
+builddependencies = [
+    ('Autotools', '20200321'),
+    ('CMake', '3.18.4'),
+    ('Doxygen', '1.8.20'),
+]
+
+dependencies = [
+    ('HDF5', '1.10.7'),
+    ('cURL', '7.72.0'),
+    ('Szip', '2.1.1'),
+]
+
+# make sure both static and shared libs are built
+configopts = [
+    "-DBUILD_SHARED_LIBS=OFF ",
+    "-DBUILD_SHARED_LIBS=ON ",
+]
+
+moduleclass = 'data'

intel-2020b/netCDF-Fortran-4.5.3-iimpi-2020b.eb

@@ -0,0 +1,25 @@
+name = 'netCDF-Fortran'
+version = '4.5.3'
+
+homepage = 'https://www.unidata.ucar.edu/software/netcdf/'
+description = """NetCDF (network Common Data Form) is a set of software libraries
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented
+ scientific data."""
+
+toolchain = {'name': 'iimpi', 'version': '2020b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['c6da30c2fe7e4e614c1dff4124e857afbd45355c6798353eccfa60c0702b495a']
+
+builddependencies = [
+    ('M4', '1.4.18'),
+]
+
+dependencies = [('netCDF', '4.7.4')]
+
+# (too) parallel build fails, but single-core build is fairly quick anyway (~1min)
+parallel = 1
+
+moduleclass = 'data'