diff --git a/l/libX11/libX11-1.6.3.eb b/l/libX11/libX11-1.6.3.eb index bcb5b714..c760d65f 100644 --- a/l/libX11/libX11-1.6.3.eb +++ b/l/libX11/libX11-1.6.3.eb @@ -13,6 +13,7 @@ source_urls = [XORG_LIB_SOURCE] dependencies = [ ('libxcb', '1.11.1'), + ('xtrans', '1.3.5'), ('fontconfig', '2.11.1'), ] diff --git a/l/libxcb/libxcb-1.11.1.eb b/l/libxcb/libxcb-1.11.1.eb index dcd24217..25975e03 100644 --- a/l/libxcb/libxcb-1.11.1.eb +++ b/l/libxcb/libxcb-1.11.1.eb @@ -23,31 +23,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': [ - 'lib/libxcb%s.a' % - x for x in [ - '', - '-local_composite', - '-damage', - '-dpms', - '-dri2', - '-glx', - '-randr', - '-record', - '-render', - '-res', - '-screensaver', - '-shape', - '-shm', - '-sync', - '-xevie', - '-xf86dri', - '-xfixes', - '-xinerama', - '-xprint', - '-xtest', - '-xv', - '-xvmc']], + 'files': [], 'dirs': [ 'include/xcb', 'lib/pkgconfig'], diff --git a/o/OpenFOAM/OpenFOAM-7-foss-2020a.eb b/o/OpenFOAM/OpenFOAM-7-foss-2020a.eb index 0d139de8..6e7a2869 100644 --- a/o/OpenFOAM/OpenFOAM-7-foss-2020a.eb +++ b/o/OpenFOAM/OpenFOAM-7-foss-2020a.eb @@ -41,7 +41,7 @@ dependencies = [ builddependencies = [ ('Bison', '3.5.3'), - ('CMake', '3.9.0', '', True), + ('CMake', '3.16.4'), ('flex', '2.6.4'), ] diff --git a/p/ParaView/ParaView-5.6.2-foss-2020a-Python-3.7.4-mpi.eb b/p/ParaView/ParaView-5.6.2-foss-2020a-Python-3.7.4-mpi.eb new file mode 100644 index 00000000..0d47fbf3 --- /dev/null +++ b/p/ParaView/ParaView-5.6.2-foss-2020a-Python-3.7.4-mpi.eb @@ -0,0 +1,82 @@ +# JH 2020 + +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.6.2' +versionsuffix = '-Python-%(pyver)s-mpi' + +homepage = "https://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2020a'} +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 = ["ParaView-v%(version)s.tar.xz"] +checksums = ['1f3710b77c58a46891808dbe23dc59a1259d9c6b7bb123aaaeaa6ddf2be882ea'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), + ('XZ', '5.2.5'), + ('HDF5', '1.10.6'), + ('netCDF', '4.7.4'), + ('libGLU', '9.0.1'), + ('X11', '20200222'), + ('Mesa', '20.0.2'), + ('Qt5', '5.14.1'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.2.2'), + ('Szip', '2.1.1'), +] + +builddependencies = [('CMake', '3.16.4')] + +separate_build_dir = True + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DBUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_QT_VERSION=5 -DQT_QMAKE_EXECUTABLE=$EBROOTQT5/bin/qmake ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_ENABLE_PYTHON=ON ' + +# Python +configopts += "-DVTK_WRAP_PYTHON=ON " +configopts += "-DVTK_PYTHON_VERSION=%(pyver)s " +configopts += "-DPYTHON_INCLUDE_DIR=$EBROOTPYTHON/include/python%(pyshortver)s " +configopts += "-DPYTHON_LIBRARY=$EBROOTPYTHON/lib/libpython%%(pyshortver)s.%s " % SHLIB_EXT + +# Third party libs +configopts += '-DVTK_USE_SYSTEM_MPI4PY=ON ' +configopts += "-DVTK_USE_SYSTEM_LZMA=ON " +configopts += "-DVTK_USE_SYSTEM_HDF5=ON " +configopts += "-DVTK_USE_SYSTEM_NETCDF=ON " + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DVTK_OPENGL_HAS_OSMESA=ON ' +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT + + +# Without internet connection turn off testing (uncomment the following line) +# configopts += '-DBUILD_TESTING=OFF ' +# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md +# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly +# Without internet connection, comment the following two lines (configopts and prebuildopts) +configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData ' + +# The ParaView server can be cranky, test downloads are quite often failing, especially in the case +# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the +# first serial attempt would fail. +prebuildopts = 'make VTKData ;' + +sanity_check_paths = { + 'files': ['bin/paraview'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib'], +} + +moduleclass = 'vis' diff --git a/r/RELION/RELION-3.1.0-gompi-2019b.eb b/r/RELION/RELION-3.1.0-gompi-2019b.eb new file mode 100644 index 00000000..f341c974 --- /dev/null +++ b/r/RELION/RELION-3.1.0-gompi-2019b.eb @@ -0,0 +1,33 @@ +# IT4Innovations 2020\ +# LK + +easyblock = 'CMakeMake' + +name = 'RELION' +version = '3.1.0' + +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 local_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': 'gompi', 'version': '2019b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/3dem/relion/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.16.2', '', True), +] + +dependencies = [ + ('X11', '20190717', '', True), + ('libpng', '1.6.37', '', True), + ('FFTW', '3.3.8'), + ('FLTK', '1.3.5', '', True), +] + +separate_build_dir = True + +moduleclass = 'bio' diff --git a/r/RELION/RELION-3.1.0-intel-2020a.eb b/r/RELION/RELION-3.1.0-intel-2020a.eb new file mode 100644 index 00000000..126527ea --- /dev/null +++ b/r/RELION/RELION-3.1.0-intel-2020a.eb @@ -0,0 +1,42 @@ +# IT4Innovations 2020 +# LK + +easyblock = 'CMakeMake' + +name = 'RELION' +version = '3.1.0' + +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': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/3dem/relion/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.16.2')] + +dependencies = [ + ('X11', '20190717', '', ('GCCcore', '8.3.0')), + ('FLTK', '1.3.5', '', True), + ('LibTIFF', '4.1.0', '', ('GCCcore', '8.3.0')), +# ('tbb', '2019_U9', '', ('GCCcore', '8.3.0')), + ('FFTW', '3.3.8'), + ('GTK+', '3.24.13', '', ('GCCcore', '8.3.0')), + ('libXrender', '0.9.9', '', True), +] + +#configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' -DMPI_INCLUDE_PATH=$EBROOTIMPI/include64 " +#configopts += "-DMPI_C_COMPILER=$EBROOTIMPI/bin64/mpiicc -DMPI_CXX_COMPILER=$EBROOTIMPI/bin64/mpiicpc " +#configopts += "-DCUDA=OFF -DCudaTexture=OFF " +#configopts += "-DALTCPU=ON -DMKLFFT=ON " +#configopts += "-DALTCPU=ON -DMKLFFT=ON -DFORCE_OWN_TBB=OFF " + +sanity_check_paths = { + 'files': ['bin/relion'], + 'dirs': [] +} + +moduleclass = 'bio'