From c809a96fcc4d632cdec7eff5138a7bb17aa28c00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= Date: Mon, 19 Jun 2017 12:56:34 +0200 Subject: [PATCH] new file: e/Embree/Embree-2.16.2.eb new file: g/GDAL/GDAL-2.1.3-Python-2.7.13-without-intel.eb new file: i/ispc/ispc-1.9.1.eb new file: o/OSPRay/OSPRay-1.3.0.eb new file: p/ParaView/ParaView-5.1.2-intel-2017a-mpi-OSPRay.eb new file: p/ParaView/Paraview-5.1.2-intel-2017a-OSPRay.eb new file: s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.eb new file: s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.patch new file: v/VASP/VASP-5.4.4-intel-2017a-03.eb modified: v/VASP/VASP-5.4.4-intel-2017a.eb --- e/Embree/Embree-2.16.2.eb | 31 ++++++++++++ .../GDAL-2.1.3-Python-2.7.13-without-intel.eb | 47 +++++++++++++++++ i/ispc/ispc-1.9.1.eb | 26 ++++++++++ o/OSPRay/OSPRay-1.3.0.eb | 35 +++++++++++++ .../ParaView-5.1.2-intel-2017a-mpi-OSPRay.eb | 50 +++++++++++++++++++ .../Paraview-5.1.2-intel-2017a-OSPRay.eb | 26 ++++++++++ s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.eb | 35 +++++++++++++ s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.patch | 20 ++++++++ v/VASP/VASP-5.4.4-intel-2017a-03.eb | 48 ++++++++++++++++++ v/VASP/VASP-5.4.4-intel-2017a.eb | 6 ++- 10 files changed, 322 insertions(+), 2 deletions(-) create mode 100644 e/Embree/Embree-2.16.2.eb create mode 100644 g/GDAL/GDAL-2.1.3-Python-2.7.13-without-intel.eb create mode 100644 i/ispc/ispc-1.9.1.eb create mode 100644 o/OSPRay/OSPRay-1.3.0.eb create mode 100644 p/ParaView/ParaView-5.1.2-intel-2017a-mpi-OSPRay.eb create mode 100644 p/ParaView/Paraview-5.1.2-intel-2017a-OSPRay.eb create mode 100644 s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.eb create mode 100644 s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.patch create mode 100644 v/VASP/VASP-5.4.4-intel-2017a-03.eb diff --git a/e/Embree/Embree-2.16.2.eb b/e/Embree/Embree-2.16.2.eb new file mode 100644 index 00000000..99b5f3bc --- /dev/null +++ b/e/Embree/Embree-2.16.2.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Embree' +version = '2.16.2' + +homepage = 'https://embree.github.io/index.html' +description = """ + Embree is a collection of high-performance ray tracing kernels, developed at Intel.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['https://github.com/embree/embree/archive'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.8.1', '', True), +] + +dependencies = [ + ('tbb', '4.4.2.152', '', True), + ('ispc', '1.9.1', '', True), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libospray.so'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' diff --git a/g/GDAL/GDAL-2.1.3-Python-2.7.13-without-intel.eb b/g/GDAL/GDAL-2.1.3-Python-2.7.13-without-intel.eb new file mode 100644 index 00000000..70f3d9a2 --- /dev/null +++ b/g/GDAL/GDAL-2.1.3-Python-2.7.13-without-intel.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.3' +versionsuffix = '-Python-%(pyver)s-without-intel' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +patches = ['GDAL-%(version)s_fix-uchar-definition.patch'] + +dependencies = [ + ('Python', '2.7.13'), +# ('netCDF', '4.4.1.1', '', ('intel', '2017a')), + ('expat', '2.2.0'), + ('GEOS', '3.6.1', '-Python-%(pyver)s'), + ('SQLite', '3.17.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.29'), + ('libjpeg-turbo', '1.5.1'), +# ('JasPer', '2.0.12', '', ('intel', '2017a')), + ('LibTIFF', '4.0.7'), + ('zlib', '1.2.11'), +# ('cURL', '7.53.1'), + ('PCRE', '8.40'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/i/ispc/ispc-1.9.1.eb b/i/ispc/ispc-1.9.1.eb new file mode 100644 index 00000000..4586780b --- /dev/null +++ b/i/ispc/ispc-1.9.1.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'ispc' +version = '1.9.1' + +homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/' +description = """Intel SPMD Program Compilers; An open-source compiler for high-performance + SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, + with extensions for 'single program, multiple data' (SPMD) programming. + Under the SPMD model, the programmer writes a program that generally appears + to be a regular serial program, though the execution model is actually that + a number of program instances execute in parallel on the hardware.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['ispc-v%(version)s-linux.tar.gz'] +source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')] + +sanity_check_paths = { + 'files': ["ispc"], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'compiler' diff --git a/o/OSPRay/OSPRay-1.3.0.eb b/o/OSPRay/OSPRay-1.3.0.eb new file mode 100644 index 00000000..28d96cf4 --- /dev/null +++ b/o/OSPRay/OSPRay-1.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'OSPRay' +version = '1.3.0' + +homepage = 'http://www.ospray.org' +description = """ + A Ray Tracing Based Rendering Engine for High-Fidelity Visualization""" +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['https://github.com/ospray/OSPRay/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.8.1', '', True), + ('tbb', '4.4.2.152', '', True) +] + +dependencies = [] + +separate_build_dir = True + +#skipsteps= ['configure', 'build'] + +sanity_check_paths = { + 'files': ['lib/libospray.so'], + 'dirs': ['bin', 'lib'], +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'vis' diff --git a/p/ParaView/ParaView-5.1.2-intel-2017a-mpi-OSPRay.eb b/p/ParaView/ParaView-5.1.2-intel-2017a-mpi-OSPRay.eb new file mode 100644 index 00000000..46eff3aa --- /dev/null +++ b/p/ParaView/ParaView-5.1.2-intel-2017a-mpi-OSPRay.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.1.2' +versionsuffix = '-mpi-OSPRay' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s.tar.gz"] + +dependencies = [ + ('X11', '20170314', '', True), + ('Mesa', '12.0.2'), + ('libGLU', '9.0.0', '', True), + ('Qt', '4.8.6', '', True), + ('zlib', '1.2.11', '', True), + ('HDF5', '1.8.17'), + ('Python', '2.7.13', '', True), +] + +builddependencies = [('CMake', '3.8.1', '', True)] + +separate_build_dir = True + +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON ' +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT +configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON -DVTK_RENDERING_BACKEND=OpenGL2 ' +# if you want to build server only Paraview, uncomment the following line: +# configopts += '-DVTK_USE_X=OFF ' + +# 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 ;' + +moduleclass = 'vis' diff --git a/p/ParaView/Paraview-5.1.2-intel-2017a-OSPRay.eb b/p/ParaView/Paraview-5.1.2-intel-2017a-OSPRay.eb new file mode 100644 index 00000000..b1bf1933 --- /dev/null +++ b/p/ParaView/Paraview-5.1.2-intel-2017a-OSPRay.eb @@ -0,0 +1,26 @@ +easyblock = 'PackedBinary' + +name = 'ParaView' +version = '5.1.2' +versionsuffix = '-OSPRay' + +homepage = "http://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'dummy', 'version': ''} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["PV5_1_2_pvOSPRay_linux_x86_64.tgz"] + +dependencies = [('intel', '2017a')] + +install_cmd = "cp -a PV5_1_2_pvOSPRay_linux_x86_64/* %(installdir)s/ && find %(installdir)s/ -type d -exec chmod 755 {} \; " + +sanity_check_paths = { + 'files': ['bin/paraview'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'vis' + diff --git a/s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.eb b/s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.eb new file mode 100644 index 00000000..3b822980 --- /dev/null +++ b/s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'Sen2Cor' +version = '2.3.1' + +homepage = 'http://step.esa.int/main/third-party-plugins-2/sen2cor/' +description = """Sen2Cor is a processor for Sentinel-2 Level 2A product generation and formatting; +it performs the atmospheric-, terrain and cirrus correction of Top-Of- Atmosphere Level 1C input data. +Sen2Cor creates Bottom-Of-Atmosphere, optionally terrain- and cirrus corrected reflectance images; +additional, Aerosol Optical Thickness-, Water Vapor-, Scene Classification Maps and Quality Indicators +for cloud and snow probabilities. Its output product format is equivalent to the Level 1C User Product: +JPEG 2000 images, three different resolutions, 60, 20 and 10 m.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://step.esa.int/thirdparties/sen2cor/%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +python = "Python" +python_version = "2.7.13" +versionsuffix = '-%s-%s' % (python, python_version) + +patches = ['%(name)s-%(version)s-Python-2.7.13.patch'] + +dependencies = [ + (python, python_version), + ('GDAL', '2.1.3', '-%s-%s' % (python, python_version)), +] + +sanity_check_paths = { + 'files': ['bin/L2A_Process', 'bin/L2A_Process-02.03.01', 'bin/L2A_Process-2.3.1'], + 'dirs': ['lib'] +} + +moduleclass = 'phys' diff --git a/s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.patch b/s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.patch new file mode 100644 index 00000000..c905efea --- /dev/null +++ b/s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.patch @@ -0,0 +1,20 @@ +--- setup.py.orig 2017-02-02 09:37:32.000000000 +0100 ++++ setup.py 2017-06-19 11:12:03.788380266 +0200 +@@ -35,7 +35,7 @@ + def copyConfiguration(): + sys.stdout.write('\nSEN2COR ' + version + ' setup script:\n') + sys.stdout.write('This will finish the configuration of the environment settings.\n') +- user_input = raw_input('\nOK to continue? [y/n]: ') ++ user_input = 'y' + if user_input == 'n': + return False + +@@ -46,7 +46,7 @@ + while True: + sys.stdout.write('\nPlease input a path for the sen2cor home directory:\n') + sys.stdout.write('default is: ' + SEN2COR_HOME + '\n') +- user_input = raw_input('Is this OK? [y/n]: ') ++ user_input = 'y' + if user_input == 'n': + SEN2COR_HOME = raw_input('New path: ') + sys.stdout.write('New path is: ' + SEN2COR_HOME + '\n') diff --git a/v/VASP/VASP-5.4.4-intel-2017a-03.eb b/v/VASP/VASP-5.4.4-intel-2017a-03.eb new file mode 100644 index 00000000..9e9d4e53 --- /dev/null +++ b/v/VASP/VASP-5.4.4-intel-2017a-03.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'VASP' +version = '5.4.4' +versionsuffix = '-O3' + +homepage = 'http://www.vasp.at' +description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale +materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, +from first principles.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +# Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code +sources = ['%s.%s.tar.gz' % (name.lower(), version)] + +dependencies = [ + ('FFTW', '3.3.6'), + ('zlib', '1.2.11', '', True), +] + +prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && ' + +# path to libfftw3xf_intel.a is hardcoded in makefile.include +prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && ' + +# remove mkl flag to prevent mixing dynamic libs with the static libs in LIBBLACS/SCALAPACK +prebuildopts += 'sed -i "s|-mkl=sequential||" makefile.include && ' + +# change -O2 to -O3 +prebuildopts += 'sed -i "s|-O2|-O3|" makefile.include && ' + +# VASP uses LIBS as a list of folders +prebuildopts += 'unset LIBS && ' + +buildopts = 'all BLACS="$LIBBLACS" SCALAPACK="$LIBSCALAPACK"' + +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': [] +} + +moduleclass = 'phys' diff --git a/v/VASP/VASP-5.4.4-intel-2017a.eb b/v/VASP/VASP-5.4.4-intel-2017a.eb index 7c8de85f..d64cbc5f 100644 --- a/v/VASP/VASP-5.4.4-intel-2017a.eb +++ b/v/VASP/VASP-5.4.4-intel-2017a.eb @@ -2,6 +2,7 @@ easyblock = 'MakeCp' name = 'VASP' version = '5.4.4' +versionsuffix = '-test-fftw' homepage = 'http://www.vasp.at' description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale @@ -12,10 +13,11 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} # Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code -sources = ['%s.%s.tar.gz' % (name.lower(), version)] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +checksums = ['8ac646b108f974371eef398973373bf6'] dependencies = [ - ('FFTW', '3.3.6'), ('zlib', '1.2.11', '', True), ]