diff --git a/b/BCFtools/BCFtools-1.6-intel-2017a.eb b/b/BCFtools/BCFtools-1.6-intel-2017a.eb new file mode 100644 index 00000000..65494590 --- /dev/null +++ b/b/BCFtools/BCFtools-1.6-intel-2017a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.6' + +homepage = 'http://www.htslib.org/' +description = """Samtools is a suite of programs for interacting with high-throughput sequencing data. + BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +#patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch'] + +dependencies = [ + ('zlib', '1.2.11', '', True), + ('HTSlib', '1.6'), + ('GSL', '2.3'), + ('XZ', '5.2.3', '', True), +] + +parallel = 1 + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1' +installopts = ' prefix=%(installdir)s' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' diff --git a/b/BWA/BWA-0.7.17-intel-2017a.eb b/b/BWA/BWA-0.7.17-intel-2017a.eb new file mode 100644 index 00000000..63e41604 --- /dev/null +++ b/b/BWA/BWA-0.7.17-intel-2017a.eb @@ -0,0 +1,18 @@ +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns + relatively short nucleotide sequences against a long reference sequence such as the human genome.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('zlib', '1.2.11', '', True), +] + +moduleclass = 'bio' diff --git a/c/Clang/Clang-3.8.1-GCC-6.3.0-2.27.eb b/c/Clang/Clang-3.8.1-GCC-6.3.0-2.27.eb new file mode 100644 index 00000000..061fbcb2 --- /dev/null +++ b/c/Clang/Clang-3.8.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.8.1" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '7.2.0-2.29'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/release/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.2', '', True), +] + +builddependencies = [ + ('CMake', '3.9.1', '', True), + ('Python', '2.7.13', '', True), + ('libxml2', '2.9.4', '', True), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/d/DMTCP/DMTCP-2.5.2.eb b/d/DMTCP/DMTCP-2.5.2.eb new file mode 100644 index 00000000..0664d3d4 --- /dev/null +++ b/d/DMTCP/DMTCP-2.5.2.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '2.5.2' + +homepage = "http://dmtcp.sourceforge.net/index.html" +description = """DMTCP (Distributed MultiThreaded Checkpointing) +transparently checkpoints a single-host or distributed computation +in user-space -- with no modifications to user code or to the O/S.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] + +configopts = '--enable-infiniband-support' + +postinstallcmds = [ + 'cp test/ %(installdir)s/test -R', + '(cd %(installdir)s/test; make -j 8)', +] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/d/DMTCP/DMTCP-3.0.eb b/d/DMTCP/DMTCP-3.0.eb new file mode 100644 index 00000000..6310df04 --- /dev/null +++ b/d/DMTCP/DMTCP-3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '3.0' + +homepage = "http://dmtcp.sourceforge.net/index.html" +description = """DMTCP (Distributed MultiThreaded Checkpointing) +transparently checkpoints a single-host or distributed computation +in user-space -- with no modifications to user code or to the O/S.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['master.tar.gz'] + +configopts = '--enable-infiniband-support' + +postinstallcmds = [ + 'cp test/ %(installdir)s/test -R', + '(cd %(installdir)s/test; make -j 8)', +] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/f/FFTW/FFTW-3.3.6-foss-2017a.eb b/f/FFTW/FFTW-3.3.6-foss-2017a.eb new file mode 100644 index 00000000..c5e5ee78 --- /dev/null +++ b/f/FFTW/FFTW-3.3.6-foss-2017a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.6' + +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': 'foss', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s-pl1.tar.gz'] +checksums = ['682a0e78d6966ca37c7446d4ab4cc2a1'] + +common_configopts = "--enable-threads --enable-openmp --with-pic" + +configopts = [ + common_configopts + " --enable-single --enable-sse2 --enable-mpi", + common_configopts + " --enable-long-double --enable-mpi", + common_configopts + " --enable-quad-precision", + common_configopts + " --enable-sse2 --enable-mpi", # default as last +] + +sanity_check_paths = { + 'files': ['bin/fftw%s' % x for x in ['-wisdom', '-wisdom-to-conf', 'f-wisdom', 'l-wisdom', 'q-wisdom']] + + ['include/fftw3%s' % x for x in ['-mpi.f03', '-mpi.h', '.f', '.f03', + '.h', 'l-mpi.f03', 'l.f03', 'q.f03']] + + ['lib/libfftw3%s%s.a' % (x, y) for x in ['', 'f', 'l'] for y in ['', '_mpi', '_omp', '_threads']] + + ['lib/libfftw3q.a', 'lib/libfftw3q_omp.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/h/HTSlib/HTSlib-1.6-intel-2017a.eb b/h/HTSlib/HTSlib-1.6-intel-2017a.eb new file mode 100644 index 00000000..e32227ca --- /dev/null +++ b/h/HTSlib/HTSlib-1.6-intel-2017a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.6' + +homepage = "http://www.htslib.org/" +description = """ A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix """ + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('zlib', '1.2.11', '', True), + ('XZ', '5.2.3', '', True), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/l/libsndfile/libsndfile-1.0.28.eb b/l/libsndfile/libsndfile-1.0.28.eb new file mode 100644 index 00000000..2894cf32 --- /dev/null +++ b/l/libsndfile/libsndfile-1.0.28.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libsndfile' +version = '1.0.28' + +homepage = 'http://www.mega-nerd.com/libsndfile' +description = """Libsndfile is a C library for reading and writing files containing sampled sound + (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.mega-nerd.com/libsndfile/files/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1ff33929f042fa333aed1e8923aa628c3ee9e1eb85512686c55092d1e5a9dfa9'] + +builddependencies = [('binutils', '2.29')] + +sanity_check_paths = { + 'files': ['include/sndfile.h', 'include/sndfile.hh', 'lib/libsndfile.a', 'lib/libsndfile.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'lib' diff --git a/m/MPC/MPC-1.0.2.eb b/m/MPC/MPC-1.0.2.eb new file mode 100644 index 00000000..6f617077 --- /dev/null +++ b/m/MPC/MPC-1.0.2.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'MPC' +version = '1.0.2' + +homepage = 'http://www.multiprecision.org/' +description = """Gnu Mpc is a C library for the arithmetic of + complex numbers with arbitrarily high precision and correct + rounding of the result. It extends the principles of the IEEE-754 + standard for fixed precision real floating point numbers to + complex numbers, providing well-defined semantics for every + operation. At the same time, speed of operation at high precision + is a major design goal.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.multiprecision.org/mpc/download/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('GMP', '6.1.2'), + ('MPFR', '3.1.5')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpc.%s' % SHLIB_EXT, 'include/mpc.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/m/MPFR/MPFR-3.1.5.eb b/m/MPFR/MPFR-3.1.5.eb new file mode 100644 index 00000000..2a763b80 --- /dev/null +++ b/m/MPFR/MPFR-3.1.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.5' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '6.1.2')] + +# runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/m/MPICH/MPICH-3.2.1-GCC-6.3.0-2.27.eb b/m/MPICH/MPICH-3.2.1-GCC-6.3.0-2.27.eb new file mode 100644 index 00000000..e600139b --- /dev/null +++ b/m/MPICH/MPICH-3.2.1-GCC-6.3.0-2.27.eb @@ -0,0 +1,18 @@ +name = 'MPICH' +version = '3.2.1' + +homepage = 'http://www.mpich.org/' +description = """MPICH v3.x is an open source high-performance MPI 3.0 implementation. +It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.mpich.org/static/tarballs/%(version)s'] + +configopts="--enable-shared" + +# Let's store the checksum in order to be sure it doesn't suddenly change +# checksums = ['f414cfa77099cd1fa1a5ae4e22db508a'] + +moduleclass = 'mpi' diff --git a/m/Mesa/Mesa-17.2.6-foss-2017a.eb b/m/Mesa/Mesa-17.2.6-foss-2017a.eb new file mode 100644 index 00000000..86e532a9 --- /dev/null +++ b/m/Mesa/Mesa-17.2.6-foss-2017a.eb @@ -0,0 +1,66 @@ +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '17.2.6' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2017a'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] +#patches = ['Mesa-17.0.2_fix-strip-llvm-flags.patch'] + +builddependencies = [ + ('flex', '2.6.4', '', True), + ('Bison', '3.0.4', '', True), + ('Autotools', '20150215', '', True), + ('pkg-config', '0.29.1', '', True), + ('Mako', '1.0.6', '-Python-2.7.13', True), + ('libxml2', '2.9.4', '-Python-2.7.13', True), +] + +dependencies = [ + ('zlib', '1.2.11', '', True), + ('nettle', '3.3'), + ('libdrm', '2.4.76', '', True), + ('LLVM', '4.0.0', '', ('GCC', '6.3.0-2.27')), + ('X11', '20170314', '', True), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/n/NLopt/NLopt-2.4.2.eb b/n/NLopt/NLopt-2.4.2.eb new file mode 100644 index 00000000..52fa5a55 --- /dev/null +++ b/n/NLopt/NLopt-2.4.2.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'NLopt' +version = '2.4.2' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/NLopt' +description = """ NLopt is a free/open-source library for nonlinear optimization, + providing a common interface for a number of different free optimization routines + available online as well as original implementations of various other algorithms. """ + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +source_urls = ['http://ab-initio.mit.edu/nlopt/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8099633de9d71cbc06cd435da993eb424bbcdbded8f803cdaa9fb8c6e09c8e89'] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['lib/libnlopt.a', 'lib/libnlopt.%s' % SHLIB_EXT, 'include/nlopt.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'numlib' diff --git a/n/nettle/nettle-3.3-foss-2017a.eb b/n/nettle/nettle-3.3-foss-2017a.eb new file mode 100644 index 00000000..41fd6fc6 --- /dev/null +++ b/n/nettle/nettle-3.3-foss-2017a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.3' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('GMP', '6.1.2', '', True), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + ['lib64/libhogweed.a', 'lib64/libhogweed.%s' % SHLIB_EXT, + 'lib64/libnettle.a', 'lib64/libnettle.%s' % SHLIB_EXT], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/o/Octave/Octave-4.2.1-intel-2017a-mic.eb b/o/Octave/Octave-4.2.1-intel-2017a-mic.eb new file mode 100644 index 00000000..fedeb33e --- /dev/null +++ b/o/Octave/Octave-4.2.1-intel-2017a-mic.eb @@ -0,0 +1,57 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '4.2.1' +versionsuffix = '-mic' + +homepage = 'http://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s_intel.patch'] + +builddependencies = [ + ('Bison', '3.0.4', '', True), + ('flex', '2.6.4', '', True), + ('Autotools', '20150215', '', True), + ('libtool', '2.4.6', '', True), + ('gperf', '3.0.4'), +] + +dependencies = [ + ('PCRE', '8.40', '', True), + ('ncurses', '6.0', '', True), + ('libreadline', '7.0', '', True), + ('arpack-ng', '3.5.0'), + ('cURL', '7.56.1', '', True), + ('FLTK', '1.3.4', '', True), + ('GLPK', '4.61'), + ('GL2PS', '1.4.0'), + ('Java', '1.8.0_121', '', True), + ('zlib', '1.2.11', '', True), + ('Qhull', '2015.2', '', True), + ('Qt5', '5.8.0', '', ('GCC', '6.3.0-2.27')), + ('HDF5', '1.8.18', '-serial'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '4.5.5', '-METIS-5.1.0'), +] + +configopts = ' CC="icc -mmic" MOC=$EBROOTQT5/bin/moc ' +configopts += 'UIC=$EBROOTQT5/bin/uic ' +configopts += 'RCC=$EBROOTQT5/bin/rcc ' +configopts += 'LRELEASE=$EBROOTQT5/bin/lrelease ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/p/PAPI/PAPI-5.5.1.eb b/p/PAPI/PAPI-5.5.1.eb new file mode 100644 index 00000000..f169c3d9 --- /dev/null +++ b/p/PAPI/PAPI-5.5.1.eb @@ -0,0 +1,56 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.5.1' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' + +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'dummy', 'version': ''} +toolchainopts = {'pic': True} + +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['49dc2c2323f6164c4a7e81b799ed690ee73158671205e71501f849391dd2c2d4'] + +builddependencies = [ + ('binutils', '2.29'), +] + +start_dir = 'src' + +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/p/PROJ/PROJ-4.9.3-foss-2017a.eb b/p/PROJ/PROJ-4.9.3-foss-2017a.eb new file mode 100644 index 00000000..4f94514e --- /dev/null +++ b/p/PROJ/PROJ-4.9.3-foss-2017a.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.3' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'foss', 'version': '2017a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/r/R/R-3.4.2-intel-2017a.eb b/r/R/R-3.4.2-intel-2017a.eb new file mode 100644 index 00000000..05d17be9 --- /dev/null +++ b/r/R/R-3.4.2-intel-2017a.eb @@ -0,0 +1,522 @@ +name = 'R' +version = '3.4.2' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" +# Actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('cairo', '1.14.8', '', True), + ('libreadline', '7.0', '', True), + ('ncurses', '6.0', '', True), + ('bzip2', '1.0.6', '', True), + ('XZ', '5.2.3', '', True), + ('zlib', '1.2.11', '', True), + ('SQLite', '3.17.0', '', True), + ('PCRE', '8.40', '', True), + ('libpng', '1.6.29', '', True), # for plotting in R + ('libjpeg-turbo', '1.5.1', '', True), # for plottting in R + ('LibTIFF', '4.0.7', '', True), + ('Java', '1.8.0_144', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.6', '', True), # for tcltk + ('Tk', '8.6.6', '', True), # for tcltk + ('cURL', '7.53.1', '', True), # for RCurl + ('libxml2', '2.9.4', '', True), # for XML + ('GDAL', '2.1.3', '-Python-2.7.13', True), # for rgdal + ('PROJ', '4.9.3'), # for rgdal + ('GMP', '6.1.2', '', True), # for igraph + ('NLopt', '2.4.2'), # for nloptr + ('FFTW', '3.3.6'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated on May 11th 2017 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified 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['kohonen-3.0.2_icpc-wd308.patch'])])), + ('base64', '2.0', ext_options), + ('doRNG', '1.6.6', ext_options), + ('nleqslv', '3.2', ext_options), + ('Deriv', '3.8.0', ext_options), + ('RGCCA', '2.1.2', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '4.0.17', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.2.0', ext_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('VennDiagram', '1.6.17', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('forecast', '8.0', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.3', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.9-2', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.6-1', ext_options), + ('goftest', '1.1-1', ext_options), + ('spatstat.utils', '1.6-0', ext_options), + ('spatstat', '1.51-0', ext_options), + ('rgdal', '1.2-7', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '2.0.4', ext_options), + ('RCurl', '1.95-4.8', ext_options), + ('bio3d', '2.3-1', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.4', ext_options), + ('cvAUC', '1.1.0', ext_options), + ('SuperLearner', '2.0-21', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('ModelMetrics', '1.1.0', ext_options), + ('caret', '6.0-76', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.10', ext_options), + ('ggvis', '0.4.3', ext_options), + ('mlr', '2.11', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-9', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.14', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.6', ext_options), + ('commonmark', '1.2', ext_options), + ('desc', '1.1.0', ext_options), + ('roxygen2', '6.0.1', ext_options), + ('git2r', '0.18.0', ext_options), + ('rversions', '1.0.3', ext_options), + ('withr', '1.0.2', ext_options), + ('devtools', '1.13.0', ext_options), + ('Rook', '1.1-1', ext_options), + ('Cairo', '1.5-9', dict(ext_options.items() + [('patches', ['Cairo-1.5-9.patch'])])), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.2-3', ext_options), + ('distillery', '1.0-2', ext_options), + ('extRemes', '2.0-8', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-10', dict(ext_options.items() + [('patches', ['multicool-0.1-10_icpc-wd308.patch'])])), + ('ks', '1.10.6', ext_options), + ('logcondens', '2.1.5', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-50', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.4.2', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.7.5', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-23.1097', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.9-3', ext_options), + ('mi', '1.0', ext_options), + ('visNetwork', '1.0.3', ext_options), + ('rgexf', '0.15.3', ext_options), + ('influenceR', '0.1.0', ext_options), + ('DiagrammeR', '0.9.0', ext_options), + ('sem', '3.1-9', ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '3.3.0', ext_options), + ('sna', '2.4', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.4.3', ext_options), + ('diveRsity', '1.9.90', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.2.0', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.1', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.3', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('purrr', '0.2.2', ext_options), + ('downloader', '0.4', ext_options), + ('imager', '0.40.2', dict(ext_options.items() + [('patches', ['imager-0.40.2_icpc-wd308.patch'])])), + ('pracma', '2.0.4', ext_options), + ('signal', '0.7-6', ext_options), + ('tuneR', '1.3.2', ext_options), + ('pastecs', '1.3-18', ext_options), + ('audio', '0.1-5', ext_options), + ('fftw', '1.0-4', ext_options), + ('seewave', '2.0.5', ext_options), + ('gsw', '1.0-3', ext_options), + ('oce', '0.9-21', ext_options), + ('ineq', '0.2-13', ext_options), + ('soundecology', '1.3.2', ext_options), +# ('KFAS', '1.2.9', ext_options), +] + +moduleclass = 'lang' diff --git a/r/R/R-3.4.3-foss-2017a.eb b/r/R/R-3.4.3-foss-2017a.eb new file mode 100644 index 00000000..fc69ec43 --- /dev/null +++ b/r/R/R-3.4.3-foss-2017a.eb @@ -0,0 +1,556 @@ +# IT4Innovations 2017 + +name = 'R' +version = '3.4.2' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2017a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +#checksums = ['02b1135d15ea969a3582caeb95594a05e830a6debcdb5b85ed2d5836a6a3fc78'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=yes --enable-R-shlib" +# actually use Tcl/Tk +configopts += ' --with-tcl-config=$EBROOTTCL/lib/tclConfig.sh --with-tk-config=$EBROOTTK/lib/tkConfig.sh ' +# Enable graphics capabilities for plotting. +configopts += " --with-cairo --with-libpng --with-jpeglib --with-libtiff" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('X11', '20170314', '', True), + ('Mesa', '17.2.6'), + ('libGLU', '9.0.0', '', True), + ('cairo', '1.14.8', '', True), + ('libreadline', '7.0', '', True), + ('ncurses', '6.0', '', True), + ('bzip2', '1.0.6', '', True), + ('XZ', '5.2.3', '', True), + ('zlib', '1.2.11', '', True), + ('SQLite', '3.17.0', '', True), + ('PCRE', '8.40', '', True), + ('libpng', '1.6.29', '', True), # for plotting in R + ('libjpeg-turbo', '1.5.1', '', True), # for plottting in R + ('LibTIFF', '4.0.7', '', True), + ('Java', '1.8.0_144', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.6', '', True), # for tcltk + ('Tk', '8.6.6', '', True), # for tcltk + ('cURL', '7.53.1', '', True), # for RCurl + ('libxml2', '2.9.4', '', True), # for XML + ('GDAL', '2.1.3', '-Python-2.7.13', True), # for rgdal + ('PROJ', '4.9.3'), # for rgdal + ('GMP', '6.1.2', '', True), # for igraph + ('NLopt', '2.4.2', '', True), # for nloptr + ('FFTW', '3.3.6'), # for fftw + ('libsndfile', '1.0.28', '', True), # for seewave + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +# packages updated and selected on August 24 2017 +exts_list = [ + # default libraries, only here to sanity check their presence + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + # non-standard libraries, should be specified with fixed versions! + ('Rmpi', '0.6-6', ext_options), + ('abind', '1.4-5', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', ext_options), + ('bit', '1.1-12', ext_options), + ('bit64', '0.9-7', ext_options), + ('filehash', '2.4-1', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '4.2', ext_options), + ('bootstrap', '2017.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.15', ext_options), + ('formatR', '1.5', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.18.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-25', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.8', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-11', ext_options), + ('mclust', '5.3', ext_options), + ('RANN', '2.5.1', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-2.1', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.4', ext_options), + ('stabledist', '0.7-1', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-18', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-8', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.62.0-1', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.9', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('backports', '1.1.0', ext_options), + ('checkmate', '1.8.3', ext_options), + ('Rcpp', '0.12.12', ext_options), + ('cubature', '1.3-11', ext_options), + ('DEoptimR', '1.0-8', ext_options), + ('digest', '0.6.12', ext_options), + ('fastmatch', '1.1-0', ext_options), + ('ffbase', '0.12.3', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.2.0', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('dotCall64', '0.9-04', ext_options), + ('spam', '2.1-1', ext_options), + ('subplex', '1.4-1', ext_options), + ('stringi', '1.1.5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.2.0', ext_options), + ('evaluate', '0.10.1', ext_options), + ('logspline', '2.1.9', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.9-4', ext_options), + ('plotrix', '3.6-6', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-40', ext_options), + ('SparseM', '1.77', ext_options), + ('tripack', '1.3-8', ext_options), + ('irace', '2.4', ext_options), + ('rJava', '0.9-8', ext_options), + ('lattice', '0.20-35', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-28', ext_options), + ('Matrix', '1.2-11', ext_options), + ('png', '0.1-7', ext_options), + ('RcppArmadillo', '0.7.960.1.1', ext_options), + ('plyr', '1.8.4', ext_options), + ('pROC', '1.9.1', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.11', ext_options), + ('fail', '1.3', ext_options), + ('rlecuyer', '0.3-4', ext_options), + ('snow', '0.4-2', ext_options), + ('MASS', '7.3-47', ext_options), + ('tree', '1.0-37', ext_options), + ('pls', '2.6-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-8', ext_options), + ('nnet', '7.3-12', ext_options), + ('nlme', '3.1-131', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.3.3.0', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.33', ext_options), + ('mgcv', '1.8-18', ext_options), + ('colorspace', '1.3-2', ext_options), + ('robustbase', '0.92-7', ext_options), + ('sp', '1.2-5', ext_options), + ('zoo', '1.8-0', ext_options), + ('lmtest', '0.9-35', ext_options), + ('vcd', '1.4-3', ext_options), + ('snowfall', '1.84-6.1', ext_options), + ('rpart', '4.1-11', ext_options), + ('survival', '2.41-3', ext_options), + ('mice', '2.30', ext_options), + ('urca', '1.3-0', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.22', ext_options), + ('akima', '0.6-2', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-20', ext_options), + ('mixtools', '1.1.0', ext_options), + ('cluster', '2.0.6', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.19-1', ext_options), + ('codetools', '0.2-15', ext_options), + ('foreach', '1.4.3', ext_options), + ('doMC', '1.3.4', ext_options), + ('DBI', '0.7', ext_options), + ('foreign', '0.8-69', ext_options), + ('gam', '1.14-4', ext_options), + ('gamlss.data', '5.0-0', ext_options), + ('gamlss.dist', '5.0-2', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.10-0', ext_options), + ('curl', '2.8.1', ext_options), + ('TTR', '0.23-2', ext_options), + ('quantmod', '0.4-10', ext_options), + ('mnormt', '1.5-5', ext_options), + ('mvtnorm', '1.0-6', ext_options), + ('pcaPP', '1.9-72', ext_options), + ('numDeriv', '2016.8-1', ext_options), + ('lava', '1.5', ext_options), + ('prodlim', '1.6.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('memoise', '1.1.0', ext_options), + ('plogr', '0.1-1', ext_options), + ('sandwich', '2.4-0', ext_options), + ('sfsmisc', '1.1-1', ext_options), + ('spatial', '7.3-11', ext_options), + ('VGAM', '1.0-4', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.8-2', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.6.1', ext_options), + ('deSolve', '1.20', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-42', ext_options), + ('fastICA', '1.2-1', ext_options), + ('R.methodsS3', '1.7.1', ext_options), + ('R.oo', '1.21.0', ext_options), + ('cgdsr', '1.2.6', ext_options), + ('R.utils', '2.5.0', ext_options), + ('R.matlab', '3.6.1', ext_options), + ('gbm', '2.1.3', ext_options), + ('dichromat', '2.0-0', ext_options), + ('Formula', '1.2-2', ext_options), + ('acepack', '1.4.1', ext_options), + ('reshape2', '1.4.2', ext_options), + ('gtable', '0.2.0', ext_options), + ('munsell', '0.4.3', ext_options), + ('labeling', '0.3', ext_options), + ('viridisLite', '0.2.0', ext_options), + ('R6', '2.2.2', ext_options), + ('scales', '0.4.1', ext_options), + ('proto', '1.0.0', ext_options), + ('lazyeval', '0.2.0', ext_options), + ('assertthat', '0.2.0', ext_options), + ('rlang', '0.1.2', ext_options), + ('tibble', '1.3.4', ext_options), + ('blob', '1.1.0', ext_options), + ('pkgconfig', '2.0.1', ext_options), + ('RSQLite', '1.1-2', ext_options), + ('BatchJobs', '1.6', ext_options), + ('ggplot2', '2.2.1', ext_options), + ('pROC', '1.10.0', ext_options), + ('gridExtra', '2.2.1', ext_options), + ('chron', '2.3-50', ext_options), + ('data.table', '1.10.4', ext_options), + ('viridis', '0.4.0', ext_options), + ('yaml', '2.1.14', ext_options), + ('jsonlite', '1.5', ext_options), + ('htmltools', '0.3.6', ext_options), + ('htmlwidgets', '0.9', ext_options), + ('knitr', '1.17', ext_options), + ('htmlTable', '1.9', ext_options), + ('Hmisc', '4.0-3', ext_options), + ('fastcluster', '1.1.24', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.10', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '2.2.1', ext_options), + ('igraph', '1.1.2', ext_options), + ('GeneNet', '1.2.13', ext_options), + ('ape', '4.1', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '3.0.1', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.5', ext_options), + ('rjson', '0.2.15', ext_options), + ('sourcetools', '0.1.6', ext_options), + ('shiny', '1.0.4', ext_options), + ('seqinr', '3.4-5', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-14', ext_options), + ('gmodels', '2.16.2', ext_options), + ('expm', '0.999-2', ext_options), + ('spdep', '0.6-13', ext_options), + ('bindr', '0.1', ext_options), + ('bindrcpp', '0.2', ext_options), + ('glue', '1.1.1', ext_options), + ('dplyr', '0.7.2', ext_options), + ('vegan', '2.4-3', ext_options), + ('adegenet', '2.0.1', ext_options), + ('prettyunits', '1.0.2', ext_options), + ('progress', '1.1.2', ext_options), + ('rncl', '0.8.2', ext_options), + ('XML', '3.98-1.9', ext_options), + ('crayon', '1.3.2', ext_options), + ('praise', '1.0.0', ext_options), + ('testthat', '1.0.2', ext_options), + ('rprojroot', '1.2', ext_options), + ('rmarkdown', '1.6', ext_options), + ('openssl', '0.9.6', ext_options), + ('httr', '1.3.1', ext_options), + ('reshape', '0.8.7', ext_options), + ('xml2', '1.1.1', ext_options), + ('triebeard', '0.3.0', ext_options), + ('urltools', '1.6.0', ext_options), + ('httpcode', '0.2.0', ext_options), + ('crul', '0.3.8', ext_options), + ('bold', '0.5.0', ext_options), + ('rredlist', '0.3.0', ext_options), + ('rentrez', '1.1.0', ext_options), + ('rotl', '3.0.3', ext_options), + ('solrium', '0.4.0', ext_options), + ('ritis', '0.5.4', ext_options), + ('worrms', '0.1.0', ext_options), + ('natserv', '0.1.4', ext_options), + ('WikipediR', '1.5.0', ext_options), + ('WikidataR', '1.3.0', ext_options), + ('wikitaxa', '0.1.4', ext_options), + ('taxize', '0.8.9', ext_options), + ('tidyselect', '0.1.1', ext_options), + ('purrr', '0.2.3', ext_options), + ('tidyr', '0.7.0', ext_options), + ('uuid', '0.1-2', ext_options), + ('RNeXML', '2.0.7', ext_options), + ('phylobase', '0.8.4', ext_options), + ('adephylo', '1.1-10', ext_options), + ('animation', '2.5', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.5.19', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-8', ext_options), + ('dismo', '1.1-4', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.4', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '9.0', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-10', ext_options), + ('rgl', '0.98.1', ext_options), + ('labdsv', '1.8-0', ext_options), + ('stabs', '0.6-3', ext_options), + ('modeltools', '0.2-21', ext_options), + ('strucchange', '1.5-1', ext_options), + ('TH.data', '1.0-8', ext_options), + ('multcomp', '1.4-6', ext_options), + ('coin', '1.2-1', ext_options), + ('party', '1.2-3', ext_options), + ('mboost', '2.8-1', ext_options), + ('msm', '1.6.4', ext_options), + ('nor1mix', '1.2-2', ext_options), + ('np', '0.60-3', ext_options), + ('polynom', '1.3-9', ext_options), + ('polspline', '1.1.12', ext_options), + ('rms', '5.1-1', ext_options), + ('RWekajars', '3.9.1-3', ext_options), + ('RWeka', '0.4-34', ext_options), + ('slam', '0.1-40', ext_options), + ('tm', '0.7-1', ext_options), + ('TraMineR', '2.0-7', ext_options), + ('chemometrics', '1.4.2', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-6', ext_options), + ('statmod', '1.4.30', ext_options), + ('miscTools', '0.6-22', ext_options), + ('maxLik', '1.3-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('optparse', '1.4.4', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '1.3.2', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.52.2', ext_options), + ('DiscriMiner', '0.1-29', ext_options), + ('ellipse', '0.3-8', ext_options), + ('leaps', '3.0', ext_options), + ('nloptr', '1.0.4', ext_options), + ('lme4', '1.1-13', ext_options), + ('pbkrtest', '0.4-7', ext_options), + ('car', '2.1-5', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.36', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-14', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.10', ext_options), + ('kohonen', '3.0.2', ext_options), + ('base64', '2.0', ext_options), + ('doRNG', '1.6.6', ext_options), + ('nleqslv', '3.3.1', ext_options), + ('Deriv', '3.8.1', ext_options), + ('RGCCA', '2.1.2', ext_options), + ('pheatmap', '1.0.8', ext_options), + ('openxlsx', '4.0.17', ext_options), + ('pvclust', '2.0-0', ext_options), + ('RCircos', '1.2.0', ext_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('VennDiagram', '1.6.17', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('forecast', '8.1', ext_options), + ('fma', '2.3', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.9-2', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.6-1', ext_options), + ('goftest', '1.1-1', ext_options), + ('spatstat.utils', '1.7-0', ext_options), + ('spatstat', '1.52-1', ext_options), + ('rgdal', '1.2-8', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '2.0.7', ext_options), + ('RCurl', '1.95-4.8', ext_options), + ('bio3d', '2.3-3', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.4', ext_options), + ('cvAUC', '1.1.0', ext_options), + ('SuperLearner', '2.0-22', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.6', ext_options), + ('ModelMetrics', '1.1.0', ext_options), + ('caret', '6.0-76', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.10', ext_options), + ('ggvis', '0.4.3', ext_options), + ('mlr', '2.11', ext_options), + ('unbalanced', '2.0', ext_options), + ('RSNNS', '0.4-9', ext_options), + ('abc.data', '1.0', ext_options), + ('abc', '2.1', ext_options), + ('lhs', '0.14', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.3', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.6', ext_options), + ('commonmark', '1.2', ext_options), + ('desc', '1.1.1', ext_options), + ('roxygen2', '6.0.1', ext_options), + ('git2r', '0.19.0', ext_options), + ('rversions', '1.0.3', ext_options), + ('withr', '2.0.0', ext_options), + ('devtools', '1.13.3', ext_options), + ('Rook', '1.1-1', ext_options), + ('Cairo', '1.5-9', dict(ext_options.items() + [('patches', ['Cairo-1.5-9.patch'])])), + ('RMTstat', '0.3', ext_options), + ('Lmoments', '1.2-3', ext_options), + ('distillery', '1.0-4', ext_options), + ('extRemes', '2.0-8', ext_options), + ('pixmap', '0.4-11', ext_options), + ('tkrplot', '0.0-23', ext_options), + ('misc3d', '0.8-4', ext_options), + ('multicool', '0.1-10', ext_options), + ('ks', '1.10.7', ext_options), + ('logcondens', '2.1.5', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-50', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.5.0', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.7.5', ext_options), + ('pbivnorm', '0.6.0', ext_options), + ('lavaan', '0.5-23.1097', ext_options), + ('matrixcalc', '1.0-3', ext_options), + ('arm', '1.9-3', ext_options), + ('mi', '1.0', ext_options), + ('visNetwork', '2.0.1', ext_options), + ('rgexf', '0.15.3', ext_options), + ('influenceR', '0.1.0', ext_options), + ('sem', '3.1-9', ext_options), + ('jpeg', '0.1-8', ext_options), + ('network', '1.13.0', ext_options), + ('statnet.common', '4.0.0', ext_options), + ('sna', '2.4', ext_options), + ('glasso', '1.8', ext_options), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.4.3', ext_options), + ('diveRsity', '1.9.90', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.2.0', ext_options), + ('geepack', '1.2-1', ext_options), + ('lubridate', '1.6.0', ext_options), + ('pim', '2.0.1', ext_options), + ('minpack.lm', '1.2-1', ext_options), + ('rootSolve', '1.7', ext_options), + ('diagram', '1.6.4', ext_options), + ('FME', '1.3.5', ext_options), + ('bmp', '0.2', ext_options), + ('readbitmap', '0.1-4', ext_options), + ('downloader', '0.4', ext_options), + ('imager', '0.40.2', ext_options), + ('bbmle', '1.0.19', ext_options), + ('unmarked', '0.12-2', ext_options), + ('AICcmodavg', '2.1-1', ext_options), + ('boot', '1.3-20', ext_options), + ('GlobalOptions', '0.0.12', ext_options), + ('circlize', '0.4.1', ext_options), + ('emdbook', '1.3.9', ext_options), + ('hash', '2.2.6', ext_options), + ('hms', '0.3', ext_options), + ('forcats', '0.2.0', ext_options), + ('feather', '0.3.1', ext_options), + ('readr', '1.1.1', ext_options), + ('DiagrammeR', '0.9.1', ext_options), + ('haven', '1.1.0', ext_options), + ('rematch', '1.0.1', ext_options), + ('cellranger', '1.1.0', ext_options), + ('readxl', '1.0.0', ext_options), + ('selectr', '0.3-1', ext_options), + ('rvest', '0.3.2', ext_options), + ('broom', '0.4.2', ext_options), + ('modelr', '0.1.1', ext_options), + ('limSolve', '1.5.5.3', ext_options), + ('MuMIn', '1.15.6', ext_options), + ('R2WinBUGS', '2.1-21', ext_options), + ('rslurm', '0.3.3', ext_options), + ('RUnit', '0.4.31', ext_options), + ('tidyverse', '1.1.1', ext_options), + ('KFAS', '1.2.9', ext_options), +] + +moduleclass = 'lang' diff --git a/s/SAMtools/SAMtools-1.6-intel-2017a.eb b/s/SAMtools/SAMtools-1.6-intel-2017a.eb new file mode 100644 index 00000000..7f802ae4 --- /dev/null +++ b/s/SAMtools/SAMtools-1.6-intel-2017a.eb @@ -0,0 +1,23 @@ +name = 'SAMtools' +version = '1.6' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +#patches = ['SAMtools-1.3_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0', '', True), + ('zlib', '1.2.11', '', True), + ('XZ', '5.2.3', '', True), +] + +moduleclass = 'bio' diff --git a/s/Singularity/Singularity-2.4.1.eb b/s/Singularity/Singularity-2.4.1.eb new file mode 100644 index 00000000..3df78cd3 --- /dev/null +++ b/s/Singularity/Singularity-2.4.1.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Singularity' +version = '2.4.1' + +homepage = 'http://gmkurtzer.github.io/singularity' +description = """Singularity is a container platform focused on supporting \"Mobility of Compute\"""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://github.com/gmkurtzer/singularity/archive/'] +sources = ['%(version)s.tar.gz'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +modextravars = {'SINGULARITY_OVERLAYFS_ENABLED': '1'} + +modluafooter = 'add_property("state","experimental")' + +moduleclass = 'tools' diff --git a/v/VASP/VASP-5.4.1-24Jun15-intel-2015b.eb b/v/VASP/VASP-5.4.1-24Jun15-intel-2015b.eb index 4ce6e0b3..44780850 100644 --- a/v/VASP/VASP-5.4.1-24Jun15-intel-2015b.eb +++ b/v/VASP/VASP-5.4.1-24Jun15-intel-2015b.eb @@ -7,7 +7,11 @@ versionsuffix = '-24Jun15' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.1-24Jun15-intel-2017.00.eb b/v/VASP/VASP-5.4.1-24Jun15-intel-2017.00.eb index 6e9fd2ae..31e35de7 100644 --- a/v/VASP/VASP-5.4.1-24Jun15-intel-2017.00.eb +++ b/v/VASP/VASP-5.4.1-24Jun15-intel-2017.00.eb @@ -7,7 +7,11 @@ versionsuffix = '-24Jun15' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2017.00'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.1-24Jun15-intel-2017a.eb b/v/VASP/VASP-5.4.1-24Jun15-intel-2017a.eb index a10aaaf8..c84a8ef1 100644 --- a/v/VASP/VASP-5.4.1-24Jun15-intel-2017a.eb +++ b/v/VASP/VASP-5.4.1-24Jun15-intel-2017a.eb @@ -7,7 +7,11 @@ versionsuffix = '-24Jun15' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2017a} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.4-intel-2015b-mkl=sequential.eb b/v/VASP/VASP-5.4.4-intel-2015b-mkl=sequential.eb index 435b1b06..0f813266 100644 --- a/v/VASP/VASP-5.4.4-intel-2015b-mkl=sequential.eb +++ b/v/VASP/VASP-5.4.4-intel-2015b-mkl=sequential.eb @@ -7,7 +7,11 @@ versionsuffix = '-mkl=sequential' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.4-intel-2016a-CUDA-8.0.44-mkl=sequential.eb b/v/VASP/VASP-5.4.4-intel-2016a-CUDA-8.0.44-mkl=sequential.eb index dab1b470..1afd94ab 100644 --- a/v/VASP/VASP-5.4.4-intel-2016a-CUDA-8.0.44-mkl=sequential.eb +++ b/v/VASP/VASP-5.4.4-intel-2016a-CUDA-8.0.44-mkl=sequential.eb @@ -7,7 +7,11 @@ versionsuffix = '-CUDA-8.0.44-mkl=sequential' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.4-intel-2017a-03.eb b/v/VASP/VASP-5.4.4-intel-2017a-03.eb index 9e9d4e53..21bdc41e 100644 --- a/v/VASP/VASP-5.4.4-intel-2017a-03.eb +++ b/v/VASP/VASP-5.4.4-intel-2017a-03.eb @@ -7,7 +7,11 @@ 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.4-intel-2017a-mkl=cluster.eb b/v/VASP/VASP-5.4.4-intel-2017a-mkl=cluster.eb index 4474a66e..e8e18734 100644 --- a/v/VASP/VASP-5.4.4-intel-2017a-mkl=cluster.eb +++ b/v/VASP/VASP-5.4.4-intel-2017a-mkl=cluster.eb @@ -7,7 +7,11 @@ versionsuffix = '-mkl=cluster' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel-test.eb b/v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel-test.eb new file mode 100644 index 00000000..1d232a5d --- /dev/null +++ b/v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel-test.eb @@ -0,0 +1,58 @@ +easyblock = 'MakeCp' + +name = 'VASP' +version = '5.4.4' +versionsuffix = '-mkl=paralel-test' + +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. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +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 = ['%(namelower)s.%(version)s.tar.gz'] + +#checksums = ['8ac646b108f974371eef398973373bf6'] + +#dependencies = [ +# ('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|-mkl=paralel|" makefile.include && ' + +# OFLAG = -O2 -xAVX +prebuildopts += 'sed -i "s|OFLAG = -O2|OFLAG = -O3 -xAVX|" makefile.include && ' + +# objects add MKLROOT +prebuildopts += 'sed -i "s|OBJECTS = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o|OBJECTS = fftmpiw.o fftmpi_map.o fft3dlib.o fftw3d.o \$\(MKLROOT\)/lib/intel64_lin/libfftw3xf_intel.a|" makefile.include && ' + +# VASP uses LIBS as a list of folders +prebuildopts += 'unset LIBS && ' + +#prebuildopts += 'exit 1' + +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-mkl=paralel.eb b/v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel.eb index f8967497..b49c05ba 100644 --- a/v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel.eb +++ b/v/VASP/VASP-5.4.4-intel-2017a-mkl=paralel.eb @@ -7,7 +7,11 @@ versionsuffix = '-mkl=paralel' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.4-intel-2017a-mkl=sequential.eb b/v/VASP/VASP-5.4.4-intel-2017a-mkl=sequential.eb index a0b8d751..343de061 100644 --- a/v/VASP/VASP-5.4.4-intel-2017a-mkl=sequential.eb +++ b/v/VASP/VASP-5.4.4-intel-2017a-mkl=sequential.eb @@ -7,7 +7,11 @@ versionsuffix = '-mkl=sequential' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.4-intel-2017a.eb b/v/VASP/VASP-5.4.4-intel-2017a.eb index d64cbc5f..23e49aac 100644 --- a/v/VASP/VASP-5.4.4-intel-2017a.eb +++ b/v/VASP/VASP-5.4.4-intel-2017a.eb @@ -7,7 +7,11 @@ versionsuffix = '-test-fftw' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} diff --git a/v/VASP/VASP-5.4.4-intel-2017b-mkl=cluster.eb b/v/VASP/VASP-5.4.4-intel-2017b-mkl=cluster.eb index 54cf0d5f..171ba528 100644 --- a/v/VASP/VASP-5.4.4-intel-2017b-mkl=cluster.eb +++ b/v/VASP/VASP-5.4.4-intel-2017b-mkl=cluster.eb @@ -7,7 +7,11 @@ versionsuffix = '-mkl=cluster' 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.""" +from first principles. + +To use VASP, You need academic licenses from University of Wiena. Follow the instructions https://www.vasp.at/index.php/faqs. + +Then send us please a list of authorized users and their ID for which you need this access. Please use only http://support.it4i.cz/rt. We are responsible to verify your licenses. After succesfull verification You will be granted to use VASP in our enviroment.""" toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'pic': True, 'usempi': True}