diff --git a/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb b/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb deleted file mode 100644 index c0357522..00000000 --- a/a/ABAQUS/ABAQUS-2017-hotfix-1721.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'ABAQUS' -version = '2017' -hotfix = '1721' -versionsuffix = '-hotfix-%s' % hotfix - -homepage = 'http://www.simulia.com/products/abaqus_fea.html' -description = """Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit - dynamics FEA.""" - -toolchain = {'name': 'dummy', 'version': ''} - -sources = [ - '%(version)s.AM_SIM_Abaqus_Extend.AllOS.1-6.tar', - '%(version)s.AM_SIM_Abaqus_Extend.AllOS.2-6.tar', - '%(version)s.AM_SIM_Abaqus_Extend.AllOS.3-6.tar', - '%(version)s.AM_SIM_Abaqus_Extend.AllOS.4-6.tar', - '%(version)s.AM_SIM_Abaqus_Extend.AllOS.5-6.tar', - '%(version)s.AM_SIM_Abaqus_Extend.AllOS.6-6.tar', - # hotfixes - '%%(version)s.FP.CFA.%s.Part_3DEXP_SimulationServices.Linux64.tar' % hotfix, - '%%(version)s.FP.CFA.%s.Part_SIMULIA_Abaqus_CAE.Linux64.tar' % hotfix, -] - -moduleclass = 'cae' diff --git a/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb b/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb deleted file mode 100644 index 440bc7a9..00000000 --- a/a/AMOS/AMOS-3.1.0-goolf-1.4.10.eb +++ /dev/null @@ -1,41 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Cedric Laczny , 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_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'AMOS' -version = '3.1.0' - -homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS' -description = """The AMOS consortium is committed to the development of open-source whole genome assembly software""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')] - -patches = ['AMOS-3.1.0_GCC-4.7.patch'] - -dependencies = [ - ('expat', '2.1.0'), - ('MUMmer', '3.23'), -] - -sanity_check_paths = { - 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], - 'dirs': [] -} - -parallel = 1 # make crashes otherwise - -moduleclass = 'bio' diff --git a/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb b/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb deleted file mode 100644 index d767191d..00000000 --- a/a/AMOS/AMOS-3.1.0-ictce-5.3.0.eb +++ /dev/null @@ -1,40 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA -# Authors:: Cedric Laczny , 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_2012-94.html -## - -easyblock = 'ConfigureMake' - -name = 'AMOS' -version = '3.1.0' - -homepage = 'http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS' -description = """The AMOS consortium is committed to the development of open-source whole genome assembly software""" - - -toolchain = {'name': 'ictce', 'version': '5.3.0'} -toolchainopts = {'optarch': True, 'pic': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = [('http://sourceforge.net/projects/amos/files/%s/%s' % (name.lower(), version), 'download')] - -dependencies = [ - ('expat', '2.1.0'), - ('MUMmer', '3.23'), -] - -sanity_check_paths = { - 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], - 'dirs': [] -} - -parallel = 1 # make crashes otherwise - -moduleclass = 'bio' diff --git a/a/ARB/ARB-5.5-goolf-1.4.10.eb b/a/ARB/ARB-5.5-goolf-1.4.10.eb deleted file mode 100644 index 41b26e29..00000000 --- a/a/ARB/ARB-5.5-goolf-1.4.10.eb +++ /dev/null @@ -1,37 +0,0 @@ -name = 'ARB' -version = '5.5' - -homepage = 'http://www.arb-home.de/' -description = """The ARB software is a graphically oriented package comprising various tools for sequence database -handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked -to the respective sequence entries is structured according to phylogeny or other user defined criteria.""" - -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -# download from http://download.arb-home.de/release/arb_5.5, and rename to include version -sources = ['%(namelower)s-%(version)s-src.tgz'] - -patches = [ - '%(name)s-%(version)s_xmkmf.patch', - '%(name)s-%(version)s_xflags.patch', -] - -dependencies = [ - ('libpng', '1.6.6'), - ('LibTIFF', '4.0.3'), - ('Java', '1.7.0_15', '', True), - ('lynx', '2.8.7'), - ('makedepend', '1.0.4'), - ('imake', '1.0.5'), - ('libXt', '1.1.4'), - ('motif', '2.3.4'), # libXm - ('libXpm', '3.5.11'), - ('libXaw', '1.0.12'), - ('Perl', '5.16.3'), - ('libxslt', '1.1.28'), - ('freeglut', '2.8.1'), - ('Sablotron', '1.0.3'), - ('libxml2', '2.9.1'), -] - -moduleclass = 'bio' diff --git a/c/CUDA/CUDA-7.5.18.eb b/c/CUDA/CUDA-7.5.18.eb deleted file mode 100644 index 51cc9d1f..00000000 --- a/c/CUDA/CUDA-7.5.18.eb +++ /dev/null @@ -1,16 +0,0 @@ -name = 'CUDA' -version = '7.5.18' - -homepage = 'https://developer.nvidia.com/cuda-toolkit' -description = """CUDA (formerly Compute Unified Device Architecture) is a parallel - computing platform and programming model created by NVIDIA and implemented by the - graphics processing units (GPUs) that they produce. CUDA gives developers access - to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" - -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major_minor)s/Prod/local_installers/'] - -sources = ['%(namelower)s_%(version)s_linux.run'] - -moduleclass = 'system' diff --git a/test.sh b/duplicate.sh similarity index 90% rename from test.sh rename to duplicate.sh index 36d4c0ae..2e5aec98 100755 --- a/test.sh +++ b/duplicate.sh @@ -37,4 +37,6 @@ done echo "" for read in `cat duplicate`; do grep "$read" it4i; done | sort -u > remove_list -rm duplicate it4i develop +for rm in `cat remove_list | cut -d ';' -f 2`; do find . -name $rm -exec rm {} \;; done + +rm duplicate it4i develop remove_list diff --git a/g/GSL/GSL-2.3-intel-2017a.eb b/g/GSL/GSL-2.3-intel-2017a.eb deleted file mode 100644 index 23a2fed6..00000000 --- a/g/GSL/GSL-2.3-intel-2017a.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GSL' -version = '2.3' - -homepage = 'http://www.gnu.org/software/gsl/' -description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. - The library provides a wide range of mathematical routines such as random number generators, special functions - and least-squares fitting.""" - -toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = [GNU_SOURCE] -sources = [SOURCELOWER_TAR_GZ] - -configopts = "--with-pic" - -moduleclass = 'numlib' diff --git a/h/HPL/HPL-2.2-intel-2017b.eb b/h/HPL/HPL-2.2-intel-2017b.eb deleted file mode 100644 index 6fb24071..00000000 --- a/h/HPL/HPL-2.2-intel-2017b.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'HPL' -version = '2.2' - -homepage = 'http://www.netlib.org/benchmark/hpl/' -description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) - arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available - implementation of the High Performance Computing Linpack Benchmark.""" - -toolchain = {'name': 'intel', 'version': '2017b'} -toolchainopts = {'usempi': True} - -sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] -checksums = ['ac7534163a09e21a5fa763e4e16dfc119bc84043f6e6a807aba666518f8df440'] - -# fix Make dependencies, so parallel build also works -patches = ['HPL_parallel-make.patch'] - -moduleclass = 'tools' diff --git a/m/Mesa/Mesa-12.0.2-intel-2016b.eb b/m/Mesa/Mesa-12.0.2-intel-2016b.eb deleted file mode 100644 index 2ac60cb5..00000000 --- a/m/Mesa/Mesa-12.0.2-intel-2016b.eb +++ /dev/null @@ -1,62 +0,0 @@ -# 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 = '12.0.2' - -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': 'intel', 'version': '2016b'} -# 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/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', -] - -builddependencies = [ - ('flex', '2.6.0'), - ('Bison', '3.0.4'), - ('Autotools', '20150215'), - ('pkg-config', '0.29.1'), - ('Mako', '1.0.4', '-Python-2.7.12'), - ('libxml2', '2.9.4', '-Python-2.7.12'), -] - -dependencies = [ - ('zlib', '1.2.8'), - ('nettle', '3.2'), - ('libdrm', '2.4.70'), - ('LLVM', '3.8.1'), - ('X11', '20160819'), -] - -# GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" -configopts += " --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" -configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " - -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/remove_list b/remove_list deleted file mode 100644 index 4c88cceb..00000000 --- a/remove_list +++ /dev/null @@ -1,12 +0,0 @@ -0515e2cba0b6b96e9a955ad98a991119;SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb -11f2dc760748e6e004378c8e2b277b70;XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb -1af592f5c53593710e9a65d4aecaa8f6;ABAQUS-2017-hotfix-1721.eb -22df523f7cc85cc59ef94b864ba42cb8;HPL-2.2-intel-2017b.eb -37a67325bd697ba16456d47f96a809e9;GSL-2.3-intel-2017a.eb -42c0a56911761bebefa424a6580e80fe;ARB-5.5-goolf-1.4.10.eb -454e580a5ededc4fc3ef984aac28bfe9;Mesa-12.0.2-intel-2016b.eb -4f649bd51dadf7c43d0b5118db54d915;AMOS-3.1.0-goolf-1.4.10.eb -515233dc386f6b025bc6c88ec8377c65;xcb-proto-1.11.eb -a47f78ce229d82b7818feb0d9e2e9480;CUDA-7.5.18.eb -d5a4360bcafc8486b843c83767044a7d;ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb -e8b947919b8aeb4a6a394d6831f5d6a4;AMOS-3.1.0-ictce-5.3.0.eb diff --git a/s/ScientificPython/ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb b/s/ScientificPython/ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb deleted file mode 100644 index 90ba2524..00000000 --- a/s/ScientificPython/ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'ScientificPython' -version = '2.9.4' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' -description = """ScientificPython is a collection of Python modules for scientific computing. - It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, - and parallelization.""" - -toolchain = {'name': 'intel', 'version': '2016a'} - -source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Python', '2.7.11'), - # older version of numpy than the one included in Python module required - # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for - ('numpy', '1.8.2', versionsuffix), -] - -options = {'modulename': 'Scientific'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/Scientific'], -} - -moduleclass = 'math' diff --git a/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb b/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb deleted file mode 100644 index 3f7ce4f2..00000000 --- a/s/SuiteSparse/SuiteSparse-4.5.5-intel-2017a-METIS-5.1.0.eb +++ /dev/null @@ -1,19 +0,0 @@ -name = 'SuiteSparse' -version = '4.5.5' -metis_ver = '5.1.0' -versionsuffix = '-METIS-%s' % metis_ver - -homepage = 'http://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" - -toolchain = {'name': 'intel', 'version': '2017a'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [('METIS', metis_ver)] - -parallel = 1 - -moduleclass = 'numlib' diff --git a/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb b/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb deleted file mode 100644 index 71416dbf..00000000 --- a/x/XML-Parser/XML-Parser-2.44-foss-2016a-Perl-5.22.1.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PerlModule' - -name = 'XML-Parser' -version = '2.44' -versionsuffix = '-Perl-%(perlver)s' - -homepage = 'http://search.cpan.org/~toddr/XML-Parser-2.41/' -description = """This is a Perl extension interface to James Clark's XML parser, expat.""" - -toolchain = {'name': 'foss', 'version': '2016a'} - -source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] -sources = [SOURCE_TAR_GZ] - -dependencies = [ - ('Perl', '5.22.1'), - ('expat', '2.1.1') -] - -options = {'modulename': 'XML::Parser'} - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML'], -} - -moduleclass = 'data' diff --git a/x/xcb-proto/xcb-proto-1.11.eb b/x/xcb-proto/xcb-proto-1.11.eb deleted file mode 100644 index 6a306d86..00000000 --- a/x/xcb-proto/xcb-proto-1.11.eb +++ /dev/null @@ -1,26 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'xcb-proto' -version = '1.11' - -homepage = 'http://xcb.freedesktop.org/' -description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, -latency hiding, direct access to the protocol, improved threading support, and extensibility.""" - -# even though xcb-proto is installed with configure-make-make install, nothing is actually built; -# only .py files are installed using Python, and some .xlm flies copied, so OK to use dummy toolchain -toolchain = {'name': 'dummy', 'version': 'dummy'} - -source_urls = ['http://xcb.freedesktop.org/dist/'] -sources = [SOURCELOWER_TAR_GZ] - -allow_system_deps = [('Python', SYS_PYTHON_VERSION)] - -pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) - -sanity_check_paths = { - 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] -} - -moduleclass = 'devel'