diff --git a/d/DOLFIN/DOLFIN-2019.1.0-intel-2020a-Py-3.7.eb b/d/DOLFIN/DOLFIN-2019.1.0-intel-2020a-Py-3.7.eb index d8c05537..7803ff27 100644 --- a/d/DOLFIN/DOLFIN-2019.1.0-intel-2020a-Py-3.7.eb +++ b/d/DOLFIN/DOLFIN-2019.1.0-intel-2020a-Py-3.7.eb @@ -1,6 +1,8 @@ # IT4Innovations 2020 # LK +easyblock = 'CMakeMake' + name = 'DOLFIN' version = '2019.1.0' versionsuffix = '-Py-3.7' @@ -17,9 +19,9 @@ sources = [SOURCELOWER_TAR_GZ] builddependencies = [ ('CMake', '3.16.2', '', True), - ('pkg-config', '0.29.2', '', True), - ('PatchELF', '0.9', '', True), -# ('pybind11', '2.2.4', versionsuffix), +# ('pkg-config', '0.29.2', '', True), +# ('PatchELF', '0.9', '', True), +# ('pybind11', '2.4.3', versionsuffix, True), ] dependencies = [ ('Py', '3.7', '', True), @@ -27,25 +29,25 @@ dependencies = [ ('FFC', '2019.1.0', versionsuffix), ('FIAT', '2019.1.0', versionsuffix), ('UFL', '2019.1.0', versionsuffix), - ('SCOTCH', '6.0.9'), - ('SuiteSparse', '5.6.0', '-METIS-5.1.0'), - ('CGAL', '4.11.1'), - ('PETSc', '3.12.4'), - ('SLEPc', '3.12.2'), - ('HDF5', '1.10.6'), +# ('SCOTCH', '6.0.9'), +# ('SuiteSparse', '5.6.0', '-METIS-5.1.0'), +# ('CGAL', '4.11.1'), +# ('PETSc', '3.12.4'), +# ('SLEPc', '3.12.2'), +# ('HDF5', '1.10.6'), # ('Trilinos', '12.12.1', versionsuffix), ('zlib', '1.2.11', '', True), ('libxml2', '2.9.9', '', True), ('Eigen', '3.3.7', '', True), # ('PLY', '3.11', versionsuffix), # ('VTK', '8.1.0', versionsuffix), -# ('petsc4py', '3.9.1', versionsuffix), -# ('slepc4py', '3.9.0', versionsuffix), +# ('petsc4py', '3.12.0', versionsuffix, True), +# ('slepc4py', '3.12.0', versionsuffix, True), # ('SUNDIALS', '2.7.0'), - ('ParMETIS', '4.0.3'), +# ('ParMETIS', '4.0.3'), ] # demos run as tests fail with 'bad X server connection', skipping for now -runtest = False +#runtest = False moduleclass = 'math' diff --git a/f/FFC/FFC-2018.1.0-conda.eb b/f/FFC/FFC-2018.1.0-conda.eb new file mode 100644 index 00000000..4d3773ee --- /dev/null +++ b/f/FFC/FFC-2018.1.0-conda.eb @@ -0,0 +1,27 @@ +# IT4Innovations 2020 +# LK + +easyblock = "Conda" + +name = 'FFC' +version = '2018.1.0' +versionsuffix = '-conda' + +homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' +description = """This software calculates phonon-phonon interaction related properties""" + +toolchain = SYSTEM + +dependencies = [ + ('Anaconda3', '2019.10'), +] + +requirements = "fenics=%(version)s mshr=%(version)s python=3.7" +channels = ['conda-forge'] + +sanity_check_paths = { + 'files': ['bin/ffc'], + 'dirs': ['bin', 'lib', 'lib64', 'include', 'sbin'] +} + +moduleclass = 'math' diff --git a/f/FFC/FFC-2019.1.0-conda.eb b/f/FFC/FFC-2019.1.0-conda.eb index da773aa4..3a3b6dd3 100644 --- a/f/FFC/FFC-2019.1.0-conda.eb +++ b/f/FFC/FFC-2019.1.0-conda.eb @@ -15,7 +15,7 @@ dependencies = [ ('Anaconda3', '2019.10'), ] -requirements = "fenics=%(version)s python=3.7" +requirements = "fenics=%(version)s mshr=%(version)s slepc=3.12 python=3.8" channels = ['conda-forge'] sanity_check_paths = { diff --git a/o/OpenMPI/OpenMPI-1.10.7-GCC-6.3.0-2.27.eb b/o/OpenMPI/OpenMPI-1.10.7-GCC-6.3.0-2.27.eb index 941a4989..8d84c213 100644 --- a/o/OpenMPI/OpenMPI-1.10.7-GCC-6.3.0-2.27.eb +++ b/o/OpenMPI/OpenMPI-1.10.7-GCC-6.3.0-2.27.eb @@ -25,7 +25,7 @@ configopts += '--disable-dlopen ' configopts += '--with-tm=/opt/pbs ' # Enable PBS # needed for --with-verbs -osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] libs = [ "mpi_cxx", diff --git a/p/PLY/PLY-3.11-intel-2020a-Py-3.7.eb b/p/PLY/PLY-3.11-intel-2020a-Py-3.7.eb new file mode 100644 index 00000000..4be3fc15 --- /dev/null +++ b/p/PLY/PLY-3.11-intel-2020a-Py-3.7.eb @@ -0,0 +1,28 @@ +# IT4Innovations 2020 +# LK + +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' +versionsuffix = "-Py-3.7" + +homepage = "http://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +dependencies = [('Py', '3.7', '', True)] + +download_dep_fail = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.7/site-packages'], +} + +moduleclass = 'lib' diff --git a/p/petsc4py/petsc4py-3.12.0-Py-3.7.eb b/p/petsc4py/petsc4py-3.12.0-Py-3.7.eb index 1c9d11e3..d8e35a76 100644 --- a/p/petsc4py/petsc4py-3.12.0-Py-3.7.eb +++ b/p/petsc4py/petsc4py-3.12.0-Py-3.7.eb @@ -1,4 +1,5 @@ # IT4Innovations 2020 +# LK easyblock = "PythonPackage" diff --git a/r/RELION/RELION-3.1.0-gompi-2019b.eb b/r/RELION/RELION-3.1.0-gompi-2019b.eb deleted file mode 100644 index f341c974..00000000 --- a/r/RELION/RELION-3.1.0-gompi-2019b.eb +++ /dev/null @@ -1,33 +0,0 @@ -# IT4Innovations 2020\ -# LK - -easyblock = 'CMakeMake' - -name = 'RELION' -version = '3.1.0' - -homepage = 'http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page' -description = """RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone local_computer - program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class - averages in electron cryo-microscopy (cryo-EM).""" - -toolchain = {'name': 'gompi', 'version': '2019b'} -toolchainopts = {'opt': True} - -source_urls = ['https://github.com/3dem/relion/archive/'] -sources = ['%(version)s.tar.gz'] - -builddependencies = [ - ('CMake', '3.16.2', '', True), -] - -dependencies = [ - ('X11', '20190717', '', True), - ('libpng', '1.6.37', '', True), - ('FFTW', '3.3.8'), - ('FLTK', '1.3.5', '', True), -] - -separate_build_dir = True - -moduleclass = 'bio' diff --git a/r/RELION/RELION-3.1.0-intel-2020a.eb b/r/RELION/RELION-3.1.0-intel-2020a.eb index 126527ea..4a77ead2 100644 --- a/r/RELION/RELION-3.1.0-intel-2020a.eb +++ b/r/RELION/RELION-3.1.0-intel-2020a.eb @@ -15,24 +15,17 @@ toolchain = {'name': 'intel', 'version': '2020a'} source_urls = ['https://github.com/3dem/relion/archive/'] sources = ['%(version)s.tar.gz'] +patches = ['fltk-ftp.patch'] -builddependencies = [('CMake', '3.16.2')] - -dependencies = [ - ('X11', '20190717', '', ('GCCcore', '8.3.0')), - ('FLTK', '1.3.5', '', True), - ('LibTIFF', '4.1.0', '', ('GCCcore', '8.3.0')), -# ('tbb', '2019_U9', '', ('GCCcore', '8.3.0')), - ('FFTW', '3.3.8'), - ('GTK+', '3.24.13', '', ('GCCcore', '8.3.0')), - ('libXrender', '0.9.9', '', True), +builddependencies = [ + ('CMake', '3.16.2'), ] -#configopts = "-DCMAKE_SHARED_LINKER_FLAGS='-lpthread' -DMPI_INCLUDE_PATH=$EBROOTIMPI/include64 " -#configopts += "-DMPI_C_COMPILER=$EBROOTIMPI/bin64/mpiicc -DMPI_CXX_COMPILER=$EBROOTIMPI/bin64/mpiicpc " -#configopts += "-DCUDA=OFF -DCudaTexture=OFF " -#configopts += "-DALTCPU=ON -DMKLFFT=ON " -#configopts += "-DALTCPU=ON -DMKLFFT=ON -DFORCE_OWN_TBB=OFF " +dependencies = [ + ('LibTIFF', '4.1.0', '', ('GCCcore', '8.3.0')), +] + +configopts = "-DMKLFFT=ON -DFORCE_OWN_FLTK=ON " sanity_check_paths = { 'files': ['bin/relion'], diff --git a/r/RELION/fltk-ftp.patch b/r/RELION/fltk-ftp.patch new file mode 100644 index 00000000..5e85a96e --- /dev/null +++ b/r/RELION/fltk-ftp.patch @@ -0,0 +1,11 @@ +--- cmake/BuildFLTK.cmake.orig 2020-07-22 12:23:50.040767719 +0200 ++++ cmake/BuildFLTK.cmake 2020-07-22 12:24:43.340803545 +0200 +@@ -36,7 +36,7 @@ + + message(STATUS "no previous fltk found, the following paths are set for libs/headers TO BE built") + +- set(FLTK_TAR_FILE ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/fltk-1.3.5-source.tar.gz) # FLTK 1.3.5 ++ set(FLTK_TAR_FILE https://www.fltk.org/pub/fltk/1.3.5/fltk-1.3.5-source.tar.gz) # FLTK 1.3.5 + set(FLTK_HASH e85017defd5a03ae82e634311db87bbf) + set(FLTK_TAR_NAME fltk-1.3.5-source.tar.gz) +