Merge branch 'master' into 'master'

Master

See merge request !13

c/Clp/Clp-1.16.10-intel-2017a.eb

@@ -0,0 +1,25 @@
+#made by PERMON team
+
+easyblock = 'ConfigureMake'
+
+name = 'Clp'
+version = '1.16.10'
+
+homepage = 'https://projects.coin-or.org/Clp'
+description = """Clp (COIN-OR linear programming) is an open-source linear programming solver written in C++. It is primarily meant to be used as a callable library, but a basic stand-alone executable version is also available. It is a part of the COIN-OR project (https://www.coin-or.org)."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = ['https://www.coin-or.org/download/source/Clp/']
+sources = [SOURCE_TGZ]
+
+dependencies = []
+
+sanity_check_paths = {
+  'files' : ['bin/clp'],
+  'dirs' : ['include/coin/','lib/'],
+}
+
+sanity_check_commands = [('clp','-h')]
+
+moduleclass = 'numlib'

l/LIBLINEAR/LIBLINEAR-2.11-intel-2017a.eb

@@ -0,0 +1,30 @@
+#made by PERMON team
+
+easyblock = 'MakeCp'
+
+name = 'LIBLINEAR'
+version = '2.11'
+
+homepage = 'http://www.csie.ntu.edu.tw/~cjlin/liblinear/'
+description = """LIBLINEAR is a simple package for solving large-scale regularized linear
+classification and regression. It supports L2-regularized logistic regression, L2-loss support vector classification
+L1-loss support vector classification, L1-regularized L2-loss support vector classification, L1-regularized logistic regression
+L2-regularized L2-loss support vector regression, L1-loss support vector regression."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = [homepage]
+sources = [SOURCELOWER_TAR_GZ]
+
+files_to_copy = [(['train', 'predict'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['train', 'predict']],
+    'dirs': [],
+}
+
+modextrapaths = {
+    'PATH': ['bin'],
+}
+
+moduleclass = 'numlib'

l/LIBSVM/LIBSVM-3.22-intel-2017a.eb

@@ -1,3 +1,5 @@
+#adapted by PERMON team
+
 easyblock = 'MakeCp'
 
 name = 'LIBSVM'
@@ -28,4 +30,4 @@ modextrapaths = {
     'PATH': ['bin', 'bin/svm-toy/qt'],
 }
 
-moduleclass = 'lib'
+moduleclass = 'numlib'

n/numpy/numpy-1.12.1-intel-2017a-Python-2.7.11.eb

@@ -0,0 +1,28 @@
+#adapted by PERMON team
+
+name = 'numpy'
+version = '1.12.1'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://www.numpy.org'
+description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things:
+ a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran
+ code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses,
+ NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be 
+ defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_ZIP]
+
+patches = ['numpy-1.12.0-mkl.patch']
+
+dependencies = [
+    ('Python', '2.7.11'),
+]
+
+# check that numpy is present in python and in proper version
+sanity_check_commands = [('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')]
+
+moduleclass = 'math'

p/PETSc/PETSc-3.7.5-intel-2017a-it4i.eb

@@ -0,0 +1,56 @@
+#made by PERMON team
+
+# BUILD ON COMPUTE NODE
+
+easyblock = 'ConfigureMake'
+name = 'PETSc'
+version = '3.7.5'
+versionsuffix = '-it4i'
+
+homepage = 'http://www.mcs.anl.gov/petsc'
+description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
+ scalable (parallel) solution of scientific applications modeled by partial differential equations."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+#build is still parallel, PETSc make doesnt support -j opt
+maxparallel = 0
+
+source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots']
+sources = [SOURCELOWER_TAR_GZ]
+
+# (build) dependencies provided through EasyBuild
+builddependencies = [('CMake', '3.7.2', '', True)]
+
+# configure installs dependencies -> remove installdir before configure
+keeppreviousinstall = True
+preconfigopts = 'rm -rf %(installdir)s;'
+
+petscArch = 'intel-opt'
+petscDir = '%(builddir)s/%(namelower)s-%(version)s'
+
+# config options
+configopts =  '--CFLAGS=-O3 -xHost --CXXFLAGS=-O3 -xHost --FFLAGS=-O3 -xHost --with-c++-support --with-pic=1 '
+configopts += '--with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --with-debugging=0 --with-gnu-compilers=0 '
+configopts += '--with-mpi=1 --with-x=0 '
+configopts += '--download-metis --download-parmetis --download-mumps --download-superlu --download-superlu_dist '
+configopts += '--with-blas-lapack-lib=[$EBROOTIMKL/mkl/lib/intel64_lin/libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a] '
+configopts += '--with-scalapack-include=$EBROOTIMKL/mkl/include '
+configopts += '--with-scalapack-lib=[$EBROOTIMKL/mkl/lib/intel64_lin/libmkl_scalapack_lp64.a,libmkl_blacs_intelmpi_lp64.a,libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a] '
+configopts += '--with-scalapack=1 '
+configopts += 'PETSC_ARCH=%s' % petscArch
+
+installopts = 'PETSC_DIR=%s PETSC_ARCH=%s' % (petscDir,petscArch)
+buildopts = installopts + ' all'
+
+modextravars = {'PETSC_DIR':'%(installdir)s'}
+
+moduleclass = 'numlib'
+
+# sanity checks
+runtest = 'test'   # run make test after make
+sanity_check_paths = {
+  'files': ['include/petscconf.h', 'lib/libpetsc.so'],
+  'dirs': []
+}
+sanity_check_commands = [('petscmpiexec','-h')]