new file: e/Embree/Embree-2.16.2.eb

new file:   g/GDAL/GDAL-2.1.3-Python-2.7.13-without-intel.eb
	new file:   i/ispc/ispc-1.9.1.eb
	new file:   o/OSPRay/OSPRay-1.3.0.eb
	new file:   p/ParaView/ParaView-5.1.2-intel-2017a-mpi-OSPRay.eb
	new file:   p/ParaView/Paraview-5.1.2-intel-2017a-OSPRay.eb
	new file:   s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.eb
	new file:   s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.patch
	new file:   v/VASP/VASP-5.4.4-intel-2017a-03.eb
	modified:   v/VASP/VASP-5.4.4-intel-2017a.eb

e/Embree/Embree-2.16.2.eb

@@ -0,0 +1,31 @@
+easyblock = 'CMakeMake'
+
+name = 'Embree'
+version = '2.16.2'
+
+homepage = 'https://embree.github.io/index.html'
+description = """
+	Embree is a collection of high-performance ray tracing kernels, developed at Intel."""
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+source_urls = ['https://github.com/embree/embree/archive']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [
+	('CMake', '3.8.1', '', True),
+]
+
+dependencies = [
+	('tbb', '4.4.2.152', '', True),
+	('ispc', '1.9.1', '', True),
+]
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ['lib/libospray.so'],
+    'dirs': ['bin', 'lib'],
+}
+
+moduleclass = 'lib'

g/GDAL/GDAL-2.1.3-Python-2.7.13-without-intel.eb

@@ -0,0 +1,47 @@
+easyblock = 'ConfigureMake'
+
+name = 'GDAL'
+version = '2.1.3'
+versionsuffix = '-Python-%(pyver)s-without-intel'
+
+homepage = 'http://www.gdal.org/'
+description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
+ Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
+ to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
+ data translation and processing."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+patches = ['GDAL-%(version)s_fix-uchar-definition.patch']
+
+dependencies = [
+    ('Python', '2.7.13'),
+#    ('netCDF', '4.4.1.1', '', ('intel', '2017a')),
+    ('expat', '2.2.0'),
+    ('GEOS', '3.6.1', '-Python-%(pyver)s'),
+    ('SQLite', '3.17.0'),
+    ('libxml2', '2.9.4'),
+    ('libpng', '1.6.29'),
+    ('libjpeg-turbo', '1.5.1'),
+#    ('JasPer', '2.0.12', '', ('intel', '2017a')),
+    ('LibTIFF', '4.0.7'),
+    ('zlib', '1.2.11'),
+#    ('cURL', '7.53.1'),
+    ('PCRE', '8.40'),
+]
+
+configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-netcdf=$EBROOTNETCDF'
+configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO'
+configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER'
+configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python'
+
+modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages']
+}
+
+moduleclass = 'data'

i/ispc/ispc-1.9.1.eb

@@ -0,0 +1,26 @@
+easyblock = 'Tarball'
+
+name = 'ispc'
+version = '1.9.1'
+
+homepage = 'http://ispc.github.io/ , https://github.com/ispc/ispc/'
+description = """Intel SPMD Program Compilers; An open-source compiler for high-performance
+ SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language,
+ with extensions for 'single program, multiple data' (SPMD) programming.
+ Under the SPMD model, the programmer writes a program that generally appears
+ to be a regular serial program, though the execution model is actually that
+ a number of program instances execute in parallel on the hardware."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['ispc-v%(version)s-linux.tar.gz']
+source_urls = [('http://sourceforge.net/projects/ispcmirror/files/v%(version)s', 'download')]
+
+sanity_check_paths = {
+    'files': ["ispc"],
+    'dirs': []
+}
+
+modextrapaths = {'PATH': ''}
+
+moduleclass = 'compiler'

o/OSPRay/OSPRay-1.3.0.eb

@@ -0,0 +1,35 @@
+easyblock = 'CMakeMake'
+
+name = 'OSPRay'
+version = '1.3.0'
+
+homepage = 'http://www.ospray.org'
+description = """
+ A Ray Tracing Based Rendering Engine for High-Fidelity Visualization"""
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+source_urls = ['https://github.com/ospray/OSPRay/archive/']
+sources = ['v%(version)s.tar.gz']
+
+builddependencies = [
+	('CMake', '3.8.1', '', True),
+	('tbb', '4.4.2.152', '', True)
+]
+
+dependencies = []
+
+separate_build_dir = True
+
+#skipsteps= ['configure', 'build']
+
+sanity_check_paths = {
+    'files': ['lib/libospray.so'],
+    'dirs': ['bin', 'lib'],
+}
+
+# add the top dir to PATH
+modextrapaths = {
+    'PATH': ''
+}
+
+moduleclass = 'vis'

p/ParaView/ParaView-5.1.2-intel-2017a-mpi-OSPRay.eb

@@ -0,0 +1,50 @@
+easyblock = 'CMakeMake'
+
+name = 'ParaView'
+version = '5.1.2'
+versionsuffix = '-mpi-OSPRay'
+
+homepage = "http://www.paraview.org"
+description = "ParaView is a scientific parallel visualizer."
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile='
+source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix]
+sources = ["ParaView-v%(version)s.tar.gz"]
+
+dependencies = [
+    ('X11', '20170314', '', True),
+    ('Mesa', '12.0.2'),
+    ('libGLU', '9.0.0', '', True),
+    ('Qt', '4.8.6', '', True),
+    ('zlib', '1.2.11', '', True),
+    ('HDF5', '1.8.17'),
+    ('Python', '2.7.13', '', True),
+]
+
+builddependencies = [('CMake', '3.8.1', '', True)]
+
+separate_build_dir = True
+
+configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DVTK_OPENGL_HAS_OSMESA=ON -DPARAVIEW_USE_MPI=ON '
+configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include -DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s ' % SHLIB_EXT
+configopts += '-DOSMESA_INCLUDE_DIR=$EBROOTMESA/include -DOSMESA_LIBRARY=$EBROOTMESA/lib/libOSMesa.%s ' % SHLIB_EXT
+configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT
+configopts += '-DVTK_USE_SYSTEM_HDF5=ON -DPARAVIEW_ENABLE_PYTHON=ON -DBUILD_SHARED_LIBS=ON -DVTK_RENDERING_BACKEND=OpenGL2 '
+# if you want to build server only Paraview, uncomment the following line:
+# configopts += '-DVTK_USE_X=OFF '
+
+# Without internet connection turn off testing (uncomment the following line)
+configopts += '-DBUILD_TESTING=OFF '
+# Or consult https://gitlab.kitware.com/vtk/vtk/blob/master/Documentation/dev/git/data.md
+# and download ExternalData to $EASYBUILD_SOURCEPATH and adjust -DExternalData_OBJECT_STORES accordingly
+# Without internet connection, comment the following two lines (configopts and prebuildopts)
+configopts += '-DExternalData_OBJECT_STORES=%(builddir)s/ExternalData '
+# The ParaView server can be cranky, test downloads are quite often failing, especially in the case
+# of parallel downloads. Using ; insted of && gives a second chance to download the test files, if the
+# first serial attempt would fail.
+prebuildopts = 'make VTKData ;'
+
+moduleclass = 'vis'

p/ParaView/Paraview-5.1.2-intel-2017a-OSPRay.eb

@@ -0,0 +1,26 @@
+easyblock = 'PackedBinary'
+
+name = 'ParaView'
+version = '5.1.2'
+versionsuffix = '-OSPRay'
+
+homepage = "http://www.paraview.org"
+description = "ParaView is a scientific parallel visualizer."
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile='
+source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix]
+sources = ["PV5_1_2_pvOSPRay_linux_x86_64.tgz"]
+
+dependencies = [('intel', '2017a')]
+
+install_cmd = "cp -a PV5_1_2_pvOSPRay_linux_x86_64/* %(installdir)s/ && find %(installdir)s/ -type d -exec chmod 755 {} \; "
+
+sanity_check_paths = {
+    'files': ['bin/paraview'],
+    'dirs': ['bin', 'lib'],
+}
+
+moduleclass = 'vis'
+

s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.eb

@@ -0,0 +1,35 @@
+easyblock = "PythonPackage"
+
+name = 'Sen2Cor'
+version = '2.3.1'
+
+homepage = 'http://step.esa.int/main/third-party-plugins-2/sen2cor/'
+description = """Sen2Cor is a processor for Sentinel-2 Level 2A product generation and formatting; 
+it performs the atmospheric-, terrain and cirrus correction of Top-Of- Atmosphere Level 1C input data.
+Sen2Cor creates Bottom-Of-Atmosphere, optionally terrain- and cirrus corrected reflectance images; 
+additional, Aerosol Optical Thickness-, Water Vapor-, Scene Classification Maps and Quality Indicators 
+for cloud and snow probabilities. Its output product format is equivalent to the Level 1C User Product: 
+JPEG 2000 images, three different resolutions, 60, 20 and 10 m."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://step.esa.int/thirdparties/sen2cor/%(version)s/']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+
+python = "Python"
+python_version = "2.7.13"
+versionsuffix = '-%s-%s' % (python, python_version)
+
+patches = ['%(name)s-%(version)s-Python-2.7.13.patch']
+
+dependencies = [
+    (python, python_version),
+    ('GDAL', '2.1.3', '-%s-%s' % (python, python_version)),
+]
+
+sanity_check_paths = {
+    'files': ['bin/L2A_Process', 'bin/L2A_Process-02.03.01', 'bin/L2A_Process-2.3.1'],
+    'dirs': ['lib']
+}
+
+moduleclass = 'phys'

s/Sen2Cor/Sen2Cor-2.3.1-Python-2.7.13.patch

@@ -0,0 +1,20 @@
+--- setup.py.orig	2017-02-02 09:37:32.000000000 +0100
++++ setup.py	2017-06-19 11:12:03.788380266 +0200
+@@ -35,7 +35,7 @@
+ def copyConfiguration():
+     sys.stdout.write('\nSEN2COR ' + version + ' setup script:\n')
+     sys.stdout.write('This will finish the configuration of the environment settings.\n')
+-    user_input = raw_input('\nOK to continue? [y/n]: ')
++    user_input = 'y'
+     if user_input == 'n':
+         return False
+ 
+@@ -46,7 +46,7 @@
+     while True:
+         sys.stdout.write('\nPlease input a path for the sen2cor home directory:\n')
+         sys.stdout.write('default is: ' + SEN2COR_HOME + '\n')
+-        user_input = raw_input('Is this OK? [y/n]: ')
++        user_input = 'y'
+         if user_input == 'n':
+             SEN2COR_HOME = raw_input('New path: ')
+             sys.stdout.write('New path is: ' + SEN2COR_HOME + '\n')

v/VASP/VASP-5.4.4-intel-2017a-03.eb

@@ -0,0 +1,48 @@
+easyblock = 'MakeCp'
+
+name = 'VASP'
+version = '5.4.4'
+versionsuffix = '-O3'
+
+homepage = 'http://www.vasp.at'
+description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
+materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics,
+from first principles."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+# Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code
+sources = ['%s.%s.tar.gz' % (name.lower(), version)]
+
+dependencies = [
+    ('FFTW', '3.3.6'),
+    ('zlib', '1.2.11', '', True),
+]
+
+prebuildopts = 'cp arch/makefile.include.linux_intel ./makefile.include && '
+
+# path to libfftw3xf_intel.a is hardcoded in makefile.include
+prebuildopts += 'sed -i "s|\$(MKLROOT)/interfaces/fftw3xf|\$(FFTW_LIB_DIR)|" makefile.include && '
+
+# remove mkl flag to prevent mixing dynamic libs with the static libs in LIBBLACS/SCALAPACK
+prebuildopts += 'sed -i "s|-mkl=sequential||" makefile.include && '
+
+# change -O2 to -O3
+prebuildopts += 'sed -i "s|-O2|-O3|" makefile.include && '
+
+# VASP uses LIBS as a list of folders
+prebuildopts += 'unset LIBS && '
+
+buildopts = 'all BLACS="$LIBBLACS" SCALAPACK="$LIBSCALAPACK"'
+
+parallel = 1
+
+files_to_copy = [(['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/vasp_std', 'bin/vasp_gam', 'bin/vasp_ncl'],
+    'dirs': []
+}
+
+moduleclass = 'phys'

v/VASP/VASP-5.4.4-intel-2017a.eb

@@ -2,6 +2,7 @@ easyblock = 'MakeCp'
 
 name = 'VASP'
 version = '5.4.4'
+versionsuffix = '-test-fftw'
 
 homepage = 'http://www.vasp.at'
 description = """The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale
@@ -12,10 +13,11 @@ toolchain = {'name': 'intel', 'version': '2017a'}
 toolchainopts = {'pic': True, 'usempi': True}
 
 # Vasp is proprietary software, see http://www.vasp.at/index.php/faqs on how to get access to the code
-sources = ['%s.%s.tar.gz' % (name.lower(), version)]
+sources = ['%(namelower)s.%(version)s.tar.gz']
+
+checksums = ['8ac646b108f974371eef398973373bf6']
 
 dependencies = [
-    ('FFTW', '3.3.6'),
     ('zlib', '1.2.11', '', True),
 ]