Merge pull request #3329 from boegel/20160712090032_new_pr_netCDF441

{data}[foss/2016b] netCDF v4.4.1, GDAL v2.1.1 (REVIEW)

easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2016b.eb

@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'Bison'
+version = '3.0.4'
+
+homepage = 'http://www.gnu.org/software/bison'
+description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar
+ into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables."""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [GNU_SOURCE]
+
+builddependencies = [('M4', '1.4.17')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"],
+    'dirs': [],
+}
+
+moduleclass = 'lang'

easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'CMake'
+version = '3.5.2'
+
+homepage = 'http://www.cmake.org'
+description = """CMake, the cross-platform, open-source build system.
+ CMake is a family of tools designed to build, test and package software."""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+
+source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s']
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = '-- -DCMAKE_USE_OPENSSL=1'
+
+dependencies = [
+    ('ncurses', '6.0'),
+    # 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', '1.0.1s'),
+]
+
+osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

easybuild/easyconfigs/c/cURL/cURL-7.49.1-foss-2016b.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'cURL'
+version = '7.49.1'
+
+homepage = 'http://curl.haxx.se'
+description = """libcurl is a free and easy-to-use client-side URL transfer library,
+ supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS,
+ POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports
+ SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload,
+ proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate,
+ Kerberos), file transfer resume, http proxy tunneling and more."""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://curl.haxx.se/download/']
+
+osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')]
+
+# dependencies = [('OpenSSL', '1.0.1t')]
+# configopts = "--with-ssl=$EBROOTOPENSSL"
+
+modextravars = {'CURL_INCLUDES': '%(installdir)s/include'}
+
+sanity_check_paths = {
+    'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'tools'

easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016b.eb

@@ -0,0 +1,21 @@
+name = 'Doxygen'
+version = '1.8.11'
+
+homepage = 'http://www.doxygen.org'
+description = """Doxygen is a documentation system for C++, C, Java, Objective-C, Python, 
+ IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D."""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+
+sources = ['%(namelower)s-%(version)s.src.tar.gz']
+source_urls = ['http://ftp.stack.nl/pub/users/dimitri/']
+
+builddependencies = [
+    ('CMake', '3.5.2'),
+    ('flex', '2.6.0'),
+    ('Bison', '3.0.4'),
+]
+
+parallel = 1
+
+moduleclass = 'devel'

easybuild/easyconfigs/e/expat/expat-2.2.0-foss-2016b.eb

@@ -0,0 +1,16 @@
+easyblock = 'ConfigureMake'
+
+name = 'expat'
+version = '2.2.0'
+
+homepage = 'http://expat.sourceforge.net/'
+description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application
+ registers handlers for things the parser might find in the XML document (like start tags)"""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+toolchainopts = {'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = [SOURCEFORGE_SOURCE]
+
+moduleclass = 'tools'

easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb

@@ -0,0 +1,16 @@
+name = 'flex'
+version = '2.6.0'
+
+homepage = 'http://flex.sourceforge.net/'
+description = """Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, 
+ sometimes called a tokenizer, is a program which recognizes lexical patterns in text."""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+toolchainopts = {'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s']
+
+dependencies = [('Bison', '3.0.4')]
+
+moduleclass = 'lang'

easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-foss-2016b.eb

@@ -0,0 +1,30 @@
+easyblock = 'ConfigureMake'
+
+name = 'GDAL'
+version = '2.1.0'
+
+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': 'foss', 'version': '2016b'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+
+dependencies = [
+    ('netCDF', '4.4.1'),
+    ('expat', '2.2.0'),
+    ('libxml2', '2.9.4'),
+    ('zlib', '1.2.8'),
+]
+
+sanity_check_paths = {
+    'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'],
+    'dirs': ['bin', 'include']
+}
+
+moduleclass = 'data'

easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb

@@ -0,0 +1,25 @@
+name = 'HDF5'
+version = '1.8.17'
+
+homepage = 'http://www.hdfgroup.org/HDF5/'
+description = """HDF5 is a unique technology suite that makes possible the management of
+ extremely large and complex data collections."""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+
+patches = [
+    'configure_libtool.patch',
+]
+
+buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"'
+
+dependencies = [
+    ('zlib', '1.2.8'),
+    ('Szip', '2.1'),
+]
+
+moduleclass = 'data'

easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016b.eb

@@ -0,0 +1,34 @@
+name = 'netCDF'
+version = '4.4.1'
+
+homepage = 'http://www.unidata.ucar.edu/software/netcdf/'
+description = """NetCDF (network Common Data Form) is a set of software libraries 
+ and machine-independent data formats that support the creation, access, and sharing of array-oriented 
+ scientific data."""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = [
+    'https://github.com/Unidata/netcdf-c/archive/'
+]
+
+dependencies = [
+    ('HDF5', '1.8.17'),
+    ('cURL', '7.49.1'),
+    ('Szip', '2.1'),
+]
+
+builddependencies = [
+    ('CMake', '3.5.2'),
+    ('Doxygen', '1.8.11'),
+]
+
+# make sure both static and shared libs are built
+configopts = [
+    "-DBUILD_SHARED_LIBS=OFF ",
+    "-DBUILD_SHARED_LIBS=ON ",
+]
+
+moduleclass = 'data'

easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2016b.eb

@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'Szip'
+version = '2.1'
+
+homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/'
+description = "Szip compression software, providing lossless compression of scientific data"
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+toolchainopts = {'pic': True}
+
+source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src']
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = "--with-pic"
+
+sanity_check_paths = {
+    'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] +
+             ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]],
+    'dirs': [],
+}
+
+moduleclass = 'tools'