new file: a/Automake/Automake-1.16.1.eb

new file:   a/Autotools/Autotools-20180311.eb
	modified:   h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.27.eb
	new file:   h/hwloc/hwloc-1.11.7-PGI-18.5-GCC-6.3.0-2.27.eb
	new file:   j/JAVA/JAVA-1.9.0+181-PGI-18.5-GCC-6.3.0-2.27.eb
	new file:   j/JAVA/Java-1.8.0_121.eb
	new file:   j/JAVA/Java-1.8.0_144.eb
	new file:   j/JAVA/Java-1.8.0_51.eb
	new file:   j/JAVA/Java-1.9.0+181.eb
	modified:   n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb
	new file:   n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb
	new file:   o/OpenMPI/OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.eb
	new file:   o/OpenMPI/OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.env
	deleted:    j/Java/Java-1.8.0_121.eb
	deleted:    j/Java/Java-1.8.0_144.eb
	deleted:    j/Java/Java-1.8.0_51.eb
	deleted:    j/Java/Java-1.9.0+181.eb


Former-commit-id: c541dab187356751c629fbe56f806eac437a361b

a/Automake/Automake-1.16.1.eb

@@ -0,0 +1,27 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'Automake'
+version = "1.16.1"
+
+homepage = 'http://www.gnu.org/software/automake/automake.html'
+
+description = "Automake: GNU Standards-compliant Makefile generator"
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['https://mirror.checkdomain.de/gnu/automake/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8']
+
+dependencies = [
+    ('Autoconf', '2.69'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/automake', 'bin/aclocal'],
+    'dirs': []
+}
+
+moduleclass = 'devel'

a/Autotools/Autotools-20180311.eb

@@ -0,0 +1,26 @@
+# IT4Innovations 2018
+
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20180311'  # date of the most recent change
+
+homepage = 'http://autotools.io'
+
+description = """
+ This bundle collect the standard GNU build tools: Autoconf, Automake
+ and libtool
+"""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+dependencies = [
+    ('Autoconf', '2.69'),    # 20120424
+    ('Automake', '1.16.1'),  # 20180311
+    ('libtool', '2.4.6'),    # 20150215
+]
+
+# Pure bundle -- no need to specify 'binutils' used when building GCCcore
+# toolchain as build dependency
+
+moduleclass = 'devel'

h/hwloc/hwloc-1.11.7-GCC-6.3.0-2.27.eb

@@ -1,23 +1,27 @@
-easyblock = 'ConfigureMake' 
- 
-name = 'hwloc' 
-version = '1.11.7' 
- 
-homepage = 'http://www.open-mpi.org/projects/hwloc/' 
-description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction 
-(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including 
-NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various 
-system attributes such as cache and memory information as well as the locality of I/O devices such as 
-network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering 
-information about modern computing hardware so as to exploit it accordingly and efficiently.""" 
- 
-toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} 
- 
-source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] 
-sources = [SOURCE_TAR_GZ] 
- 
-dependencies = [('numactl', '2.0.11')] 
- 
-configopts = "--enable-libnuma=$EBROOTNUMACTL" 
- 
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'hwloc'
+version = '1.11.7'
+
+homepage = 'http://www.open-mpi.org/projects/hwloc/'
+description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction
+(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including
+NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various
+system attributes such as cache and memory information as well as the locality of I/O devices such as
+network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering
+information about modern computing hardware so as to exploit it accordingly and efficiently."""
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/']
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+   ('numactl', '2.0.11', '', ('GCCcore', '6.3.0')),
+]
+
+configopts = "--enable-libnuma=$EBROOTNUMACTL"
+
 moduleclass = 'system'

h/hwloc/hwloc-1.11.7-PGI-18.5-GCC-6.3.0-2.27.eb

@@ -0,0 +1,28 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'hwloc'
+version = '1.11.7'
+
+homepage = 'http://www.open-mpi.org/projects/hwloc/'
+description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction
+(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including
+NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various
+system attributes such as cache and memory information as well as the locality of I/O devices such as
+network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering
+information about modern computing hardware so as to exploit it accordingly and efficiently."""
+
+toolchain = {'name': 'PGI', 'version': '18.5-GCC-6.3.0-2.27'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://download.open-mpi.org/release/hwloc/v1.11/']
+sources = ['hwloc-1.11.7.tar.gz']
+
+dependencies = [
+   ('numactl', '2.0.11', '', ('GCCcore', '6.3.0'))
+]
+
+configopts = "--enable-libnuma=$EBROOTNUMACTL"
+
+moduleclass = 'system'

j/JAVA/JAVA-1.9.0+181-PGI-18.5-GCC-6.3.0-2.27.eb

@@ -0,0 +1,13 @@
+name = 'JAVA'
+version = "1.9.0+181"
+
+homepage = 'http://java.com/'
+description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy
+ Java applications on desktops and servers."""
+
+toolchain = {'name': 'PGI', 'version': '18.5-GCC-6.3.0-2.27'}
+
+# download the tar.gz directly from http://www.oracle.com/technetwork/java/javase/downloads/index.html
+sources = ['jdk-9_linux-x64_bin.tar.gz']
+
+moduleclass = 'lang'

n/numactl/numactl-2.0.11-GCC-6.3.0-2.27.eb

@@ -1,23 +1,27 @@
-easyblock = 'ConfigureMake' 
- 
-name = 'numactl' 
-version = '2.0.11' 
- 
-homepage = 'http://oss.sgi.com/projects/libnuma/' 
-description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. 
-It does this by supplying a NUMA memory policy to the operating system before running your program. 
-The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" 
- 
-toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'numactl'
+version = '2.0.11'
+
+homepage = 'http://oss.sgi.com/projects/libnuma/'
+description = """The numactl program allows you to run your application program on specific cpu's and memory nodes.
+It does this by supplying a NUMA memory policy to the operating system before running your program.
+The libnuma library provides convenient ways for you to add NUMA memory policies into your own program."""
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/numactl/numactl/archive/']
+sources = [SOURCE_TAR_GZ]
+checksums = ['3e099a59b2c527bcdbddd34e1952ca87462d2cef4c93da9b0bc03f02903f7089']
+
+preconfigopts = "./autogen.sh && "
+
+sanity_check_paths = {
+    'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'],
+    'dirs': ['share/man', 'include']
+}
 
-source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] 
-sources = [SOURCE_TAR_GZ] 
- 
-checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] 
- 
-sanity_check_paths = { 
-    'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], 
-    'dirs': ['share/man', 'include'] 
-} 
- 
 moduleclass = 'tools'

n/numactl/numactl-2.0.11-GCCcore-6.3.0.eb

@@ -0,0 +1,32 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'numactl'
+version = '2.0.11'
+
+homepage = 'http://oss.sgi.com/projects/libnuma/'
+description = """The numactl program allows you to run your application program on specific cpu's and memory nodes.
+It does this by supplying a NUMA memory policy to the operating system before running your program.
+The libnuma library provides convenient ways for you to add NUMA memory policies into your own program."""
+
+toolchain = {'name': 'GCCcore', 'version': '6.3.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/numactl/numactl/archive/']
+sources = ['v2.0.12.tar.gz']
+checksums = ['a4d2292af28fb20007ddb9706f8bb1cc']
+
+builddependencies = [
+    ('binutils', '2.27'),
+    ('Autotools', '20180311', '', True),
+]
+
+preconfigopts = "./autogen.sh && "
+
+sanity_check_paths = {
+    'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'],
+    'dirs': ['share/man', 'include']
+}
+
+moduleclass = 'tools'

o/OpenMPI/OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.eb

@@ -0,0 +1,51 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'OpenMPI'
+version = '1.10.7'
+
+homepage = 'http://www.open-mpi.org/'
+description = """The Open MPI Project is an open source MPI-2 implementation."""
+
+toolchain = {'name': 'PGI', 'version': '18.5-GCC-6.3.0-2.27'}
+toolchainopts = {'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads']
+
+dependencies = [('hwloc', '1.11.7')]
+
+configopts = '--with-threads=posix --enable-shared --enable-static --enable-mpi-thread-multiple --with-verbs '
+configopts += '--enable-mpirun-prefix-by-default '  # suppress failure modes in relation to mpirun path
+configopts += '--with-hwloc=$EBROOTHWLOC '  # hwloc support
+configopts += '--disable-dlopen '  # statically link component, don't do dynamic loading
+configopts += '--with-tm=/opt/pbs/default '  # Enable PBS
+configopts += '--with-cxxrtlib="-lgcc_s -lstdc++"' # for vt-mpi-unify
+
+# for PBS Pro 13
+preconfigopts = 'export LIBS="-ldl" && '
+
+# needed for --with-verbs
+osdependencies = [('libibverbs-dev', 'libibverbs-devel')]
+
+libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] +
+             ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] +
+             ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]],
+    'dirs': ["include/openmpi/ompi/mpi/cxx"],
+}
+
+sanity_check_commands = [
+   ('mpicc --version | grep pgcc', ''),
+   ('mpicxx --version | grep pgc++', ''),
+   ('mpifort --version | grep pgfortran', ''),
+]
+
+modextravars = {'OMPI_MCA_btl_openib_if_include': 'mlx4_0',
+                'OMPI_MCA_oob_tcp_if_include': '10.0.0.0/8',
+}
+
+moduleclass = 'mpi'

o/OpenMPI/OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.env

@@ -0,0 +1,19 @@
+#!/bin/bash
+# script to set up build environment as defined by EasyBuild v3.6.2 for OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.eb
+# usage: source OpenMPI-1.10.7-PGI-18.5-GCC-6.3.0-2.27.env
+
+# toolchain & dependency modules
+module load PGI/18.5-GCC-6.3.0-2.27
+module load hwloc/1.11.7-PGI-18.5-GCC-6.3.0-2.27
+module load Java/1.9.0+181
+
+# build environment
+export CC='pgcc'
+export CPPFLAGS='-I/apps/all/hwloc/1.11.7-PGI-18.5-GCC-6.3.0-2.27/include -I/apps/all/Java/1.9.0+181/include'
+export CXX='pgc++'
+export F77='pgf77'
+export F90='pgfortran'
+export FC='pgfortran'
+export LDFLAGS='-L/apps/all/hwloc/1.11.7-PGI-18.5-GCC-6.3.0-2.27/lib -L/apps/all/Java/1.9.0+181/lib'
+export OPTFLAGS='-O3'
+export LIBS="-ldl"