Merge branch 'gromacs_gpu' into 'master'

Gromacs gpu

See merge request Pmodules/buildblocks!32

MPI/gromacs/2019/variants

@@ -0,0 +1 @@
+gromacs/2019.3_sp  stable   gcc/7.4.0 openmpi/3.1.4_merlin6 cuda/10.0.130 Python/2.7.16 b:cmake/3.14.0

MPI/gromacs/build

@@ -1,21 +1,34 @@
-#!/usr/bin/env modbuild
+#!/usr/bin/env modbuild 
 
 pbuild::set_download_url "http://ftp.gromacs.org/pub/$P/$P-${V_PKG}.tar.gz"
 
 pbuild::add_to_group 'MPI'
 
-pbuild::install_docfiles ACKNOWLEDGMENTS COPYING MANIFEST README.txt
+if (( V_MAJOR <= 2018 )); then
+  pbuild::install_docfiles ACKNOWLEDGMENTS COPYING MANIFEST README.txt
+else
+  pbuild::install_docfiles AUTHORS COPYING README
+fi
 
 pbuild::pre_configure() {
-	pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=RELEASE"
-	pbuild::add_configure_args "-DGMX_MPI=on"
-        
+  # For enabling GPU, set to 'yes'
+  local enable_gpu='yes'
+
+  echo here
+  pbuild::add_configure_args "-DCMAKE_BUILD_TYPE=RELEASE"
+  pbuild::add_configure_args "-DGMX_MPI=on"
+
   if pbuild::use_flag dp ; then
-		pbuild::add_configure_args "-DGFMX_DOUBLE=on"
+    pbuild::add_configure_args "-DGFMX_DOUBLE=on"
   else # pbuild::use_flag sp
-		pbuild::add_configure_args "-DGFMX_DOUBLE=off"
+    pbuild::add_configure_args "-DGFMX_DOUBLE=off"
   fi
+
+  if [[ "${enable_gpu}" == 'yes' ]]; then
+ 	pbuild::add_configure_args "-DGMX_GPU=on"
+  else
  	pbuild::add_configure_args "-DGMX_GPU=off"
-	# To remove: pbuild::add_configure_args "-DGMX_SIMD=SSE2"
-	pbuild::add_configure_args "-DGMX_BUILD_OWN_FFTW=on"
+  fi
+  # To remove: pbuild::add_configure_args "-DGMX_SIMD=SSE2"
+  pbuild::add_configure_args "-DGMX_BUILD_OWN_FFTW=on"
 }

Programming/Java/12.0.2/variants

@@ -0,0 +1 @@
+Java/12.0.2   stable

Programming/Java/build

@@ -0,0 +1,55 @@
+#!/usr/bin/env modbuild 
+
+pbuild::set_download_url "https://download.java.net/java/GA/jdk12.0.2/e482c34c86bd4bf8b56c0b35558996b9/10/GPL/openjdk-12.0.2_linux-x64_bin.tar.gz"
+
+pbuild::add_to_group 'Programming'
+
+pbuild::compile_in_sourcetree
+
+pbuild::install_docfiles "legal/jdk.net/LICENSE" "release"
+
+pbuild::compile() {
+  :
+}
+
+pbuild::install() {
+  install -m 0755 -d "${PREFIX}/bin"
+  for binary_file in $(ls ${SRC_DIR}/bin/*)
+  do
+    install -m 0755 "${binary_file}" "${PREFIX}/bin"
+  done
+
+  for java_dir in $(echo "lib lib/security lib/jfr lib/server")
+  do
+    mkdir -p "${PREFIX}/${java_dir}"
+    install -m 0755 -d "${PREFIX}/${java_dir}"
+    for library_file in $(find ${SRC_DIR}/${java_dir} -maxdepth 1 -type f)
+    do
+      install -m 0755 "${library_file}" "${PREFIX}/${java_dir}"
+    done
+  done
+
+  for java_dir in $(echo "conf conf/management conf/security conf/security/policy conf/security/policy/unlimited conf/security/policy/limited conf/sdp")
+  do
+    mkdir -p "${PREFIX}/${java_dir}"
+    install -m 0755 -d "${PREFIX}/${java_dir}"
+    for library_file in $(find ${SRC_DIR}/${java_dir} -maxdepth 1 -type f)
+    do
+      install -m 0755 "${library_file}" "${PREFIX}/${java_dir}"
+    done
+  done
+
+  for java_dir in $(echo "jmods")
+  do
+    mkdir -p "${PREFIX}/${java_dir}"
+    install -m 0755 -d "${PREFIX}/${java_dir}"
+    for library_file in $(find ${SRC_DIR}/${java_dir} -maxdepth 1 -type f)
+    do
+      install -m 0755 "${library_file}" "${PREFIX}/${java_dir}"
+    done
+  done
+}
+
+pbuild::cleanup_src() {
+  :
+}

Programming/Java/modulefile

@@ -0,0 +1,21 @@
+#%Module1.0
+
+module-whatis		"Java Development Kit builds, from Oracle"
+module-url		"http://jdk.java.net/"
+module-license		"See PREFIX/share/doc/COPYING"
+module-maintainer	"Marc Caubet <marc.caubet@psi.ch>"
+module-help		"
+Open Java Development Kit) is a free and open-source 
+implementation of the Java Platform, Standard Edition 
+(Java SE). It is the result of an effort Sun Microsystems 
+began in 2006. 
+
+The implementation is licensed under the GNU General 
+Public License (GNU GPL) version 2 with a linking 
+exception. Were it not for the GPL linking exception, 
+components that linked to the Java class library would be
+subject to the terms of the GPL license. 
+
+OpenJDK is the official reference implementation of Java 
+SE.
+"