Merge branch 'master' of git.psi.ch:Pmodules/buildblocks

Compiler/boost/build

@@ -1,8 +1,5 @@
 #!/usr/bin/env modbuild
 
-# :TODO: detect compiler
-TOOLSET=intel-linux
-
 BOOST_BUILD_PATH="${MODULE_BUILDDIR}"
 
 pbuild::configure() {
@@ -11,7 +8,6 @@ pbuild::configure() {
 		--prefix="${PREFIX}" \
 		--with-libraries=all \
 		--with-python-root="${PYTHON_PREFIX}" \
-		-with-toolset=${TOOLSET} \
 		|| exit 1
 }
 
@@ -23,7 +19,7 @@ pbuild::build() {
 		--layout=system \
 		--without-mpi \
 		variant=release \
-		link=static \
+		link=shared \
 		threading=multi \
 		stage
 }
@@ -36,7 +32,7 @@ pbuild::install() {
 		--layout=system \
 		--without-mpi \
 		variant=release \
-		link=static \
+		link=shared \
 		threading=multi \
 		install
 }

Compiler/roger/build

@@ -0,0 +1,19 @@
+#!/usr/bin/env modbuild
+
+pbuild::pre_configure() {
+	./autogen.sh
+}
+
+pbuild::configure() {
+	"${MODULE_SRCDIR}"/configure \
+		--prefix="${PREFIX}"
+}
+
+declare JOBS=1
+pbuild::compile_in_sourcetree
+
+pbuild::add_to_group 'Compiler'
+pbuild::set_runtime_dependencies "${COMPILER}" 'hdf5_serial' 'root'
+pbuild::set_build_dependencies 'autoconf' 'automake' 'libtool' "${COMPILER}" 'hdf5_serial' 'H5hut_serial' 'gsl' 'root' 'boost'
+pbuild::make_all
+

Compiler/roger/modulefile

@@ -0,0 +1,10 @@
+#%Module1.0
+
+set whatis	"visualization tool for H5hut files"
+set url		"http://amas.psi.ch/"
+set license	"PSI"
+set maintainer	"Achim Gsell <achim.gsell@psi.ch>"
+set help	"
+"
+
+source		$env(PSI_LIBMODULES)

Compiler/roger/with_modules

@@ -0,0 +1,6 @@
+gcc/4.8.3
+hdf5_serial/1.8.12
+H5hut_serial/1.99.13
+gsl/1.15
+root/5.34.34
+boost/1.60.0

Compiler/root/build

@@ -5,6 +5,22 @@ module use Libraries
 INSTANTCLIENT_INCLUDE_DIR='/usr/include/oracle/12.1/client64'
 INSTANTCLIENT_LIBRARY_DIR='/usr/lib/oracle/12.1/client64/lib'
 
+declare -a EXTRA_LIBS=()
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libclntshcore.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libclntshcore.so.12.1" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libclntsh.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libclntsh.so.12.1" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libipc1.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libmql1.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libnnz12.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libocci.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libocci.so.12.1" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libociei.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libocijdbc12.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/libons.so" )
+EXTRA_LIBS+=( "${INSTANTCLIENT_LIBRARY_DIR}/liboramysql12.so" )
+
+
 case ${OS} in
 Darwin )
 	# cocoa doesn't work with GCC!?
@@ -22,12 +38,12 @@ esac
 #
 pbuild::configure() {
 	"${MODULE_SRCDIR}"/configure \
-		--disable-asimage \
+		--enable-asimage \
+		--enable-mathmore \
 		--disable-ldap \
 		--disable-mysql \
 		--disable-opengl \
 		--disable-python \
-		--enable-mathmore \
 		--with-cc=${CC} \
 		--with-cxx=${CXX} \
 		--with-f77=${F77} \
@@ -45,6 +61,17 @@ pbuild::build() {
 pbuild::install() {
 	make clean
 
+	mkdir -p "${PREFIX}"
+	cp -rv * "${PREFIX}"
+	mkdir -p "${DOCDIR}"
+	rsync --archive --verbose	 "${PREFIX}/LICENSE"	"${DOCDIR}/LICENSE"
+	rsync --archive --verbose	 "${PREFIX}/man/"	"${PREFIX}/share/man/"
+	rsync --archive --verbose	 "${PREFIX}/README/"	"${DOCDIR}/README/" 
+
+	rm -rf	 "${PREFIX}/LICENSE"
+	rm -rf	 "${PREFIX}/man/"
+	rm -rf	 "${PREFIX}/README"
+
 	rm -f  Makefile
 	rm -rf config.*
 	rm -rf core
@@ -66,20 +93,12 @@ pbuild::install() {
 	rm -rf tmva
 	rm -rf tutorials
 	rm -rf rootx
-
-	mkdir -p share
-	mv man share
-
-	mkdir -p "${PREFIX}"
-	cp -rv * "${PREFIX}"
-	mkdir -p "${DOCDIR}"
-	mv -f "${PREFIX}/LICENSE" "${DOCDIR}"
-	rm -f "${DOCDIR}/README"
-	mv -f "${PREFIX}/README"  "${DOCDIR}"
 }
 
-pbuild::postinstall() {
-	cp -av "${INSTANTCLIENT_LIBRARY_DIR}/"libocci.so* "${PREFIX}"/lib
+pbuild::post_install() {
+	for lib in "${EXTRA_LIBS[@]}"; do
+		cp -av "${lib}" "${PREFIX}"/lib
+	done
 }
 
 module use unstable

Compiler/root/modulefile

@@ -1,16 +1,12 @@
 #%Module1.0
 
-set whatis	"CERN root"
-set url		"http://root.cern.ch/"
-set license	"GNU LGPL v2"
-set maintainer	"Achim Gsell <achim.gsell@psi.ch>"
-set help	"
+module-whatis		"CERN root"
+module-url		"http://root.cern.ch/"
+module-license		"GNU LGPL v2"
+module-maintainer	"Achim Gsell <achim.gsell@psi.ch>"
+module-help	"
 ROOT is an object-oriented framework aimed at solving the data analysis
-challenges of high-energy physics. There are two key words in this
-definition, object oriented and framework. First, we explain what we
-mean by a framework and then why it is an object-oriented framework.
+challenges of high-energy physics.
 "
 
-source		$env(PSI_LIBMODULES)
-
 setenv	ROOTSYS	$PREFIX	

Compiler/root/with_modules

@@ -0,0 +1,2 @@
+gsl/1.15
+Python/3.4.3

Libraries/tiff/build

@@ -3,6 +3,9 @@
 pbuild::configure() {
 	"${MODULE_SRCDIR}"/configure \
 		--prefix="${PREFIX}" \
+		--with-pic=yes \
+		--disable-shared \
+		--disable-jpeg \
 		|| exit 1
 }
 

Libraries/tiff/modulefile

@@ -1,15 +1,13 @@
 #%Module1.0
 
-set whatis	"set of C functions that support the manipulation of TIFF image files."
-set url		"http://www.libtiff.org/"
-set license	"BSD-like, see: http://libtiff.org/misc.html"
-set maintainer	"Achim Gsell <achim.gsell@psi.ch>"
+module-whatis		"set of C functions that support the manipulation of TIFF image files."
+module-url		"http://www.remotesensing.org/libtiff/"
+module-license		"BSD-like, see: http://libtiff.org/misc.html"
+module-maintainer	"Achim Gsell <achim.gsell@psi.ch>"
 
-set help	"
+module-help	"
 This software provides support for the Tag Image File Format (TIFF), a
 widely used format for storing image data. The latest version of the TIFF
 specification is available on-line in several different formats, as are a
 number of Technical Notes (TTN's).
 "
- 
-source		$env(PSI_LIBMODULES)

MPI/cpmd/LINUX-X86_64-PMODULE

@@ -0,0 +1,30 @@
+#INFO#
+#INFO# Configuration to build a 64-bit parallel CPMD executable for
+#INFO# Fedora Linux (version 6 and up). Required packages:
+#INFO# gcc-mpif90, atlas-devel, fftw2-devel, openmpi-devel
+#INFO# 
+#INFO#
+
+     IRAT=2
+     FC='mpif90'
+     CC='mpicc'
+     LD='mpif90'
+     CPP=''
+     CPPFLAGS='-D__Linux -D__GNU  -D__PARALLEL -D__HAS_FFT_DEFAULT -D__x86_64'
+     FFLAGS_GROMOS='-ffixed-form $(FFLAGS)' 
+     FFLAGS_GROMOS_MODULES=' $(FFLAGS)' 
+     if [ $debug ]; then
+       FFLAGS='-g -O0'
+       CFLAGS='-g -O0'
+     else
+       FFLAGS='-O2'
+       CFLAGS='-O2 -Wall'
+     fi
+     if [ $omp ]; then
+       FFLAGS=${FFLAGS}' -fopenmp'
+       OMP3_DISABLED=`{ ${FC} -v; } 2>&1 | ${GREP} version | ${AWK} '{ print ( $3 < "4.7.0" ) ? "true" : "false" }'`
+       LIBS='-L/usr/lib64/atlas/ -llapack -lblas'
+     else
+       LIBS='-L/usr/lib64/atlas/ -llapack -lblas'
+     fi
+     LFLAGS=' '${LIBS}

MPI/cpmd/build

@@ -4,7 +4,7 @@
 
 case $OS in 
 	Linux )
-		target='LINUX-X86_64-FEDORA-MPI-FFTW'
+		target='LINUX-X86_64-PMODULE'
 		;;
 	Darwin )
 		target='MACOSX-GFORTRAN-INTEL-MPI'
@@ -12,6 +12,7 @@ case $OS in
 esac
 
 pbuild::configure() {
+	cp -v "${BUILD_BLOCK_DIR}/${target}" "${MODULE_BUILDDIR}/configure"
 	./configure.sh "${target}" || exit 1
 }
 

MPI/hdf5/build

@@ -15,6 +15,7 @@ pbuild::configure() {
 		--enable-cxx \
 		--enable-fortran \
 		--enable-unsupported \
+		--enable-threadsafe \
 		--with-pic \
 		|| exit 1
 }

MX/phenix/build

@@ -0,0 +1,20 @@
+#!/usr/bin/env modbuild
+
+pbuild::configure() {
+	:
+}
+
+pbuild::build() {
+	:
+}
+
+pbuild::install() {
+	cd "${MODULE_SRCDIR}"
+	./install --prefix="${PREFIX%/*}"
+}
+
+
+pbuild::add_to_group 'MX'
+pbuild::set_build_dependencies ''
+pbuild::make_all
+

MX/phenix/modulefile

@@ -0,0 +1,12 @@
+#%Module1.0
+
+module-whatis	        "Python-based Hierarchical ENvironment for Integrated Xtallography"
+module-url		"http://www.phenix-online.org/"
+module-license	        "NON-COMMERCIAL END USER SOURCE  CODE  LICENSE"
+module-maintainer	"Dmitry Ozerov <dmitry.ozerov@psi.ch>"
+
+module-help	"
+PHENIX is a software suite for the automated determination of molecular structures using X-ray crystallography and other methods.
+Citing PHENIX:
+PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010).
+"

Tools/emacs/build

@@ -2,12 +2,11 @@
 
 module use 'Libraries'
 
-build_dependencies="${COMPILER} libungif tiff"
+build_dependencies="libungif tiff"
 
 case ${OS} in
 Darwin )
-	configure_args='--with-ns'
-	build_dependencies="libungif tiff"
+	configure_args='--with-ns --with-jpeg=no'
 	CC=''
 	CXX=''
 	COMPILER=''

Tools/emacs/with_modules

@@ -0,0 +1,2 @@
+libungif/4.1.4
+tiff/4.0.6