[gentoo-commits] proj/sci:master commit in: sci-physics/abinit/

[Honza Macháček]

commit:     4f1c3ab6bcdefdade71186214b625663eada8a77
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Fri Jun 27 13:53:49 2014 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Fri Jun 27 13:53:49 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4f1c3ab6

Version bumped to 7.6.4. ScaLAPACK support, and use of the MPI implementation of sci-libs/fftw added. Minor attempts on enhancements and cleanup.

Package-Manager: portage-2.2.10

---
 sci-physics/abinit/ChangeLog           |   9 +-
 sci-physics/abinit/abinit-7.6.4.ebuild | 388 +++++++++++++++++++++++++++++++++
 sci-physics/abinit/metadata.xml        |  23 +-
 3 files changed, 415 insertions(+), 5 deletions(-)

diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog
index 6baa378..11dd22a 100644
--- a/sci-physics/abinit/ChangeLog
+++ b/sci-physics/abinit/ChangeLog
@@ -1,7 +1,14 @@
 # ChangeLog for sci-physics/abinit
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*abinit-7.6.4 (27 Jun 2014)
+
+  27 Jun 2014; Honza Macháček <Hloupy.Honza@×××××××.cz> +abinit-7.6.4.ebuild,
+  metadata.xml:
+  Version bumped to 7.6.4. ScaLAPACK support, and use of the MPI implementation
+  of sci-libs/fftw added. Minor attempts on enhancements and cleanup.
+
   10 Oct 2013; Honza Macháček <Hloupy.Honza@×××××××.cz> abinit-7.4.2.ebuild,
   +files/7.4.2-cuda_link_stdc++.patch:
   Added a patch to link libstdc++ with the C++ CUDA objects.

diff --git a/sci-physics/abinit/abinit-7.6.4.ebuild b/sci-physics/abinit/abinit-7.6.4.ebuild
new file mode 100644
index 0000000..6947f11
--- /dev/null
+++ b/sci-physics/abinit/abinit-7.6.4.ebuild
@@ -0,0 +1,388 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_5,2_6,2_7} )
+
+inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs
+
+DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory"
+HOMEPAGE="http://www.abinit.org/"
+SRC_URI="http://ftp.abinit.org/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw fftw-mpi +fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp python scalapack scripts -test +threads wannier"
+
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+#"			scalapack? ( !bigdft )"
+
+RDEPEND="virtual/blas
+	virtual/lapack
+	${PYTHON_DEPS}
+	dev-python/numpy
+	atompaw? ( >=sci-physics/atompaw-3.0.1.9-r1[libxc?] )
+	bigdft? ( ~sci-libs/bigdft-abi-1.0.4[scalapack?] )
+	cuda? ( dev-util/nvidia-cuda-sdk )
+	etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 )
+	fftw? (
+		sci-libs/fftw:3.0
+		fftw-threads? (
+			openmp? ( sci-libs/fftw:3.0[openmp] )
+			!openmp? ( sci-libs/fftw:3.0[threads] )
+			)
+		fftw-mpi? (
+			sci-libs/fftw:3.0[mpi]
+			openmp? ( sci-libs/fftw:3.0[openmp] )
+			!openmp? ( sci-libs/fftw:3.0[threads] )
+			)
+		)
+	fox? ( >=sci-libs/fox-4.1.2-r2[sax] )
+	gsl? ( sci-libs/gsl )
+	hdf5? ( sci-libs/hdf5[fortran] )
+	levmar? ( sci-libs/levmar )
+	libxc? ( =sci-libs/libxc-2.0*[fortran] )
+	netcdf? (
+		sci-libs/netcdf[hdf5?]
+		|| (
+			sci-libs/netcdf[fortran]
+			sci-libs/netcdf-fortran
+			)
+		)
+	mpi? ( virtual/mpi )
+	scalapack? ( virtual/scalapack )
+	scripts? ( dev-python/PyQt4 )
+	wannier? ( >=sci-libs/wannier90-1.2-r1 )"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	dev-perl/Text-Markdown"
+
+S=${WORKDIR}/${P%[a-z]}
+
+DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING
+	README README.ChangeLog README.GPU README.xlf RELNOTES THANKS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+	# Doesn't compile with gcc-4.0, only >=4.1
+	if [[ $(tc-getFC) == *gfortran ]]; then
+		if [[ $(gcc-major-version) -eq 4 ]] \
+			&& [[ $(gcc-minor-version) -lt 1  ]]; then
+				die "Requires gcc-4.1 or newer"
+		fi
+	fi
+
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export F77="mpif77"
+		export CC="mpicc"
+		export CXX="mpic++"
+	else
+		tc-export FC F77 CC CXX
+	fi
+
+	# Preprocesor macross can make some lines really long
+	append-fflags -ffree-line-length-none
+
+	# This should be correct:
+	#   It is gcc-centric because toolchain-funcs.eclass is gcc-centric.
+	#   Should a bug be filed against toolchain-funcs.eclass?
+	# if use openmp; then
+	#         tc-has-openmp || \
+	#                 die "Please select an openmp capable compiler like gcc[openmp]"
+	# fi
+	#
+	# This is completely wrong:
+	#   If other compilers than Gnu Compiler Collection can be used by portage,
+	#   their support of OpenMP should be properly tested. This code limits the test
+	#   to gcc, and blindly supposes that other compilers do support OpenMP.
+	# if use openmp && [[ $(tc-getCC)$ == *gcc* ]] &&	! tc-has-openmp; then
+	# 	die "Please select an openmp capable compiler like gcc[openmp]"
+	# fi
+	#
+	# Luckily Abinit is a fortran package.
+	#   fortran-2.eclass has its own test for OpenMP support,
+	#   more general than toolchain-funcs.eclass
+	#   The test itself proceeds inside fortran-2_pkg_setup
+	if use openmp; then FORTRAN_NEED_OPENMP=1; fi
+
+	fortran-2_pkg_setup
+
+	if use openmp; then
+		# based on _fortran-has-openmp() of fortran-2.eclass
+		local code=ebuild-openmp-flags
+		local ret
+		local openmp
+
+		pushd "${T}"
+		cat <<- EOF > "${code}.c"
+		# include <omp.h>
+		main () {
+			int nthreads;
+			nthreads=omp_get_num_threads();
+		}
+		EOF
+
+		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+			${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log
+			ret=$?
+			(( ${ret} )) || break
+		done
+
+		rm -f "${code}.*"
+		popd
+
+		if (( ${ret} )); then
+			die "Please switch to an openmp compatible C compiler"
+		else
+			export CC="${CC} ${openmp}"
+			export CXX="${CXX} ${openmp}"
+		fi
+
+		pushd "${T}"
+		cat <<- EOF > "${code}.f"
+		1     call omp_get_num_threads
+		2     end
+		EOF
+
+		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+			${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log
+			ret=$?
+			(( ${ret} )) || break
+		done
+
+		rm -f "${code}.*"
+		popd
+
+		if (( ${ret} )); then
+			die "Please switch to an openmp compatible fortran compiler."
+		else
+			export FC="${FC} ${openmp}"
+			export F77="${F77} ${openmp}"
+		fi
+	fi
+
+	# Sort out some USE options
+	if use fftw-threads && ! use fftw; then
+		ewarn "fftw-threads set but fftw not used, ignored."
+	fi
+	if use fftw-mpi; then
+		if ! use fftw; then
+			ewarn "fftw-mpi set but fftw not used, ignored."
+		elif ! use mpi; then
+			ewarn "fftw-mpi set but mpi not used, ignored."
+		elif ! use fftw-threads; then
+			ewarn "fftw-mpi set but fftw-threads not. Will use a threaded fftw nevertheless, required with MPI."
+		fi
+	fi
+	if use cuda-double && ! use cuda; then
+		ewarn "cuda-double set but cuda not used, ignored"
+	fi
+
+	python-single-r1_pkg_setup
+
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/6.2.2-change-default-directories.patch \
+		"${FILESDIR}"/6.12.1-autoconf.patch \
+		"${FILESDIR}"/6.12.1-xmalloc.patch \
+		"${FILESDIR}"/7.6.3-libabinit_options.patch \
+		"${FILESDIR}"/7.4.2-levmar_diag_scaling.patch \
+		"${FILESDIR}"/7.4.2-syntax.patch \
+		"${FILESDIR}"/7.4.2-cuda_link_stdc++.patch
+	eautoreconf
+	sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure
+	python_fix_shebang "${S}"
+}
+
+src_configure() {
+	local modules="$(FoX-config --sax --fcflags)"
+	local FoX_libs="$(FoX-config --sax --libs)"
+
+	local trio_flavor=""
+	use etsf_io && trio_flavor="${trio_flavor}+etsf_io"
+	use fox && trio_flavor="${trio_flavor}+fox"
+	use netcdf && trio_flavor="${trio_flavor}+netcdf"
+	test "no${trio_flavor}" = "no" && trio_flavor="none"
+
+	local netcdff_libs="-lnetcdff"
+	use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran"
+
+#	local linalg_flavor="atlas"
+	local linalg_flavor="custom"
+	local mylapack="lapack"
+	use scalapack && mylapack="scalapack" && linalg_flavor="${linalg_flavor}+scalapack"
+
+	local dft_flavor=""
+	use atompaw && dft_flavor="${dft_flavor}+atompaw"
+	use bigdft && dft_flavor="${dft_flavor}+bigdft"
+	use libxc && dft_flavor="${dft_flavor}+libxc"
+	use wannier && dft_flavor="${dft_flavor}+wannier90"
+	test "no${dft_flavor}" = "no" && dft_flavor="none"
+
+	local fft_flavor="fftw3"
+	local fft_libs=""
+	# The fftw threads support is protected by black magick.
+	# Anybody removes it, dies.
+	# New USE flag "fftw-threads" was added to control usage
+	# of the threaded fftw variant. Since fftw-3.3 has expanded
+	# the paralel options by MPI and OpenMP support, analogical
+	# USE flags should be added to select them in future;
+	# unusable with previous FFTW versions, they are postponed
+	# for now.
+	if use mpi && use fftw-mpi; then
+		fft_flavor="fftw3-mpi"
+		fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_mpi)"
+		fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_mpi)"
+		if use openmp; then
+			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)"
+			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)"
+		else
+			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)"
+			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)"
+		fi
+	elif use fftw-threads; then
+		fft_flavor="fftw3-threads"
+		if use openmp; then
+			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)"
+			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)"
+		else
+			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)"
+			fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)"
+		fi
+	else
+		fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3)"
+		fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f)"
+	fi
+
+	local gpu_flavor="none"
+	if use cuda; then
+		gpu_flavor="cuda-single"
+		if use cuda-double; then
+			gpu_flavor="cuda-double"
+		fi
+	fi
+
+	local myeconfargs=(
+		--enable-clib
+		--enable-exports
+		--enable-pkg-check
+		$(use_enable debug debug enhanced)
+		$(use_enable mpi)
+		$(use_enable mpi mpi-io)
+		$(use_enable openmp)
+		$(use_enable lotf)
+		$(use_enable cuda gpu)
+		"$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")"
+		"$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")"
+		"$(use gsl && echo "--with-math-flavor=gsl")"
+		"$(use gsl && echo "--with-math-incs=$($(tc-getPKG_CONFIG) --cflags gsl)")"
+		"$(use gsl && echo "--with-math-libs=$($(tc-getPKG_CONFIG) --libs gsl)")"
+		"$(use levmar && echo "--with-algo-flavor=levmar")"
+		"$(use levmar && echo "--with-algo-libs=-llevmar")"
+		--with-linalg-flavor="${linalg_flavor}"
+		--with-linalg-libs="$($(tc-getPKG_CONFIG) --libs "${mylapack}")"
+		--with-trio-flavor="${trio_flavor}"
+		"$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")"
+		"$(use netcdf && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
+		"$(use fox && echo "--with-fox-incs=${modules}")"
+		"$(use fox && echo "--with-fox-libs=${FoX_libs}")"
+		"$(use etsf_io && echo "--with-etsf-io-incs=${modules}")"
+		"$(use etsf_io && echo "--with-etsf-io-libs=-letsf_io -letsf_io_utils -letsf_io_low_level")"
+		--with-dft-flavor="${dft_flavor}"
+		"$(use atompaw && echo "--with-atompaw-incs=${modules}")"
+		"$(use atompaw && echo "--with-atompaw-libs=-latompaw")"
+		"$(use bigdft && echo "--with-bigdft-incs=${modules}")"
+		"$(use bigdft && echo "--with-bigdft-libs=$($(tc-getPKG_CONFIG) --libs bigdft)")"
+		"$(use libxc && echo "--with-libxc-incs=${modules}")"
+		"$(use libxc && echo "--with-libxc-libs=$($(tc-getPKG_CONFIG) --libs libxc)")"
+		"$(use wannier && echo "--with-wannier90-bins=/usr/bin")"
+		"$(use wannier && echo "--with-wannier90-incs=${modules}")"
+		"$(use wannier && echo "--with-wannier90-libs=-lwannier $($(tc-getPKG_CONFIG) --libs blas lapack)")"
+		"$(use fftw && echo "--with-fft-flavor=${fft_flavor}")"
+		"$(use fftw && echo "--with-fft-incs=-I/usr/include")"
+		"$(use fftw && echo "--with-fft-libs=${fft_libs}")"
+		--with-timer-flavor="abinit"
+		LD="$(tc-getLD)"
+		FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include"
+		)
+
+	MARKDOWN=Markdown.pl autotools-utils_src_configure
+}
+
+src_compile() {
+	autotools-utils_src_compile
+
+	# Apparently libabinit.a is not built by default
+	# Used by BigDFT. Should probably be built separately,
+	# as a package of its own: BigDFT used by Abinit.
+	# Does libabinit.a depend on BigDFT, if used?
+	# Can Abinit use external libabinit.a?
+	use libabinit && autotools-utils_src_compile libabinit.a
+
+	sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc
+}
+
+src_test() {
+	einfo "The complete tests take quite a while, easily several hours or even days."
+	# autotools-utils_src_test expanded and modified
+	_check_build_dir
+	pushd "${BUILD_DIR}" > /dev/null || die
+
+	einfo "Running the internal tests."
+	emake tests_in || die 'The internal tests failed.'
+
+	einfo "Running the thorough tests. Be patient, please."
+	"${S}"/tests/runtests.py || ewarn "The package has not passed the thorough tests."
+
+	popd > /dev/null || die
+}
+
+src_install() {
+	#autotools-utils_src_install() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	emake DESTDIR="${D}" install || die "make install failed"
+
+	use libabinit && dolib libabinit.a
+
+	if use test; then
+		for dc in results.tar.gz results.txt suite_report.html; do
+			test -e Test_suite/"${dc}" && dodoc Test_suite/"${dc}" || ewarn "Copying tests results ${dc} failed"
+		done
+	fi
+
+	popd > /dev/null
+
+	# XXX: support installing them from builddir as well!!!
+	if [[ ${DOCS} ]]; then
+		dodoc "${DOCS[@]}" || die "dodoc failed"
+	else
+		local f
+		# same list as in PMS
+		for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \
+				THANKS BUGS FAQ CREDITS CHANGELOG; do
+			if [[ -s ${f} ]]; then
+				dodoc "${f}" || die "(default) dodoc ${f} failed"
+			fi
+		done
+	fi
+	if [[ ${HTML_DOCS} ]]; then
+		dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed"
+	fi
+
+	if use scripts; then
+		insinto /usr/share/"${P}"
+		doins -r scripts
+	fi
+
+	# Remove libtool files and unnecessary static libs
+	prune_libtool_files
+}

diff --git a/sci-physics/abinit/metadata.xml b/sci-physics/abinit/metadata.xml
index 192c6f3..eb0c4e6 100644
--- a/sci-physics/abinit/metadata.xml
+++ b/sci-physics/abinit/metadata.xml
@@ -36,7 +36,12 @@ ABINIT code, different utility programs are provided.
   </use>
   <use>
     <flag name="fftw-threads">
-   Use the threaded version of <pkg>sci-libs/fftw</pkg>
+   Use the threaded (openMP or pthreads) version of <pkg>sci-libs/fftw</pkg>
+  </flag>
+  </use>
+  <use>
+    <flag name="fftw-mpi">
+   Use the MPI version of <pkg>sci-libs/fftw</pkg> (always with either openMP or pthreads too)
   </flag>
   </use>
   <use>
@@ -45,7 +50,7 @@ ABINIT code, different utility programs are provided.
   <use>
     <flag name="gui">
       Build the abinit GUI (requires java);
-      since 7.4.x a separate package
+      since 7.4.0 a separate package
     </flag>
   </use>
   <use>
@@ -67,12 +72,22 @@ ABINIT code, different utility programs are provided.
     <flag name="lotf">Activate the Learn on The Fly method (LOTF) for Molecular Dynamics</flag>
   </use>
   <use>
+    <flag name="scalapack">
+      Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing
+    </flag>
+  </use>
+  <use>
     <flag name="scripts">Install helper scripts, mostly Python</flag>
   </use>
   <use>
-    <flag name="vdwxc">Activate van der Waals exchange-correlation correction</flag>
+    <flag name="vdwxc">
+      Activate van der Waals exchange-correlation correction. Since 7.4.0
+      no longer optional
+    </flag>
   </use>
   <use>
-    <flag name="wannier">Enable support for wannier90, a maximally localized Wannier functions (MLWFs) calculator</flag>
+    <flag name="wannier">
+      Enable support for wannier90, a maximally localized Wannier functions (MLWFs) calculator
+    </flag>
   </use>
 </pkgmetadata>