[gentoo-commits] proj/sci:master commit in: sci-physics/bigdft/, sci-physics/bigdft/files/

["Honza Macháček" <Hloupy.Honza@centrum.cz>]

commit:     3b97a12c0c2fe8f6968c9cdd84b67b404e280797
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Mon Jun 17 12:51:05 2013 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Mon Jun 17 12:51:05 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3b97a12c

Version of bigdft bumped to 1.7_pre24, moved from sci-libs to sci-physics. No longer used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used upstream.

---
 sci-physics/bigdft/ChangeLog                       | 147 +++++++++++++++++++++
 sci-physics/bigdft/bigdft-1.7_pre24.ebuild         | 140 ++++++++++++++++++++
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  25 ++++
 3 files changed, 312 insertions(+)

diff --git a/sci-physics/bigdft/ChangeLog b/sci-physics/bigdft/ChangeLog
new file mode 100644
index 0000000..0c32817
--- /dev/null
+++ b/sci-physics/bigdft/ChangeLog
@@ -0,0 +1,147 @@
+# ChangeLog for sci-physics/bigdft
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bigdft-1.7_pre24 (17 Jun 2013)
+
+  17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +bigdft-1.7_pre24.ebuild, +files/bigdft-1.7-dev.24-nolib_mods.patch:
+  Version bumped to 1.7_pre24. Moved from sci-libs to sci-physics, no longer
+  used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned
+  in favour of /usr/include, as used upstream.
+
+  03 Mar 2013; Justin Lecher <jlec@gentoo.org> bigdft-1.7_pre12.ebuild:
+  Fix issue 52
+
+  03 Mar 2013; Justin Lecher <jlec@gentoo.org> bigdft-1.7_pre12.ebuild:
+  Fix issue 52
+
+  22 Feb 2013; Justin Lecher <jlec@gentoo.org> -bigdft-1.6_pre1-r4.ebuild,
+  bigdft-1.6.0-r2.ebuild, bigdft-1.7_pre12.ebuild, metadata.xml:
+  Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config;
+  drop old
+
+  20 Feb 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+  bigdft-1.7_pre12.ebuild:
+  The setup of python for the compilation of the GPU support in
+  bigdft-1.7_pre12 improved.
+
+  20 Feb 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+  bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-GPUlink.patch:
+  Compilation of GPU support in bigdft-1.7_pre12 improved. Yet to be tested.
+
+*bigdft-1.7_pre12 (17 Jan 2013)
+
+  17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-libxc_dir_include.patch,
+  +files/bigdft-1.7-dev.12-nolib_mods.patch,
+  +files/bigdft-1.7-dev.12-tests.tar.bz2:
+  New version 1.7-dev.12 (1.7_pre12) from the Abinit site added; used by
+  sci-physics/abinit-7.0.4 but apparently segfaults it.
+
+*bigdft-1.6_pre1-r4 (01 Sep 2012)
+
+  01 Sep 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -bigdft-1.6_pre1-r3.ebuild, +bigdft-1.6_pre1-r4.ebuild,
+  -files/bigdft-1.6-tuto.1-GPUlibs.patch,
+  +files/bigdft-1.6-tuto.1-GPUlibs-1.patch,
+  -files/bigdft-1.6-tuto.1-bigdft.pc.patch,
+  +files/bigdft-1.6-tuto.1-bigdft.pc-1.patch:
+  Patches to install GPU support corrected not to break linking against the
+  compiled libraries
+
+  10 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  files/bigdft-1.6-tuto.1-GPUlibs.patch:
+  bigdft-1.6-tuto.1-GPUlibs.patch updated not to forget the pkg-config file
+
+*bigdft-1.6_pre1-r3 (04 Jul 2012)
+
+  04 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -bigdft-1.6_pre1-r2.ebuild, +bigdft-1.6_pre1-r3.ebuild,
+  +files/bigdft-1.6-tuto.1-GPUlibs.patch,
+  +files/bigdft-1.6-tuto.1-gcc-4.6.patch:
+  bigdft-1.6_pre1 from -r2 to -r3: patched to install necessary libraries for
+  GPU support and to compile with gcc-4.6
+
+  22 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> bigdft-1.6.0-r2.ebuild,
+  bigdft-1.6_pre1-r2.ebuild:
+  [sci-libs/bigdft] add ~amd64-linux
+
+*bigdft-1.6.0-r2 (19 Jun 2012)
+*bigdft-1.6_pre1-r2 (19 Jun 2012)
+
+  19 Jun 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -bigdft-1.6_pre1-r1.ebuild, +bigdft-1.6_pre1-r2.ebuild,
+  -bigdft-1.6.0-r1.ebuild, +bigdft-1.6.0-r2.ebuild:
+  Reflect the split of the fortran interface out of sci-libs/netcdf
+
+  22 May 2012; Justin Lecher <jlec@gentoo.org> bigdft-1.6_pre1-r1.ebuild,
+  bigdft-1.6.0-r1.ebuild:
+  Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits
+
+*bigdft-1.6.0-r1 (15 May 2012)
+*bigdft-1.6_pre1-r1 (15 May 2012)
+
+  15 May 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -bigdft-1.6_pre1.ebuild, +bigdft-1.6_pre1-r1.ebuild, -bigdft-1.6.0.ebuild,
+  +bigdft-1.6.0-r1.ebuild:
+  pkg-config file corrected
+
+  30 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  -bigdft-1.2.0.2.ebuild, -files/bigdft-1.2.0.2-0001.patch,
+  -files/bigdft-1.2.0.2-0002.patch, -files/bigdft-1.2.0.2-0003.patch,
+  -files/bigdft-1.2.0.2-0004.patch, -files/bigdft-1.2.0.2-testH.patch,
+  -bigdft-1.2.0.5.ebuild, -files/bigdft-1.2.0.5-0001.patch,
+  -bigdft-1.6_pre0.ebuild, -files/bigdft-1.6-tuto-bigdft.pc.patch,
+  -files/bigdft-1.6-tuto-libxc_dir_include.patch:
+  Clean-up.
+
+*bigdft-1.6_pre1 (22 Mar 2012)
+*bigdft-1.6_pre0 (22 Mar 2012)
+
+  22 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild, +bigdft-1.6_pre0.ebuild,
+  +bigdft-1.6_pre1.ebuild, bigdft-1.6.0.ebuild,
+  +files/bigdft-1.6.0-libxc_dir_include.patch,
+  +files/bigdft-1.6-tuto.1-bigdft.pc.patch,
+  +files/bigdft-1.6-tuto.1-libxc_dir_include.patch,
+  +files/bigdft-1.6-tuto-bigdft.pc.patch,
+  +files/bigdft-1.6-tuto-libxc_dir_include.patch:
+  Old versions used by old versions of abinit ressurected. May be removed
+  forever if nobody complains about the latest abinit. 1.6.0 corrected,
+  1.6_pre0 and 1.6_pre1 added; 1.6_pre1 is used by sci-physics/abinit-6.12.1.
+
+*bigdft-1.6.0 (18 Feb 2012)
+
+  18 Feb 2012; Justin Lecher <jlec@gentoo.org> -bigdft-1.2.0.2.ebuild,
+  -bigdft-1.2.0.5.ebuild, +bigdft-1.6.0.ebuild, metadata.xml:
+  Move to EAPI=4 and autotools-util.eclass
+
+*bigdft-1.2.0.5 (14 Dec 2011)
+
+  14 Dec 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
+  bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild,
+  +files/bigdft-1.2.0.5-0001.patch:
+  Version bump to 1.2.0.5 for sci-physics/abinit-6.10.3; still not much
+  progress towards the current version (1.5.2 and 1.6-tuto)
+
+  11 Jul 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
+  bigdft-1.2.0.2.ebuild:
+  The MPI support, broken by fortran-2.eclass usage, made work again.
+
+  24 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild:
+  Streamlined fortran-2 eclass usage
+
+  21 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild,
+  +metadata.xml:
+  Added fortran-2.eclass support
+
+*bigdft-1.2.0.2 (17 Jan 2011)
+
+  17 Jan 2011; Honza Macháček <Hloupy.Honza@centrum.cz>
+  +bigdft-1.2.0.2.ebuild, +files/bigdft-1.2.0.2-0001.patch,
+  +files/bigdft-1.2.0.2-0002.patch, +files/bigdft-1.2.0.2-0003.patch,
+  +files/bigdft-1.2.0.2-0004.patch, +files/bigdft-1.2.0.2-testH.patch:
+  A bigDFT ebuild for sci-physics/abinit; not the latest version but the abinit
+  compatible one.
+

diff --git a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
new file mode 100644
index 0000000..d74906a
--- /dev/null
+++ b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
@@ -0,0 +1,140 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_5 python2_6 python2_7 )
+
+inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs
+
+REAL_PV="${PV/_pre/-dev.}"
+
+DESCRIPTION="A DFT electronic structure code using a wavelet basis set"
+HOMEPAGE="http://bigdft.org/"
+SRC_URI="http://launchpad.net/${PN}/master/${REAL_PV}/+download/${PN}-${REAL_PV}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux"
+IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
+
+RDEPEND="
+	>=sci-libs/libxc-1.0[fortran]
+	virtual/blas
+	virtual/fortran
+	virtual/lapack
+	dev-libs/libyaml
+	mpi? ( virtual/mpi )
+	cuda? ( dev-util/nvidia-cuda-sdk )
+	opencl? ( virtual/opencl )
+	etsf_io? ( sci-libs/etsf_io )
+	netcdf? ( || (
+				sci-libs/netcdf[fortran]
+				sci-libs/netcdf-fortran
+				)
+			)"
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	>=sys-devel/autoconf-2.59
+	doc? ( virtual/latex-base )
+	${PYTHON_DEPS}
+	dev-python/pyyaml[libyaml]
+	app-arch/tar
+	app-arch/gzip"
+
+S="${WORKDIR}/${PN}-${REAL_PV}"
+
+DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
+
+FORTRAN_STANDARD=90
+
+pkg_setup() {
+	# fortran-2.eclass does not handle mpi wrappers
+	if use mpi; then
+		export FC="mpif90"
+		export F77="mpif77"
+		export CC="mpicc"
+	else
+		tc-export FC F77 CC
+	fi
+
+	fortran-2_pkg_setup
+	if use openmp && [[ $(tc-getCC)$ == *gcc* ]] &&	! tc-has-openmp; then
+		die "Please select an openmp capable compiler like gcc[openmp]"
+	fi
+	python-any-r1_pkg_setup
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/"${PN}-${REAL_PV}"-nolib_mods.patch
+
+	eautoreconf
+}
+
+src_configure() {
+	local openmp=""
+	use openmp && openmp="-fopenmp"
+	local modules="${EPREFIX}/usr/include"
+	local netcdff_libs="-lnetcdff"
+	filter-flags '-m*' '-O*' "-pipe"
+	local nvcflags="${CFLAGS}"
+	_filter-var nvcflags '-m*' '-O*' "-pipe" "-W*"
+	local myeconfargs=(
+		$(use_enable mpi)
+		--enable-optimised-convolution
+		--enable-pseudo
+		--enable-libbigdft
+		--enable-binaries
+		--disable-minima-hopping
+		--disable-internal-libyaml
+		--enable-internal-libabinit
+		--with-moduledir="${modules}"
+		--with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l lapack) \
+			$($(tc-getPKG_CONFIG) --libs-only-l blas)"
+		--with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L lapack) \
+			$($(tc-getPKG_CONFIG) --libs-only-L blas)"
+		--with-libxc="yes"
+		--disable-internal-libxc
+		$(use_enable cuda cuda-gpu)
+		$(use_with cuda cuda-path /opt/cuda)
+		$(use_with cuda nvcc-flags "${nvcflags}")
+		$(use_enable opencl)
+		$(use_with etsf_io etsf-io)
+		"$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
+		PKG_CONFIG="$(tc-getPKG_CONFIG)"
+		FCFLAGS="${FCFLAGS} ${openmp} -I${modules}"
+		LD="$(tc-getLD)"
+		CPP="$(tc-getCPP)"
+		)
+	autotools-utils_src_configure
+}
+
+src_compile() {
+	#autotools-utils_src_compile() expanded
+	_check_build_dir
+	pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null
+	emake -j1
+	sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc
+	popd > /dev/null
+
+	#autotools-utils_src_compile
+	use doc && autotools-utils_src_compile doc
+}
+
+src_test() {
+	if use test; then
+		#autotools-utils_src_test() expanded
+		_check_build_dir
+		pushd "${BUILD_DIR}" > /dev/null || die
+		# Run default src_test as defined in ebuild.sh
+		cd tests
+		emake -j1 check
+		popd > /dev/null
+	fi
+}
+
+src_install() {
+	autotools-utils_src_install HAVE_LIBXC=1
+}

diff --git a/sci-physics/bigdft/files/bigdft-1.7-dev.24-nolib_mods.patch b/sci-physics/bigdft/files/bigdft-1.7-dev.24-nolib_mods.patch
new file mode 100644
index 0000000..de3555b
--- /dev/null
+++ b/sci-physics/bigdft/files/bigdft-1.7-dev.24-nolib_mods.patch
@@ -0,0 +1,25 @@
+diff -Naurp bigdft-1.7-dev.24.orig/src/Makefile.am bigdft-1.7-dev.24/src/Makefile.am
+--- bigdft-1.7-dev.24.orig/src/Makefile.am	2013-03-12 12:56:53.000000000 +0000
++++ bigdft-1.7-dev.24/src/Makefile.am	2013-04-10 09:29:31.073319847 +0000
+@@ -56,6 +56,9 @@ bigdft_library_rpath =
+ endif
+ if BUILD_LIB_BIGDFT
+ lib_bigdft = libbigdft.a libdft_common.a
++else
++lib_bigdft =
++endif
+ PS_SOURCES = PSolver/Build_Kernel.f90 \
+ 	PSolver/xcenergy.f90 \
+ 	PSolver/3Dgradient.f90 \
+@@ -64,11 +67,6 @@ PS_SOURCES = PSolver/Build_Kernel.f90 \
+ 	PSolver/wofz.f90 \
+ 	lib/fft/fft3d.f90
+ PS_MODULES = PSolver/Poisson_Solver.f90
+-else
+-lib_bigdft =
+-PS_SOURCES =
+-PS_MODULES =
+-endif
+ if BUILD_BINARIES
+ binaries_sources = bigdft memguess splsad NEB frequencies MDanalysis $(minima_hopping_sources) bart abscalc BigDFT2Wannier WaCo NEB_images
+ local_binaries = test_forces