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

[Honza Macháček]

commit:     fba081143ca9e86c13f5cfb561d4b6a9fd6e9d8b
Author:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
AuthorDate: Fri Sep  5 13:06:33 2014 +0000
Commit:     Honza Macháček <Hloupy.Honza <AT> centrum <DOT> cz>
CommitDate: Fri Sep  5 13:06:33 2014 +0000
URL:        http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fba08114

sci-physics/bigdft bumped to 1.7.5, after a long pause.

Package-Manager: portage-2.2.8-r1

---
 sci-physics/bigdft/ChangeLog                       |  11 ++-
 ...bigdft-1.7_pre24.ebuild => bigdft-1.7.5.ebuild} |  77 +++++++++++----
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  25 -----
 .../bigdft/files/bigdft-1.7.5-dynamic_memory.patch | 106 +++++++++++++++++++++
 .../bigdft/files/bigdft-1.7.5-pkgconfig.patch      |  10 ++
 sci-physics/bigdft/metadata.xml                    |  30 ++++++
 6 files changed, 213 insertions(+), 46 deletions(-)

diff --git a/sci-physics/bigdft/ChangeLog b/sci-physics/bigdft/ChangeLog
index 3a27413..a0d1fa4 100644
--- a/sci-physics/bigdft/ChangeLog
+++ b/sci-physics/bigdft/ChangeLog
@@ -1,7 +1,16 @@
 # ChangeLog for sci-physics/bigdft
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*bigdft-1.7.5 (05 Sep 2014)
+
+  05 Sep 2014; Honza Macháček <Hloupy.Honza@×××××××.cz>
+  -bigdft-1.7_pre24.ebuild, +bigdft-1.7.5.ebuild,
+  +files/bigdft-1.7.5-dynamic_memory.patch,
+  +files/bigdft-1.7.5-pkgconfig.patch,
+  -files/bigdft-1.7-dev.24-nolib_mods.patch, +metadata.xml:
+  Version bump, after a long pause.
+
   19 Jun 2013; Honza Macháček <Hloupy.Honza@×××××××.cz>
   bigdft-1.7_pre24.ebuild:
   Filter LDFLAGS for cuda use not to break nvcc.

diff --git a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild b/sci-physics/bigdft/bigdft-1.7.5.ebuild
similarity index 62%
rename from sci-physics/bigdft/bigdft-1.7_pre24.ebuild
rename to sci-physics/bigdft/bigdft-1.7.5.ebuild
index 2b0e95e..6782e66 100644
--- a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild
+++ b/sci-physics/bigdft/bigdft-1.7.5.ebuild
@@ -8,16 +8,15 @@ 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"
+SRC_URI="http://launchpad.net/${PN}/${PV%.*}/${PV}/+download/${P}.tar.xz"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux"
-IUSE="cuda doc etsf_io mpi netcdf openmp opencl test"
+IUSE="cuda doc etsf_io glib mpi netcdf openmp opencl scalapack test"
 
 RDEPEND="
 	>=sci-libs/libxc-1.2.0-r1[fortran]
@@ -28,12 +27,14 @@ RDEPEND="
 	mpi? ( virtual/mpi )
 	cuda? ( dev-util/nvidia-cuda-sdk )
 	opencl? ( virtual/opencl )
-	etsf_io? ( sci-libs/etsf_io )
+	glib? ( >=dev-libs/glib-2.22 )
+	etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 )
 	netcdf? ( || (
 				sci-libs/netcdf[fortran]
 				sci-libs/netcdf-fortran
 				)
-			)"
+			)
+	scalapack? ( virtual/scalapack )"
 DEPEND="${RDEPEND}
 	virtual/pkgconfig
 	>=sys-devel/autoconf-2.59
@@ -44,8 +45,6 @@ DEPEND="${RDEPEND}
 	app-arch/tar
 	app-arch/gzip"
 
-S="${WORKDIR}/${PN}-${REAL_PV}"
-
 DOCS=( README INSTALL ChangeLog AUTHORS NEWS )
 
 FORTRAN_STANDARD=90
@@ -56,47 +55,70 @@ pkg_setup() {
 		export FC="mpif90"
 		export F77="mpif77"
 		export CC="mpicc"
+		export CXX="mpic++"
 	else
-		tc-export FC F77 CC
+		tc-export FC F77 CC CXX
 	fi
 
+	use openmp && FORTRAN_NEED_OPENMP=1
+
 	fortran-2_pkg_setup
-	if use openmp && [[ $(tc-getCC)$ == *gcc* ]] &&	! tc-has-openmp; then
-		die "Please select an openmp capable compiler like gcc[openmp]"
+
+	if use openmp; then
+		# based on _fortran-has-openmp() of fortran-2.eclass
+		local openmp=""
+		local fcode=ebuild-openmp-flags.f
+		local _fc=$(tc-getFC)
+
+		pushd "${T}"
+		cat <<- EOF > "${fcode}"
+		1     call omp_get_num_threads
+		2     end
+		EOF
+
+		for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do
+			"${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break
+		done
+
+		rm -f "${fcode}.*"
+		popd
+
+		append-flags "${openmp}"
 	fi
+
 	python-any-r1_pkg_setup
 }
 
 src_prepare() {
 	epatch \
-		"${FILESDIR}"/"${PN}-${REAL_PV}"-nolib_mods.patch
+		"${FILESDIR}"/"${P}"-pkgconfig.patch \
+		"${FILESDIR}"/"${P}"-dynamic_memory.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*"
 	use cuda && filter-ldflags '-m*' '-O*' "-pipe" "-W*"
+	local mylapack="lapack"
+	use scalapack && mylapack="scalapack"
 	local myeconfargs=(
 		$(use_enable mpi)
 		--enable-optimised-convolution
 		--enable-pseudo
 		--enable-libbigdft
 		--enable-binaries
+		--disable-bindings
 		--disable-minima-hopping
 		--disable-internal-libyaml
 		--enable-internal-libabinit
 		--with-moduledir="${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-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l "${mylapack}")"
+		--with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L "${mylapack}")"
 		--with-libxc="yes"
 		--disable-internal-libxc
 		$(use_enable cuda cuda-gpu)
@@ -105,8 +127,13 @@ src_configure() {
 		$(use_enable opencl)
 		$(use_with etsf_io etsf-io)
 		"$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")"
+		$(use_with glib gobject)
+		$(use_with scalapack)
+		$(use_with scalapack scalapack-path "${EPREFIX}/usr/$(get_libdir)")
+		$(use_with scalapack blacs)
+		$(use_with scalapack blacs-path "${EPREFIX}/usr/$(get_libdir)")
 		PKG_CONFIG="$(tc-getPKG_CONFIG)"
-		FCFLAGS="${FCFLAGS} ${openmp} -I${modules}"
+		FCFLAGS="${FCFLAGS} -I${modules}"
 		LD="$(tc-getLD)"
 		CPP="$(tc-getCPP)"
 		)
@@ -122,7 +149,10 @@ src_compile() {
 	popd > /dev/null
 
 	#autotools-utils_src_compile
-	use doc && autotools-utils_src_compile doc
+	if use doc; then
+		VARTEXFONTS="${T}/fonts"
+		autotools-utils_src_compile doc
+	fi
 }
 
 src_test() {
@@ -138,5 +168,12 @@ src_test() {
 }
 
 src_install() {
-	autotools-utils_src_install HAVE_LIBXC=1
+	autotools-utils_src_install
+	if use test; then
+		_check_build_dir
+		pushd "${BUILD_DIR}" > /dev/null || die
+		insinto /usr/share/"${P}"
+		doins -r tests
+		popd > /dev/null
+	fi
 }

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
deleted file mode 100644
index de3555b..0000000
--- a/sci-physics/bigdft/files/bigdft-1.7-dev.24-nolib_mods.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-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

diff --git a/sci-physics/bigdft/files/bigdft-1.7.5-dynamic_memory.patch b/sci-physics/bigdft/files/bigdft-1.7.5-dynamic_memory.patch
new file mode 100644
index 0000000..7271223
--- /dev/null
+++ b/sci-physics/bigdft/files/bigdft-1.7.5-dynamic_memory.patch
@@ -0,0 +1,106 @@
+diff -Naurp bigdft-1.7.5_orig/src/wavelib/i-o-etsf.f90 bigdft-1.7.5/src/wavelib/i-o-etsf.f90
+--- bigdft-1.7.5_orig/src/wavelib/i-o-etsf.f90	2014-07-09 12:56:18.000000000 +0000
++++ bigdft-1.7.5/src/wavelib/i-o-etsf.f90	2014-09-04 07:05:36.256646737 +0000
+@@ -178,6 +178,7 @@ module internal_etsf
+    subroutine etsf_gcoordToLocreg(n1, n2, n3, nvctr_c, nvctr, gcoord, lr)
+       use module_defs
+       use module_types
++      use dynamic_memory
+ 
+       implicit none
+ 
+@@ -401,6 +402,7 @@ subroutine read_waves_from_list_etsf(ipr
+       &   wfd,psi,norb,nspinor,iorbparr,isorb,eval)
+    use module_base
+    use module_types
++   use dynamic_memory
+    use etsf_io_low_level
+    use etsf_io
+    use internal_etsf
+@@ -744,11 +746,18 @@ subroutine read_waves_etsf(iproc,filenam
+    character(len = *), intent(in) :: filename
+    ! Local variables
+    integer :: i
++   real(wp), dimension(:), allocatable :: eval
++
++   eval = f_malloc(size(orbs%eval),id='eval')
++   eval = orbs%eval
+ 
+    i = 0
+    call read_waves_from_list_etsf(iproc,filename,n1,n2,n3,hx,hy,hz,at,rxyz_old,rxyz, & 
+       &   wfd,psi,orbs%norbp,orbs%nspinor,(/ (i, i=1, orbs%norbp*orbs%nspinor) /), &
+-      & orbs%isorb,orbs%eval(orbs%isorb + 1))
++      & orbs%isorb,eval(orbs%isorb + 1))
++
++   orbs%eval = eval
++   call f_free(eval)
+ END SUBROUTINE read_waves_etsf
+ 
+ subroutine read_one_wave_etsf(iproc,filename,iorbp,isorb,nspinor,n1,n2,n3,&
+@@ -765,14 +774,16 @@ subroutine read_one_wave_etsf(iproc,file
+    real(gp), dimension(3,at%astruct%nat), intent(out) :: rxyz_old
+    real(wp), dimension(wfd%nvctr_c+7*wfd%nvctr_f,nspinor), intent(out) :: psi
+    character(len = *), intent(in) :: filename
++   real(wp), dimension(1) :: eval1
+ 
+    if (nspinor == 1) then
+       call read_waves_from_list_etsf(iproc,filename,n1,n2,n3,hx,hy,hz,at,rxyz_old,rxyz, & 
+-         &   wfd,psi,1,nspinor,(/ iorbp /),isorb,eval)
++         &   wfd,psi,1,nspinor,(/ iorbp /),isorb,eval1)
+    else
+       call read_waves_from_list_etsf(iproc,filename,n1,n2,n3,hx,hy,hz,at,rxyz_old,rxyz, & 
+-         &   wfd,psi,1,nspinor,(/ 2 * iorbp - 1, 2 * iorbp /),isorb,eval)
++         &   wfd,psi,1,nspinor,(/ 2 * iorbp - 1, 2 * iorbp /),isorb,eval1)
+    end if
++   eval = eval1(1)
+ END SUBROUTINE read_one_wave_etsf
+ 
+ subroutine write_psi_compress_etsf(ncid, iorbp, orbs, nvctr, wfd, psi)
+@@ -1062,7 +1073,7 @@ subroutine write_waves_etsf(iproc,filena
+       end do
+       znucl = f_malloc(at%astruct%ntypes,id='znucl')
+       znucl = real(at%nzatom)
+-      spnames = f_malloc(at%astruct%ntypes,id='spnames')
++      spnames = f_malloc_str(etsf_chemlen,at%astruct%ntypes,id='spnames')
+       do iat = 1, at%astruct%ntypes, 1
+          !call nzsymbol(at%nzatom(iat), spnames(iat))
+          call atomic_info(at%nzatom(iat),at%nelpsp(iat),symbol=spnames(iat))
+@@ -1080,7 +1091,7 @@ subroutine write_waves_etsf(iproc,filena
+       if (.not. lstat) call etsf_error(error)
+       call f_free(xred)
+       call f_free(znucl)
+-      call f_free(spnames)
++      call f_free_str(etsf_chemlen,spnames)
+       ! The eigenvalues & occupation.
+       if (dims%number_of_spins == 1) then
+          elec%eigenvalues%data1D => orbs%eval
+@@ -1138,6 +1149,8 @@ subroutine write_waves_etsf(iproc,filena
+    END SUBROUTINE etsf_write_global
+ 
+    subroutine build_grid(n1,n2,n3,nvctr, gcoord, wfd)
++      use dynamic_memory
++
+       integer, intent(in) :: n1, n2, n3
+       type(wavefunctions_descriptors), intent(in) :: wfd
+       integer, intent(out) :: nvctr(wfd%nvctr_c)
+diff -Naurp bigdft-1.7.5_orig/src/wavelib/plotting-etsf.f90 bigdft-1.7.5/src/wavelib/plotting-etsf.f90
+--- bigdft-1.7.5_orig/src/wavelib/plotting-etsf.f90	2014-06-05 14:07:35.000000000 +0000
++++ bigdft-1.7.5/src/wavelib/plotting-etsf.f90	2014-09-04 07:04:42.335813661 +0000
+@@ -141,7 +141,7 @@ subroutine write_etsf_density(filename,m
+   end do
+   znucl = f_malloc(at%astruct%ntypes,id='znucl')
+   znucl = real(at%nzatom)
+-  spnames = f_malloc(at%astruct%ntypes,id='spnames')
++  spnames = f_malloc_str(etsf_chemlen,at%astruct%ntypes,id='spnames')
+   do iat = 1, at%astruct%ntypes, 1
+      !call nzsymbol(at%nzatom(iat), spnames(iat))
+      call atomic_info(at%nzatom(iat),at%nelpsp(iat),symbol=spnames(iat))
+@@ -159,7 +159,7 @@ subroutine write_etsf_density(filename,m
+   end if
+   call f_free(xred)
+   call f_free(znucl)
+-  call f_free(spnames)
++  call f_free_str(etsf_chemlen,spnames)
+ 
+   ! We switch to write mode.
+   call etsf_io_low_set_write_mode(ncid, lstat, error_data = error)

diff --git a/sci-physics/bigdft/files/bigdft-1.7.5-pkgconfig.patch b/sci-physics/bigdft/files/bigdft-1.7.5-pkgconfig.patch
new file mode 100644
index 0000000..fdf5937
--- /dev/null
+++ b/sci-physics/bigdft/files/bigdft-1.7.5-pkgconfig.patch
@@ -0,0 +1,10 @@
+diff -Naurp bigdft-1.7.1.orig/bigdft.pc.in bigdft-1.7.1/bigdft.pc.in
+--- bigdft-1.7.1.orig/bigdft.pc.in	2013-12-11 09:31:00.000000000 +0000
++++ bigdft-1.7.1/bigdft.pc.in	2014-01-27 10:17:14.314387505 +0000
+@@ -7,5 +7,5 @@ Name: libbigdft
+ Description: Library for DFT calculation over wavelets.
+ Requires: 
+ Version: @VERSION@
+-Libs: -L${libdir} @LIBS_DEPENDENCIES@ @FCLIBS@
++Libs: -L${libdir} @LIBS_SHORT_DEPS@ @FCLIBS@
+ Cflags: -I${includedir}

diff --git a/sci-physics/bigdft/metadata.xml b/sci-physics/bigdft/metadata.xml
new file mode 100644
index 0000000..855d625
--- /dev/null
+++ b/sci-physics/bigdft/metadata.xml
@@ -0,0 +1,30 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-physics</herd>
+  <longdescription lang="en">
+BigDFT is a DFT massively parallel electronic structure code (GPL license) using a wavelet basis set. Wavelets form a real space basis set distributed on an adaptive mesh (two levels of resolution in our implementation). GTH or HGH pseudopotentials are used to remove the core electrons. Thanks to our Poisson solver based on a Green function formalism, periodic systems, surfaces and isolated systems can be simulated with the proper boundary conditions. 
+</longdescription>
+  <use>
+    <flag name="cuda">Enable support for nVidia CUDA GPU acceleration</flag>
+  </use>
+  <use>
+    <flag name="etsf_io">
+      Enable support for reading and writing the European Theoretical
+      Spectroscopy facility (ETSF) file format.
+    </flag>
+  </use>
+  <use>
+    <flag name="glib">
+      Compile with GLib Object System support
+    </flag>
+  </use>
+  <use>
+    <flag name="opencl">Enable support for OpenCL GPU acceleration</flag>
+  </use>
+  <use>
+    <flag name="scalapack">
+      Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing
+    </flag>
+  </use>
+</pkgmetadata>