From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001 From: V3n3RiX Date: Mon, 9 Oct 2017 18:53:29 +0100 Subject: reinit the tree, so we can have metadata --- sci-libs/gerris/Manifest | 10 ++++ .../files/gerris-20130531-hypre-no-mpi.patch | 22 +++++++ .../files/gerris-20130531-lis-matrix-csr.patch | 11 ++++ .../gerris-20130531-use-blas-lapack-system.patch | 33 ++++++++++ ...erris-20131206-DEFAULT_SOURCE-replacement.patch | 16 +++++ .../files/gerris-20131206-lis-api-change.patch | 18 ++++++ sci-libs/gerris/gerris-20131206-r1.ebuild | 70 ++++++++++++++++++++++ sci-libs/gerris/metadata.xml | 15 +++++ 8 files changed, 195 insertions(+) create mode 100644 sci-libs/gerris/Manifest create mode 100644 sci-libs/gerris/files/gerris-20130531-hypre-no-mpi.patch create mode 100644 sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch create mode 100644 sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch create mode 100644 sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch create mode 100644 sci-libs/gerris/files/gerris-20131206-lis-api-change.patch create mode 100644 sci-libs/gerris/gerris-20131206-r1.ebuild create mode 100644 sci-libs/gerris/metadata.xml (limited to 'sci-libs/gerris') diff --git a/sci-libs/gerris/Manifest b/sci-libs/gerris/Manifest new file mode 100644 index 000000000000..782a0e9f9e9a --- /dev/null +++ b/sci-libs/gerris/Manifest @@ -0,0 +1,10 @@ +AUX gerris-20130531-hypre-no-mpi.patch 644 SHA256 4d7fab9f49325ded81589242dafe95008fb2fff350bd77870e4118f8de3e7d9c SHA512 01dd5e4c159b81ee47e653173361b41b5ab5ddc05f0595cfad862d40f1d6f041c4de4860b76a1ab691c296cec7c2b4258d7ea269c8c58d37a1c8f6d17f4b0ac5 WHIRLPOOL 0e6d26f2336ad1e606226c196b0bee7157a413a128647eae06a990edad6177f74830ecafe861754692ec9457d9aad65ce91f22af3d797ae43dd13e9c97ea8637 +AUX gerris-20130531-lis-matrix-csr.patch 265 SHA256 8a9e90bff38b0933b5a9f56d7dbb5cad9ec3f7332cd00093949747b995f3ef5e SHA512 1b64fb1847e213829471c0baac812cbc9e1599c202e299a84114db598970fec911cbf6abf2cf158acca1dd472d0d3df0164956b5e41f1411a2be5e19b83d168c WHIRLPOOL 40a1f511926cce03248d6965f38c1a6de7dbfcb02da71342a42f982fe9fad4a003e08f421a43f45f654596a46e9fcbc3b39660eb7770c952a61233e7bd70aa82 +AUX gerris-20130531-use-blas-lapack-system.patch 1466 SHA256 0759033b4c3790879c0a4c161047a490d087ae71cb7cbbce205f04f10cee0d65 SHA512 4ff7f35c1d8698cc6ce2ed31708e0d05fd1cd6c8829d2ab7cc589fb5e4e1ea080df27587a7bf59ec7303c0dcfaa159da625a330a5eb5d1901ecfa45a762d41e4 WHIRLPOOL b68d2f15c1934617b31c9e5571e2e22b34f67429e74b70ae5fc7b3409bb47888f20479c6e9959ae8a7b2ebbcfc2b59b77d78c11ac22db440c89538ef9f3336c7 +AUX gerris-20131206-DEFAULT_SOURCE-replacement.patch 728 SHA256 feb7eb02a40cca753dc096418e2fb9e58edbfb009029ccbdf3e4628e449e3f27 SHA512 b1ca792b4b9ffe88964f58e12a3caff23ec3ba31f8f43136acf9adc106c57d10f75f32d2ec7a6769cdd130324e9de9a1621fc4c90be834eef330690f765159c7 WHIRLPOOL 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MPI ++# hypre does not need mpi + AC_CHECK_LIB(HYPRE, HYPRE_IJMatrixCreate, hypre="yes", hypre="no", [-lm]) + if test x$hypre = xyes; then + AC_CHECK_HEADERS(HYPRE.h, hypre="yes", hypre="no") +@@ -344,7 +344,7 @@ + if test x$hypre = xno; then + AC_MSG_WARN([HYPRE not found. hypre Module won't be available.]) + fi +-fi ++ + AM_CONDITIONAL(BUILD_HYPRE, test x$hypre = xyes) + + # Build lis module if lis is installed diff --git a/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch new file mode 100644 index 000000000000..d4c7bfae15bb --- /dev/null +++ b/sci-libs/gerris/files/gerris-20130531-lis-matrix-csr.patch @@ -0,0 +1,11 @@ +--- a/modules/lis.c ++++ b/modules/lis.c +@@ -45,7 +45,7 @@ + g_array_index (stencil->coeff, double, j), + A); + } +- lis_matrix_set_type (A, LIS_MATRIX_CRS); ++ lis_matrix_set_type (A, LIS_MATRIX_CSR); + lis_matrix_assemble (A); + + LIS_VECTOR b, x; diff --git a/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch new file mode 100644 index 000000000000..1c25a8f516b6 --- /dev/null +++ b/sci-libs/gerris/files/gerris-20130531-use-blas-lapack-system.patch @@ -0,0 +1,33 @@ +--- a/modules/Makefile.am ++++ b/modules/Makefile.am +@@ -105,7 +105,7 @@ + libstokes2D_la_LIBADD = $(GFS2D_LIBS) + + libwavewatch2D_la_SOURCES = wavewatch.c +-libwavewatch2D_la_LIBADD = $(GFS2D_LIBS) -Lwavewatch -lwavewatch -L/usr/lib/gcc/i486-linux-gnu/4.2 -lgfortran ++libwavewatch2D_la_LIBADD = $(GFS2D_LIBS) -Lwavewatch -lwavewatch + libwavewatch2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1 \ + -DW3SRCE=`nm wavewatch/libwavewatch.a | grep w3srce | awk '{ if ($$2 == "T") print $$3; }'` \ + -DGFSW3INIT=`nm wavewatch/libwavewatch.a | grep gfsw3_init | awk '{ if ($$2 == "T") print $$3; }'` +@@ -164,17 +164,17 @@ + + liblis3D_la_SOURCES = lis.c + liblis3D_la_CFLAGS = $(AM_CFLAGS) +-liblis3D_la_LIBADD = $(GFS3D_LIBS) -llis -lgfortran -lm ++liblis3D_la_LIBADD = $(GFS3D_LIBS) -llis -lm + liblis2D_la_SOURCES = lis.c + liblis2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1 +-liblis2D_la_LIBADD = $(GFS2D_LIBS) -llis -lgfortran -lm ++liblis2D_la_LIBADD = $(GFS2D_LIBS) -llis -lm + + libagmg3D_la_SOURCES = agmg.c dagmg.f90 + libagmg3D_la_CFLAGS = $(AM_CFLAGS) +-libagmg3D_la_LIBADD = $(GFS3D_LIBS) -llapack -lblas -lgfortran -lm ++libagmg3D_la_LIBADD = $(GFS3D_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) -lm + libagmg2D_la_SOURCES = agmg.c dagmg.f90 + libagmg2D_la_CFLAGS = $(AM_CFLAGS) -DFTT_2D=1 +-libagmg2D_la_LIBADD = $(GFS2D_LIBS) -llapack -lblas -lgfortran -lm ++libagmg2D_la_LIBADD = $(GFS2D_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) -lm + + libokada3D_la_SOURCES = okada.c + libokada3D_la_CFLAGS = $(AM_CFLAGS) diff --git a/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch b/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch new file mode 100644 index 000000000000..d20df635512c --- /dev/null +++ b/sci-libs/gerris/files/gerris-20131206-DEFAULT_SOURCE-replacement.patch @@ -0,0 +1,16 @@ +Silence warnings due to _BSD_SOURCE being deprecated by glib: +* /usr/include/features.h:148:3: warning: #warning "_BSD_SOURCE and +* _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" [-Wcpp] +* # warning "_BSD_SOURCE and _SVID_SOURCE are deprecated, use _DEFAULT_SOURCE" + +--- a/configure.ac ++++ b/configure.ac +@@ -108,7 +108,7 @@ + AC_PROG_CC + + # -D_GNU_SOURCE is only necessary for old (< 2.10) glibc implementations of open_memstream() +-CFLAGS="$CFLAGS -D_XOPEN_SOURCE=700 -D_BSD_SOURCE -D_GNU_SOURCE" ++CFLAGS="$CFLAGS -D_XOPEN_SOURCE=700 -D_DEFAULT_SOURCE -D_GNU_SOURCE" + if test x$GCC = xyes ; then + CFLAGS="$CFLAGS -Wall -Werror-implicit-function-declaration -Wmissing-prototypes -Wmissing-declarations -pipe -std=c99" + fi diff --git a/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch b/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch new file mode 100644 index 000000000000..28892ddadedf --- /dev/null +++ b/sci-libs/gerris/files/gerris-20131206-lis-api-change.patch @@ -0,0 +1,18 @@ +sci-libs/lis changed some of its function prototypes by renaming +lis_solver_get_iters to lis_solver_get_iter in version 1.4.43 from 17 July 2014 + +See also: +http://www.ssisc.org/lis/ChangeLog.txt +https://bugs.gentoo.org/show_bug.cgi?id=593282 + +--- a/modules/lis.c ++++ b/modules/lis.c +@@ -67,7 +67,7 @@ + + lis_solve (A, b, x, solver); + int iter; +- lis_solver_get_iters (solver, &iter); ++ lis_solver_get_iter (solver, &iter); + par->niter = iter; + + lis_vector_get_values (x, 0, lp->lhs->len, (double *) lp->lhs->data); diff --git a/sci-libs/gerris/gerris-20131206-r1.ebuild b/sci-libs/gerris/gerris-20131206-r1.ebuild new file mode 100644 index 000000000000..d17000bbe95f --- /dev/null +++ b/sci-libs/gerris/gerris-20131206-r1.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit autotools flag-o-matic toolchain-funcs + +MY_P=${P/-20/-snapshot-} + +DESCRIPTION="Gerris Flow Solver" +HOMEPAGE="http://gfs.sourceforge.net/" +SRC_URI="http://gerris.dalembert.upmc.fr/gerris/tarballs/${MY_P}.tar.gz" + +LICENSE="GPL-2" + +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples mpi static-libs" + +# all these deps could be optional +# but the configure.in would have to be modified +# heavily for the automagic +RDEPEND=" + dev-libs/glib:2 + dev-games/ode + sci-libs/netcdf:= + sci-libs/gsl:= + sci-libs/gts + sci-libs/hypre[mpi?] + sci-libs/lis[mpi?] + sci-libs/proj + sci-libs/fftw:3.0= + virtual/lapack + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MY_P}" + +# buggy tests, need extra packages and require gerris to be installed +RESTRICT=test + +PATCHES=( + "${FILESDIR}"/${PN}-20130531-hypre-no-mpi.patch + "${FILESDIR}"/${PN}-20130531-lis-matrix-csr.patch + "${FILESDIR}"/${PN}-20130531-use-blas-lapack-system.patch + "${FILESDIR}"/${PN}-20131206-lis-api-change.patch + "${FILESDIR}"/${PN}-20131206-DEFAULT_SOURCE-replacement.patch +) + +src_prepare() { + default + eautoreconf +} + +src_configure() { + append-cppflags "-I${EPREFIX}/usr/include/hypre" + econf \ + --enable-shared \ + $(use_enable static-libs static) \ + $(use_enable mpi) \ + LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" +} + +src_install() { + default + use examples && dodoc -r doc/examples + + find "${D}" -name '*.la' -delete || die +} diff --git a/sci-libs/gerris/metadata.xml b/sci-libs/gerris/metadata.xml new file mode 100644 index 000000000000..cbf216a39022 --- /dev/null +++ b/sci-libs/gerris/metadata.xml @@ -0,0 +1,15 @@ + + + + + sci@gentoo.org + Gentoo Science Project + + + Gerris Flow Solver is a software program for the solution of the partial + differential equations describing fluid flow. + + + gfs + + -- cgit v1.2.3