Suite sparse

sci-libs/suitesparse/Manifest

@@ -0,0 +1 @@
+DIST suitesparse-5.4.0.tar.gz 52594099 BLAKE2B e7e2400d2d24c5e029cad7b6afd572077333e341d74c4f065e9eea793f6d5dad466d762153a97a57dbec40a86790c2db144122957beb68de083b15c6f5ebd204 SHA512 8328bcc2ef5eb03febf91b9c71159f091ff405c1ba7522e53714120fcf857ceab2d2ecf8bf9a2e1fc45e1a934665a341e3a47f954f87b59934f4fce6164775d6

sci-libs/suitesparse/files/suitesparse-5.4.0-0001-Suitesparse_config-Suitesparse_config.mk-drop-RPATH.patch

@@ -0,0 +1,26 @@
+From 9ec0dbdc11267e940c9932a2a02ea3cceea78673 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <[email protected]>
+Date: Sat, 20 Jul 2019 16:47:32 +0200
+Subject: [PATCH 1/2] Suitesparse_config/Suitesparse_config.mk: drop RPATH
+
+Signed-off-by: Bernd Waibel <[email protected]>
+---
+ SuiteSparse_config/SuiteSparse_config.mk | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/SuiteSparse_config/SuiteSparse_config.mk b/SuiteSparse_config/SuiteSparse_config.mk
+index 19a3903..c70c237 100644
+--- a/SuiteSparse_config/SuiteSparse_config.mk
++++ b/SuiteSparse_config/SuiteSparse_config.mk
+@@ -358,7 +358,7 @@ SUITESPARSE_VERSION = 5.4.0
+
+     ifeq ($(UNAME),Linux)
+         # add the realtime library, librt, and SuiteSparse/lib
+-        LDLIBS += -lrt -Wl,-rpath=$(INSTALL_LIB)
++        LDLIBS += -lrt
+     endif
+
+     #---------------------------------------------------------------------------
+-- 
+2.22.0
+

sci-libs/suitesparse/files/suitesparse-5.4.0-0002-AMD-Lib-Makefile-also-build-shared-library.patch

@@ -0,0 +1,64 @@
+From 7394b9923afb8703322dfeb8927c1dcf8144a67f Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <[email protected]>
+Date: Sat, 20 Jul 2019 16:48:56 +0200
+Subject: [PATCH 2/2] AMD/Lib/Makefile: also build shared library
+
+Signed-off-by: Bernd Waibel <[email protected]>
+---
+ AMD/Lib/Makefile | 19 +++++++++++++++++--
+ 1 file changed, 17 insertions(+), 2 deletions(-)
+
+diff --git a/AMD/Lib/Makefile b/AMD/Lib/Makefile
+index 3b92f6a..5b558a5 100644
+--- a/AMD/Lib/Makefile
++++ b/AMD/Lib/Makefile
+@@ -11,7 +11,7 @@ default: library
+ include ../../SuiteSparse_config/SuiteSparse_config.mk
+
+ # AMD depends on SuiteSparse_config
+-LDLIBS += -lsuitesparseconfig
++LDLIBS += -lsuitesparseconfig -lgfortran
+
+ # compile and install in SuiteSparse/lib
+ library:
+@@ -62,7 +62,7 @@ $(AR_TARGET): $(OBJ)
+ # compile the Fortran versions and the libamdf77.a library (static only)
+ #-------------------------------------------------------------------------------
+
+-fortran: libamdf77.a
++fortran: libamdf77.a libamdf77.so.$(VERSION)
+
+ AMDF77 = amd.o amdbar.o
+
+@@ -76,6 +76,12 @@ libamdf77.a: $(AMDF77)
+ 	$(ARCHIVE) libamdf77.a $^
+ 	- $(RANLIB) libamdf77.a
+
++libamdf77.so.$(VERSION): $(AMDF77)
++	$(CC) $(SO_OPTS) $^ -o $@ $(LDLIBS)
++	ln -sf $@ libamdf77.so.$(SO_VERSION)
++	ln -sf $@ libamdf77.so
++	chmod 755 $@
++
+ #-------------------------------------------------------------------------------
+ # install (shared C version only)
+ #-------------------------------------------------------------------------------
+@@ -98,6 +104,15 @@ $(INSTALL_LIB)/$(SO_TARGET): $(OBJ)
+ 	chmod 644 $(INSTALL_DOC)/AMD_UserGuide.pdf
+ 	chmod 644 $(INSTALL_DOC)/AMD_README.txt
+
++install-fortran: $(INSTALL_LIB)/libamdf77.so.$(VERSION)
++
++$(INSTALL_LIB)/libamdf77.so.$(VERSION): fortran
++	@mkdir -p $(INSTALL_LIB)
++	$(CC) $(SO_OPTS) $(AMDF77) -o $@ $(LDLIBS)
++	( cd $(INSTALL_LIB) ; ln -sf libamdf77.so.$(VERSION) libamdf77.so.$(SO_VERSION) )
++	( cd $(INSTALL_LIB) ; ln -sf libamdf77.so.$(VERSION) libamdf77.so )
++	chmod 755 $(INSTALL_LIB)/libamdf77.so.$(VERSION)
++
+ # uninstall AMD
+ uninstall:
+ 	$(RM) $(INSTALL_LIB)/$(SO_TARGET)
+-- 
+2.22.0
+

sci-libs/suitesparse/metadata.xml

@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<maintainer type="project">
+	<email>[email protected]</email>
+	<name>Gentoo Science Project</name>
+</maintainer>
+<longdescription lang="en">
+<!-- FIXME: rework this -->
+SuiteSparse is a suite of sparse matrix libraries from University of
+Florida Computer Science Department. Currently, this includes:
+	* AMD: symmetric approximate minimum degree
+	* BTF: permutation to block triangular form
+	* CAMD: symmetric approximate minimum degree
+	* CCOLAMD: constrained column approximate minimum degree
+	* COLAMD: column approximate minimum degree
+	* CHOLMOD: sparse supernodal Cholesky factorization and update/downdate
+	* CSparse: a concise sparse matrix package
+	* CXSparse: an extended version of CSparse
+	* GraphBLAS: graph algorithms implemented with BLAS
+	* KLU: sparse LU factorization, for circuit simulation
+	* LDL: a simple LDL^T factorization
+	* Mongoose: graph partioning package
+	* RBio: read/write sparse matrices in Rutherford / Boeing format
+	* SPQR: multifrontal sparse QT factorization
+	* SuiteSparse_config: common configuration for all but CSparse
+	* UMFPACK: sparse multifrontal LU factorization
+The Gentoo package does not include the suitesparse MATLAB tools from
+upstream, from the packages above and the following MATLAB-only packages:
+	* LINFACTOR: solve Ax=b using LU or CHOL
+	* MESHND: 2D and 3D mesh generation and nested dissection
+	* SSMULT: sparse matrix times sparse matrix 
+</longdescription>
+<use>
+	<flag name="cuda">Use CUDA for cholmod and spqr</flag>
+	<flag name="tbb">Use Intel's <pkg>dev-cpp/tbb</pkg> for threading</flag>
+</use>
+</pkgmetadata>

sci-libs/suitesparse/suitesparse-5.4.0.ebuild

@@ -0,0 +1,168 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+# FIXME: currently this is a safety measure. Is it really needed by the
+#	fortran modules?
+FORTRAN_NEED_OPENMP=1
+
+# FIXME: how to handle cmake without having a root CMakeLists.txt?
+inherit fortran-2 multiprocessing toolchain-funcs
+
+MY_PN="SuiteSparse"
+
+DESCRIPTION="Package for a suite of sparse matrix tools"
+HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html"
+SRC_URI="http://faculty.cse.tamu.edu/davis/${MY_PN}/${MY_PN}-${PV}.tar.gz -> ${P}.tar.gz"
+
+# BSD: amd, camd, ccolamd, colamd, ssget
+# LGPL-2.1+: btf, cholmod/Check, choldmod/Cholesky, cholmod/Core,
+#	cholmod/Partition, cxsparse, klu, ldl
+# GPL-2+: choldmod/Demo, cholmod/Matlab, cholmod/MatrixOps,
+#	cholmod/Modify, cholmod/Supernodal, cholmod/Tcov, cholmod/Valgrind,
+#	GPUQREngine, RBio, spqr, SuiteSparse_GPURuntime, umfpack
+# Apache-2.0: GraphBLAS
+# GPL-3: Mongoose
+LICENSE="Apache-2.0 BSD GPL-2+ GPL-3 LGPL-2.1+"
+SLOT="0"
+
+KEYWORDS="~amd64 ~x86"
+
+FORTRAN_NEEDED="amd"
+
+# FIXME: currently not included:
+#	Piro_Band, Skyline_SVD
+# GraphBLAS and Mongoose are cmake based builds
+# SuiteSparse_GPURuntime and GPUQREngine are part of spqr[cuda]
+# FIXME: cuda is not compiling due to C/C++ mixing
+# FIXME: testing
+IUSE="cuda fortran tbb test"
+
+# Tests currently fail in cholmod library
+#RESTRICT="!test? ( test )"
+RESTRICT="test"
+
+# FIXME: Exclude the old packages. These could be removed once the package
+# and revdeps are fully updated.
+RDEPEND="
+	!<sci-libs/suitesparse-5
+	!sci-libs/amd
+	!sci-libs/btf
+	!sci-libs/camd
+	!sci-libs/ccolamd
+	!sci-libs/cholmod
+	!sci-libs/colamd
+	!sci-libs/cxsparse
+	!sci-libs/klu
+	!sci-libs/ldl
+	!sci-libs/spqr
+	!sci-libs/suitesparseconfig
+	!sci-libs/umfpack
+	|| ( >=sci-libs/metis-5.1.0-r3[openmp(+)] >=sci-libs/parmetis-4.0.3[openmp(+)] )
+	virtual/blas
+	virtual/lapack
+	cuda? (
+		>=dev-util/nvidia-cuda-toolkit-9.2.88:=
+		>=sci-libs/magma-2.4.0
+	)
+	tbb? ( >=dev-cpp/tbb-2017.20161128 )
+"
+
+DEPEND="
+	${RDEPEND}
+	sys-devel/m4
+	test? ( >=app-shells/tcsh-6.20.00 )
+"
+BDEPEND=">=sys-apps/grep-3.1"
+
+S=${WORKDIR}/${MY_PN}
+
+PATCHES=(
+	"${FILESDIR}/${P}-0001-Suitesparse_config-Suitesparse_config.mk-drop-RPATH.patch"
+	"${FILESDIR}/${P}-0002-AMD-Lib-Makefile-also-build-shared-library.patch"
+)
+
+DOCS=( README.txt )
+
+pkg_setup() {
+	# several of the packages need openmp support, so check for it early
+	tc-check-openmp || die "Need OpenMP to build ${P}"
+}
+
+src_compile() {
+	local myblas=$($(tc-getPKG_CONFIG) --libs blas)
+	local mylapack=$($(tc-getPKG_CONFIG) --libs lapack)
+	# FIXME: AUTOCC auto-enables intel compilers
+	local mymakeopts="OPTIMIZATION= AUTOCC=no JOBS=$(makeopts_jobs)"
+	mymakeopts="${mymakeopts} INSTALL=${ED}/usr INSTALL_LIB=${ED}/usr/$(get_libdir)"
+	mymakeopts="${mymakeopts} LAPACK=\"${mylapack}\" BLAS=\"${myblas}\""
+	mymakeopts="${mymakeopts} MY_METIS_LIB=-lmetis"
+	if use cuda; then
+		mymakeopts="${mymakeopts} CUDA=yes magma_inc=${EPREFIX}/usr magma_lib=${EPREFIX}/usr/$(get_libdir) -lmagma"
+		mymakeopts="${mymakeopts} CHOLDMOD_CONFIG+=-DGPU_BLAS SPQR_CONFIG+=-DGPU_BLAS"
+	else
+		mymakeopts="${mymakeopts} CUDA=no"
+	fi
+	if use fortran; then
+		local myf77=$(tc-getF77)
+		mymakeopts="${mymakeopts} F77=${myf77}"
+	fi
+	if use tbb; then
+		mymakeopts="${mymakeopts} TBB=-ltbb SPQR_CONFIG+=-DHAVE_TBB"
+	fi
+	use test && mymakeopts="${mymakeopts} TCOV=yes"
+	export LD_LIBRARY_PATH="${S}/lib"
+#	emake ${mymakeopts} config # FIXME: remove on final ebuild
+	emake ${mymakeopts} library
+#	use static-libs && emake ${mymakeopts} static
+	if use fortran; then
+		emake -C "${S}/AMD" ${mymakeopts} fortran
+	fi
+}
+
+src_test() {
+	local myblas=$($(tc-getPKG_CONFIG) --libs blas)
+	local mylapack=$($(tc-getPKG_CONFIG) --libs lapack)
+	local mytestargs="OPTIMIZATION= AUTOCC=no BLAS=${myblas} LAPACK=${mylapack}"
+	mytestargs="${mytestargs} MY_METIS_LIB=-lmetis"
+	if use cuda; then
+		mytestargs="${mytestargs} CUDA=yes magma_inc=${EPREFIX}/usr magma_lib=${EPREFIX}/usr/$(get_libdir) -lmagma"
+		mytestargs="${mytestargs} CHOLDMOD_CONFIG+=-DGPU_BLAS SPQR_CONFIG+=-DGPU_BLAS"
+	else
+		mytestargs="${mytestargs} CUDA=no"
+	fi
+	if use fortran; then
+		local myf77=$(tc-getF77)
+		mytestargs="${mytestargs} F77=${myf77}"
+	fi
+	if use tbb; then
+		mytestargs="${mytestargs} TBB=-ltbb SPQR_CONFIG+=-DHAVE_TBB"
+	fi
+	export LD_LIBRARY_PATH="${S}/lib"
+	emake ${mytestargs} cov
+}
+
+src_install() {
+	local myblas=$($(tc-getPKG_CONFIG) --libs blas)
+	local mylapack=$($(tc-getPKG_CONFIG) --libs lapack)
+	local myinstallargs="INSTALL=${ED}/usr INSTALL_LIB=${ED}/usr/$(get_libdir)"
+	myinstallargs="${myinstallargs} BLAS=${myblas} LAPACK=${mylapack} MY_METIS_LIB=-lmetis"
+	if use cuda; then
+		myinstallargs="${myinstallargs} CUDA=yes magma_inc=${EPREFIX}/usr magma_lib=${EPREFIX}/usr/$(get_libdir) -lmagma"
+		myinstallargs="${myinstallargs} CHOLMOD_CONFIG+=-DGPU_BLAS SPQR_CONFIG+=-DGPU_BLAS"
+	else
+		myinstallargs="${myinstallargs} CUDA=no"
+	fi
+	if use fortran; then
+		local myf77=$(tc-getF77)
+		myinstallargs="${myinstallargs} F77=${myf77}"
+	fi
+	if use tbb; then
+		myinstallargs="${myinstallargs} TBB=-ltbb SPQR_CONFIG+=-DHAVE_TBB"
+	fi
+	emake ${myinstallargs} install
+	if use fortran; then
+		emake -C "${S}/AMD/Lib" ${myinstallargs} install-fortran
+	fi
+}