From 0bc2ece8d2c7b10b9e116e12561ee591f65a91da Mon Sep 17 00:00:00 2001 From: Kyle Guinn Date: Tue, 9 Jun 2015 00:47:19 -0500 Subject: academic/cholmod: Updated for version 3.0.5. Signed-off-by: Kyle Guinn --- academic/cholmod/autotoolize.diff | 83 ++++++++++++++++++++++++++----------- academic/cholmod/cholmod.SlackBuild | 44 ++++++++++---------- academic/cholmod/cholmod.info | 8 ++-- 3 files changed, 85 insertions(+), 50 deletions(-) (limited to 'academic/cholmod') diff --git a/academic/cholmod/autotoolize.diff b/academic/cholmod/autotoolize.diff index 5e93cf2f1cb2..8c87d18771f5 100644 --- a/academic/cholmod/autotoolize.diff +++ b/academic/cholmod/autotoolize.diff @@ -2,7 +2,7 @@ diff --git a/Check/Makefile.am b/Check/Makefile.am new file mode 100644 --- /dev/null +++ b/Check/Makefile.am -@@ -0,0 +1,24 @@ +@@ -0,0 +1,26 @@ +AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) + +EXTRA_DIST = \ @@ -20,9 +20,11 @@ new file mode 100644 + libcheck.la + +libchecki_la_SOURCES = $(CHECKSRC) ++libchecki_la_LIBADD = $(SUITESPARSECONFIG_LIBS) +libchecki_la_CPPFLAGS= $(AM_CPPFLAGS) + +libcheckl_la_SOURCES = $(CHECKSRC) ++libcheckl_la_LIBADD = $(SUITESPARSECONFIG_LIBS) +libcheckl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG + +libcheck_la_SOURCES = @@ -64,11 +66,11 @@ new file mode 100644 + libcholesky.la + +libcholeskyi_la_SOURCES = $(CHOLESKYSRC) -+libcholeskyi_la_LIBADD = $(COLAMD_LIBS) $(AMD_LIBS) -lm ++libcholeskyi_la_LIBADD = $(COLAMD_LIBS) $(AMD_LIBS) $(SUITESPARSECONFIG_LIBS) -lm +libcholeskyi_la_CPPFLAGS = $(AM_CPPFLAGS) + +libcholeskyl_la_SOURCES = $(CHOLESKYSRC) -+libcholeskyl_la_LIBADD = $(COLAMD_LIBS) $(AMD_LIBS) -lm ++libcholeskyl_la_LIBADD = $(COLAMD_LIBS) $(AMD_LIBS) $(SUITESPARSECONFIG_LIBS) -lm +libcholeskyl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG + +libcholesky_la_SOURCES = @@ -113,11 +115,11 @@ new file mode 100644 + libcore.la + +libcorei_la_SOURCES = $(CORESRC) -+libcorei_la_LIBADD = -lm ++libcorei_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm +libcorei_la_CPPFLAGS = $(AM_CPPFLAGS) + +libcorel_la_SOURCES = $(CORESRC) -+libcorel_la_LIBADD = -lm ++libcorel_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm +libcorel_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG + +libcore_la_SOURCES = @@ -628,11 +630,41 @@ new file mode 100644 + +CLEANFILES = _*.awk _*.tex *.dvi *.aux *.log *.lof *.lot *.toc *.bak *.bbl *.blg +MAINTAINERCLEANFILES = $(dist_pdf_DATA) +diff --git a/GPU/Makefile.am b/GPU/Makefile.am +new file mode 100644 +--- /dev/null ++++ b/GPU/Makefile.am +@@ -0,0 +1,25 @@ ++AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) ++ ++GPUSRC = \ ++ cholmod_gpu.c ++ ++EXTRA_DIST = \ ++ cholmod_gpu_kernels.c \ ++ cholmod_gpu_kernels.cu ++ ++noinst_HEADERS = \ ++ t_cholmod_gpu.c ++ ++noinst_LTLIBRARIES = \ ++ libgpui.la \ ++ libgpul.la \ ++ libgpu.la ++ ++libgpui_la_SOURCES = $(GPUSRC) ++libgpui_la_CPPFLAGS = $(AM_CPPFLAGS) ++ ++libgpul_la_SOURCES = $(GPUSRC) ++libgpul_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG ++ ++libgpu_la_SOURCES = ++libgpu_la_LIBADD = libgpui.la libgpul.la diff --git a/Include/Makefile.am b/Include/Makefile.am new file mode 100644 --- /dev/null +++ b/Include/Makefile.am -@@ -0,0 +1,42 @@ +@@ -0,0 +1,45 @@ +EXTRA_DIST = \ + License.txt \ + README.txt @@ -645,10 +677,13 @@ new file mode 100644 + cholmod.h \ + cholmod_blas.h \ + cholmod_core.h \ ++ cholmod_function.h \ ++ cholmod_gpu.h \ + cholmod_io64.h + +noinst_HEADERS = \ + cholmod_complexity.h \ ++ cholmod_gpu_kernels.h \ + cholmod_internal.h \ + cholmod_template.h + @@ -755,7 +790,7 @@ diff --git a/Makefile.am b/Makefile.am new file mode 100644 --- /dev/null +++ b/Makefile.am -@@ -0,0 +1,43 @@ +@@ -0,0 +1,46 @@ +SUBDIRS = Include Core +EXTRA_DIST = README.txt + @@ -766,7 +801,7 @@ new file mode 100644 + +libcholmod_la_SOURCES = +libcholmod_la_LIBADD = $(top_builddir)/Core/libcore.la -+libcholmod_la_LDFLAGS = -no-undefined -version-number 2:1:2 ++libcholmod_la_LDFLAGS = -no-undefined -release $(PACKAGE_VERSION) + +if MOD_CHECK +SUBDIRS += Check @@ -798,6 +833,9 @@ new file mode 100644 +libcholmod_la_LIBADD += $(top_builddir)/Supernodal/libsupernodal.la +endif + ++#SUBDIRS += GPU ++#libcholmod_la_LIBADD += $(top_builddir)/GPU/libgpu.la ++ +SUBDIRS += MATLAB Demo Doc diff --git a/MatrixOps/Makefile.am b/MatrixOps/Makefile.am new file mode 100644 @@ -830,11 +868,11 @@ new file mode 100644 + libmatrixops.la + +libmatrixopsi_la_SOURCES = $(MATRIXOPSSRC) -+libmatrixopsi_la_LIBADD = -lm ++libmatrixopsi_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm +libmatrixopsi_la_CPPFLAGS = $(AM_CPPFLAGS) + +libmatrixopsl_la_SOURCES = $(MATRIXOPSSRC) -+libmatrixopsl_la_LIBADD = -lm ++libmatrixopsl_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm +libmatrixopsl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG + +libmatrixops_la_SOURCES = @@ -865,11 +903,11 @@ new file mode 100644 + libmodify.la + +libmodifyi_la_SOURCES = $(MODIFYSRC) -+libmodifyi_la_LIBADD = -lm ++libmodifyi_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm +libmodifyi_la_CPPFLAGS = $(AM_CPPFLAGS) + +libmodifyl_la_SOURCES = $(MODIFYSRC) -+libmodifyl_la_LIBADD = -lm ++libmodifyl_la_LIBADD = $(SUITESPARSECONFIG_LIBS) -lm +libmodifyl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG + +libmodify_la_SOURCES = @@ -898,11 +936,11 @@ new file mode 100644 + libpartition.la + +libpartitioni_la_SOURCES = $(PARTITIONSRC) -+libpartitioni_la_LIBADD = $(METIS_LIBS) $(CCOLAMD_LIBS) $(CAMD_LIBS) -lm ++libpartitioni_la_LIBADD = $(METIS_LIBS) $(CCOLAMD_LIBS) $(CAMD_LIBS) $(SUITESPARSECONFIG_LIBS) -lm +libpartitioni_la_CPPFLAGS = $(AM_CPPFLAGS) + +libpartitionl_la_SOURCES = $(PARTITIONSRC) -+libpartitionl_la_LIBADD = $(METIS_LIBS) $(CCOLAMD_LIBS) $(CAMD_LIBS) -lm ++libpartitionl_la_LIBADD = $(METIS_LIBS) $(CCOLAMD_LIBS) $(CAMD_LIBS) $(SUITESPARSECONFIG_LIBS) -lm +libpartitionl_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG + +libpartition_la_SOURCES = @@ -966,7 +1004,7 @@ diff --git a/Supernodal/Makefile.am b/Supernodal/Makefile.am new file mode 100644 --- /dev/null +++ b/Supernodal/Makefile.am -@@ -0,0 +1,39 @@ +@@ -0,0 +1,35 @@ +AM_CPPFLAGS = -I$(top_srcdir)/Include $(SUITESPARSECONFIG_CFLAGS) + +EXTRA_DIST = \ @@ -979,7 +1017,6 @@ new file mode 100644 + cholmod_super_symbolic.c + +noinst_HEADERS = \ -+ t_cholmod_gpu.c \ + t_cholmod_super_numeric.c \ + t_cholmod_super_solve.c + @@ -989,17 +1026,14 @@ new file mode 100644 + libsupernodal.la + +libsupernodali_la_SOURCES = $(SUPERNODALSRC) -+libsupernodali_la_LIBADD = $(LAPACK_LIBS) $(BLAS_LIBS) ++libsupernodali_la_LIBADD = $(LAPACK_LIBS) $(BLAS_LIBS) $(SUITESPARSECONFIG_LIBS) +libsupernodali_la_CPPFLAGS = $(AM_CPPFLAGS) + +libsupernodall_la_SOURCES = $(SUPERNODALSRC) -+libsupernodall_la_LIBADD = $(LAPACK_LIBS) $(BLAS_LIBS) ++libsupernodall_la_LIBADD = $(LAPACK_LIBS) $(BLAS_LIBS) $(SUITESPARSECONFIG_LIBS) +libsupernodall_la_CPPFLAGS = $(AM_CPPFLAGS) -DDLONG + -+if TIMING -+libsupernodali_la_LIBADD += $(SUITESPARSECONFIG_LIBS) -+libsupernodall_la_LIBADD += $(SUITESPARSECONFIG_LIBS) -+else ++if !TIMING +libsupernodali_la_CPPFLAGS += -DNTIMER +libsupernodall_la_CPPFLAGS += -DNTIMER +endif @@ -1407,12 +1441,12 @@ diff --git a/configure.ac b/configure.ac new file mode 100644 --- /dev/null +++ b/configure.ac -@@ -0,0 +1,215 @@ +@@ -0,0 +1,216 @@ +# -*- Autoconf -*- +# Process this file with autoconf to produce a configure script. + +AC_PREREQ([2.69]) -+AC_INIT([CHOLMOD],[2.1.2],[DrTimothyAldenDavis@gmail.com],[cholmod],[http://www.suitesparse.com/]) ++AC_INIT([CHOLMOD],[3.0.5],[DrTimothyAldenDavis@gmail.com],[cholmod],[http://www.suitesparse.com/]) +AC_CONFIG_SRCDIR([Core/cholmod_common.c]) +AC_CONFIG_HEADERS([config.h Include/cholmod_config.h]) +AM_INIT_AUTOMAKE([foreign]) @@ -1616,6 +1650,7 @@ new file mode 100644 + Core/Makefile + Demo/Makefile + Doc/Makefile ++ GPU/Makefile + Include/Makefile + MATLAB/Makefile + MatrixOps/Makefile diff --git a/academic/cholmod/cholmod.SlackBuild b/academic/cholmod/cholmod.SlackBuild index 519778987155..24dcc2ecac4b 100644 --- a/academic/cholmod/cholmod.SlackBuild +++ b/academic/cholmod/cholmod.SlackBuild @@ -2,29 +2,31 @@ # Slackware build script for CHOLMOD -# Copyright 2013 Kyle Guinn , USA +# Copyright 2013-2015 Kyle Guinn , USA # All rights reserved. # # Redistribution and use of this script, with or without modification, is # permitted provided that the following conditions are met: # # 1. Redistributions of this script must retain the above copyright -# notice, this list of conditions and the following disclaimer. +# notice, this list of conditions and the following disclaimer. # -# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED -# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO -# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, -# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; -# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, -# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR -# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF -# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. PRGNAM=cholmod -SRCNAM=CHOLMOD -VERSION=${VERSION:-2.1.2} +SRCNAM=SuiteSparse +SUBDIR=CHOLMOD +VERSION=${VERSION:-3.0.5} +SRCVER=${SRCVER:-4.4.4} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} @@ -59,7 +61,7 @@ else fi # Recommended by SuiteSparse -SLKCFLAGS="$SLKCFLAGS -fexceptions -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE" +SLKCFLAGS="$SLKCFLAGS -fexceptions -D_FILE_OFFSET_BITS=64" set -e @@ -67,14 +69,10 @@ rm -rf $PKG mkdir -p $TMP $PKG $OUTPUT cd $TMP rm -rf $SRCNAM -tar xvf $CWD/$SRCNAM-$VERSION.tar.gz -cd $SRCNAM +tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz +cd $SRCNAM/$SUBDIR chown -R root:root . -find -L . \ - \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ - -o -perm 511 \) -exec chmod 755 {} \; -o \ - \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ - -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; +chmod -R u+w,go-w,a+rX-st . patch -p1 < $CWD/autotoolize.diff patch -p1 < $CWD/atlas-threaded-blas.diff @@ -99,6 +97,8 @@ make make check make install-strip DESTDIR=$PKG +find $PKG/usr/lib${LIBDIRSUFFIX} -name '*.la' -delete + mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cp -a $DOCS $PKG/usr/doc/$PRGNAM-$VERSION for i in $MODULE_DOCS; do diff --git a/academic/cholmod/cholmod.info b/academic/cholmod/cholmod.info index 6f45c6001d36..b998ea9b3491 100644 --- a/academic/cholmod/cholmod.info +++ b/academic/cholmod/cholmod.info @@ -1,8 +1,8 @@ PRGNAM="cholmod" -VERSION="2.1.2" -HOMEPAGE="https://www.cise.ufl.edu/research/sparse/cholmod/" -DOWNLOAD="https://www.cise.ufl.edu/research/sparse/cholmod/CHOLMOD-2.1.2.tar.gz" -MD5SUM="0c55ade78bb1b1f1e7b6a6cba024f70d" +VERSION="3.0.5" +HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html" +DOWNLOAD="http://faculty.cse.tamu.edu/davis/SuiteSparse/SuiteSparse-4.4.4.tar.gz" +MD5SUM="e0af74476935c9ff6d971df8bb6b82fc" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES="blas lapack suitesparseconfig amd camd colamd ccolamd" -- cgit v1.2.3