academic/cholmod: Updated for version 3.0.5.

Signed-off-by: Kyle Guinn <elyk03@gmail.com>

3 files changed, 85 insertions, 50 deletions

diff --git a/academic/cholmod/autotoolize.diff b/academic/cholmod/autotoolize.diff
index 5e93cf2f1cb29..8c87d18771f5b 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 5197789871556..24dcc2ecac4b6 100644
--- a/academic/cholmod/cholmod.SlackBuild
+++ b/academic/cholmod/cholmod.SlackBuild
@@ -2,29 +2,31 @@
 
 # Slackware build script for CHOLMOD
 
-# Copyright 2013 Kyle Guinn <elyk03@gmail.com>, USA
+# Copyright 2013-2015 Kyle Guinn <elyk03@gmail.com>, 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 6f45c6001d368..b998ea9b34919 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"