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Accepting request 1146515 from science

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OBS-URL: https://build.opensuse.org/request/show/1146515
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/suitesparse?expand=0&rev=46
This commit is contained in:
Ana Guerrero 2024-02-15 19:58:50 +00:00 committed by Git OBS Bridge
commit 537337b6c9
47 changed files with 3672 additions and 589 deletions
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Before commiting content to devel project, you must first update the tests sources.
The script `list-mongoose-test-sources.py` is a modified version of the `runTests` python script
located at `Mongoose/Tests/`. Please read the script and modify it as needed
e.g. change of min id default or max id default or reading the IDs indicated from the
the tests section of Mongoose's CMakeLists.txt.
Check if there are new sources and if there are, add it as new content sources for the RPM specfile.
Check that the specfile has those new sources copied to `Mongoose/Tests/Matrix` and `Mongoose/Matrix`. As for `ssstats.csv`, that should
be in `Mongoose/Tests/`.

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<physicalmemory>
<size unit="G">7</size>
</physicalmemory>
<disk>
<size unit="G">40</size>
</disk>
</hardware>
<overwrite>
<conditions>
@ -25,3 +28,4 @@
</hardware>
</overwrite>
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@ -1,19 +0,0 @@
diff -urN SuiteSparse.orig/SuiteSparse_config/SuiteSparse_config.h SuiteSparse/SuiteSparse_config/SuiteSparse_config.h
--- SuiteSparse.orig/SuiteSparse_config/SuiteSparse_config.h 2014-10-10 00:19:51.000000000 +0200
+++ SuiteSparse/SuiteSparse_config/SuiteSparse_config.h 2014-10-22 09:40:49.041061515 +0200
@@ -153,13 +153,13 @@
) ;
/* determine which timer to use, if any */
-#ifndef NTIMER
+/*#ifndef NTIMER*/
#ifdef _POSIX_C_SOURCE
#if _POSIX_C_SOURCE >= 199309L
#define SUITESPARSE_TIMER_ENABLED
#endif
#endif
-#endif
+/*#endif*/
/* SuiteSparse printf macro */
#define SUITESPARSE_PRINTF(params) \

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@ -1,193 +0,0 @@
From: toddrme2178@gmail.com
Date: 2018-03-07
Subject: Build shared CSparse
Upstream does not support installing CSparse as a shared library.
We need it is a shared library. This patch modifies the
makefil to make sure it is installed correctly.
--- a/CSparse/Demo/Makefile
+++ b/CSparse/Demo/Makefile
@@ -1,36 +1,48 @@
-CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O
-I = -I../Include
+# CC = cc
+# CF = -O
+
+default: all
+
+include ../../SuiteSparse_config/SuiteSparse_config.mk
LDLIBS += -lm
-CS = $(LDFLAGS) ../Lib/libcsparse.a $(LDLIBS)
-all: lib cs_demo1 cs_demo2 cs_demo3
+I = -I../../include
+
+CS = $(LDFLAGS) -L../../lib -lcsparse $(LDLIBS)
+
+all: library cs_demo1 cs_demo2 cs_demo3 \
+ tests
+
+library:
+ ( cd ../Lib ; $(MAKE) )
+
+tests: library test
+
+test: cs_demo1 cs_demo2 cs_demo3
- ./cs_demo1 < ../Matrix/t1
- ./cs_demo2 < ../Matrix/t1
- - ./cs_demo2 < ../Matrix/ash219
- - ./cs_demo2 < ../Matrix/bcsstk01
- ./cs_demo2 < ../Matrix/fs_183_1
- - ./cs_demo2 < ../Matrix/mbeacxc
- ./cs_demo2 < ../Matrix/west0067
- ./cs_demo2 < ../Matrix/lp_afiro
- - ./cs_demo2 < ../Matrix/bcsstk16
+ - ./cs_demo2 < ../Matrix/ash219
+ - ./cs_demo2 < ../Matrix/mbeacxc
+ - ./cs_demo2 < ../Matrix/bcsstk01
- ./cs_demo3 < ../Matrix/bcsstk01
+ - ./cs_demo2 < ../Matrix/bcsstk16
- ./cs_demo3 < ../Matrix/bcsstk16
-lib:
- ( cd ../Lib ; $(MAKE) )
-
-cs_demo1: lib cs_demo1.c Makefile
+cs_demo1: cs_demo1.c Makefile
$(CC) $(CF) $(I) -o cs_demo1 cs_demo1.c $(CS)
-cs_demo2: lib cs_demo2.c cs_demo.c cs_demo.h Makefile
+cs_demo2: cs_demo2.c cs_demo.c cs_demo.h Makefile
$(CC) $(CF) $(I) -o cs_demo2 cs_demo2.c cs_demo.c $(CS)
-cs_demo3: lib cs_demo3.c cs_demo.c cs_demo.h Makefile
+cs_demo3: cs_demo3.c cs_demo.c cs_demo.h Makefile
$(CC) $(CF) $(I) -o cs_demo3 cs_demo3.c cs_demo.c $(CS)
clean:
- - $(RM) *.o
+ - $(RM) -r $(CLEAN)
purge: distclean
--- a/CSparse/Lib/Makefile
+++ b/CSparse/Lib/Makefile
@@ -15,16 +15,22 @@
# CSparse/Lib. It does not install it for system-wide usage.
LIBRARY = libcsparse
-CF = $(CFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -O
+VERSION = _
+SO_VERSION = _
-I = -I../Include
-RANLIB = ranlib
-ARCHIVE = $(AR) $(ARFLAGS)
-CP = cp -f
+default: library
-AR_TARGET = $(LIBRARY).a
+include ../../SuiteSparse_config/SuiteSparse_config.mk
-all: install
+LDLIBS += -lm
+
+# compile and install in SuiteSparse/lib
+library:
+ $(MAKE) install INSTALL=$(SUITESPARSE)
+
+I = -I../../SuiteSparse_config -I../Include
+
+all: library
CS = cs_add.o cs_amd.o cs_chol.o cs_cholsol.o cs_counts.o cs_cumsum.o \
cs_droptol.o cs_dropzeros.o cs_dupl.o cs_entry.o \
@@ -39,25 +45,43 @@
$(CS): ../Include/cs.h Makefile
%.o: ../Source/%.c ../Include/cs.h
- $(CC) $(CF) $(I) -c $<
+ $(CC) $(CF) $(I) -c $< -o $@
static: $(AR_TARGET)
$(AR_TARGET): $(CS)
- $(ARCHIVE) $@ $^
+ $(ARCHIVE) $@ $^
- $(RANLIB) $@
-# install CSparse in this directory
-install: $(AR_TARGET)
-
-# uninstall CSparse
-uninstall: purge
-
clean:
- - $(RM) *.o
+ - $(RM) -r $(CLEAN)
purge: distclean
distclean: clean
- - $(RM) *.a *.obj *.dll *.dylib *.so *.so.*
+ - $(RM) -r $(PURGE)
+
+# install CSparse
+install: $(AR_TARGET) $(INSTALL_LIB)/$(SO_TARGET)
+
+$(INSTALL_LIB)/$(SO_TARGET): $(CS)
+ @mkdir -p $(INSTALL_LIB)
+ @mkdir -p $(INSTALL_INCLUDE)
+ @mkdir -p $(INSTALL_DOC)
+ $(CC) $(SO_OPTS) $^ -o $@ $(LDLIBS)
+ ( cd $(INSTALL_LIB) ; ln -sf $(SO_TARGET) $(SO_PLAIN) )
+ ( cd $(INSTALL_LIB) ; ln -sf $(SO_TARGET) $(SO_MAIN) )
+ $(CP) ../Include/cs.h $(INSTALL_INCLUDE)
+ $(CP) ../README.txt $(INSTALL_DOC)/CSPARSE_README.txt
+ chmod 755 $(INSTALL_LIB)/$(SO_TARGET)
+ chmod 644 $(INSTALL_INCLUDE)/cs.h
+ chmod 644 $(INSTALL_DOC)/CSPARSE_README.txt
+
+# uninstall CSparse
+uninstall:
+ $(RM) $(INSTALL_LIB)/$(SO_TARGET)
+ $(RM) $(INSTALL_LIB)/$(SO_PLAIN)
+ $(RM) $(INSTALL_LIB)/$(SO_MAIN)
+ $(RM) $(INSTALL_INCLUDE)/cs.h
+ $(RM) $(INSTALL_DOC)/CSPARSE_README.txt
--- a/CSparse/Makefile
+++ b/CSparse/Makefile
@@ -2,6 +2,13 @@
# CSparse Makefile
#------------------------------------------------------------------------------
+SUITESPARSE ?= $(realpath $(CURDIR)/..)
+export SUITESPARSE
+
+default: C
+
+include ../SuiteSparse_config/SuiteSparse_config.mk
+
C:
( cd Lib ; $(MAKE) )
( cd Demo ; $(MAKE) )
@@ -34,9 +41,11 @@
distclean: purge
-install: library
+# install CSparse
+install:
( cd Lib ; $(MAKE) install )
+# uninstall CSparse
uninstall:
( cd Lib ; $(MAKE) uninstall )

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@ -0,0 +1,42 @@
diff -ruN SuiteSparse-7.5.0.orig/Mongoose/CMakeLists.txt SuiteSparse-7.5.0/Mongoose/CMakeLists.txt
--- SuiteSparse-7.5.0.orig/Mongoose/CMakeLists.txt 2024-01-15 06:06:06.714855174 +0800
+++ SuiteSparse-7.5.0/Mongoose/CMakeLists.txt 2024-01-15 06:08:20.629179796 +0800
@@ -316,13 +316,13 @@
RUNTIME_OUTPUT_DIRECTORY ${TESTING_OUTPUT_PATH} )
add_test ( NAME Mongoose_Edge_Separator_Test
- COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -min 1 -max 15 -t edgesep )
+ COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -min 1 -max 15 -t edgesep -k )
add_test ( NAME Mongoose_Edge_Separator_Test_2
- COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -t edgesep -i 21 39 191 1557 1562 353 2468 1470 1380 505 182 201 2331 760 1389 2401 2420 242 250 1530 1533 360 1437 )
+ COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -t edgesep -i 21 39 191 1557 1562 353 2468 1470 1380 505 182 201 2331 760 1389 2401 2420 242 250 1530 1533 360 1437 -k )
add_test ( NAME Mongoose_Weighted_Edge_Separator_Test
- COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -t edgesep -i 2624 )
+ COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -t edgesep -i 2624 -k )
add_test ( NAME Mongoose_Target_Split_Test
- COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -min 1 -max 15 -t edgesep -s 0.3 )
+ COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -min 1 -max 15 -t edgesep -s 0.3 -k )
# Memory Tests
add_executable ( mongoose_test_memory
@@ -338,7 +338,7 @@
RUNTIME_OUTPUT_DIRECTORY ${TESTING_OUTPUT_PATH} )
add_test ( NAME Mongoose_Memory_Test
- COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -min 1 -max 15 -t memory )
+ COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -min 1 -max 15 -t memory -k )
# Performance Test
add_executable ( mongoose_test_performance
@@ -354,9 +354,9 @@
RUNTIME_OUTPUT_DIRECTORY ${TESTING_OUTPUT_PATH} )
add_test ( NAME Mongoose_Performance_Test
- COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -min 1 -max 15 -t performance -p )
+ COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -min 1 -max 15 -t performance -k )
add_test ( NAME Mongoose_Performance_Test_2
- COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -t performance -i 21 39 1557 1562 353 2468 1470 1380 505 182 201 2331 760 1389 2401 2420 242 250 1530 1533 -p )
+ COMMAND ${Python_EXECUTABLE} ${PROJECT_SOURCE_DIR}/Tests/runTests -t performance -i 21 39 1557 1562 353 2468 1470 1380 505 182 201 2331 760 1389 2401 2420 242 250 1530 1533 -k )
if ( WIN32 AND BUILD_SHARED_LIBS )
set_tests_properties ( Mongoose_IO_Test

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from subprocess import call, check_output
import os # For filesystem access
import sys # For sys.exit()
import argparse # For parsing command-line arguments
import urllib.request, urllib.parse, urllib.error # For downloading the ssget index
import ssl
import tarfile # For un-tar/unzipping matrix files
import csv # For reading the ssget index
import shutil # For using 'which'
import platform
# We only need the following matrix ids:
MATRIX_IDs = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 39, 57, 182, 191, 201, 242, 250, 353, 360, 505, 760, 1380, 1389, 1437, 1470, 1530, 1533, 1557, 1562, 2331, 2401, 2420, 2468, 2624]
def getMatrixDirectory():
matrix_dir = "."
if (not os.path.exists(matrix_dir)):
os.makedirs(matrix_dir)
return matrix_dir
def downloadStatsFile(matrix_dir):
stats_file = "ssstats.csv"
url = "http://sparse.tamu.edu/files/ssstats.csv"
with urllib.request.urlopen(url) as response, open(stats_file, 'wb') as out_file:
shutil.copyfileobj(response, out_file)
return stats_file
def runTests():
# Create or locate matrix temporary storage directory
matrix_dir = getMatrixDirectory()
# Download the matrix stats csv file
stats_file = downloadStatsFile(matrix_dir)
with open(stats_file, 'r') as f:
reader = csv.reader(f)
# Matrix IDs are not listed in the stats file - we just have to keep count
matrix_id = 0
sources_initial_num = 4
for row in reader:
if len(row) == 13: # Only rows with 13 elements represent matrix data
matrix_id += 1
# Check if the matrix ID is in the proper range and
# that the matrix is real and symmetric
isInBounds = ((matrix_id >= 1) and (matrix_id <= 2757))
isSquare = (row[2] == row[3])
isReal = (row[5] == '1')
if (isInBounds and isSquare and isReal):
if True:
matrix_name = row[0] + '/' + row[1] + '.tar.gz'
gzip_path = matrix_dir + row[0] + '_' + row[1] + '.tar.gz'
matrix_path = matrix_dir + row[1] + '/' + row[1] + ".mtx"
# print("matrix_name: " + matrix_name)
# print("gzip_path: " + gzip_path)
# print("matrix_path: " + matrix_path)
matrix_exists = os.path.isfile(gzip_path)
if False:
print("matrix exists at gzip_path")
tar = tarfile.open(gzip_path, mode='r:gz')
matrix_files = tar.getnames()
print(matrix_files)
else:
# Download matrix if it doesn't exist
if matrix_id in MATRIX_IDs:
sources_initial_num += 1
try:
url = "https://sparse.tamu.edu/MM/" + matrix_name
print("Source" + str(sources_initial_num) + ": " + url)
except:
url = "http://sparse.tamu.edu/MM/" + matrix_name
print("Source" + str(sources_initial_num) + ": " + url)
runTests()

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addFilter("no-binary")

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-------------------------------------------------------------------
Fri Feb 9 10:10:31 UTC 2024 - Soc Virnyl Estela <uncomfy+openbuildservice@uncomfyhalomacro.pl>
- Cleanup specfile
* Inform that keep-mongoose-test-sources.patch is not for upstream
* Inform that the python file is for convenience for fetching test
sources. See README-suse-maintenance.md.
-------------------------------------------------------------------
Wed Jan 24 13:39:23 UTC 2024 - Atri Bhattacharya <badshah400@gmail.com>
- Set up cmake options just once -- during %build alone.
- Drop usage of cmake internal macros when specifying install
paths.
- CMake >= 3.22 is now required for build; this automatically
drops support for openSUSE < 1650 (i.e. Leap 15.x).
- Drop conditionals for old unsupported distro versions, they
cannot support builds on account of the previous change anyway.
- Drop use of '-ffat-lto-objects' when building with LTO: this is
only needed for static libs, not built here.
- Only unset MALLOC_* when LTO is being used.
- Use once consistent version for all libraries, set to source
tarball.
- Drop more than five-year old Obsoletes/Provides; developers
should use pkgconfig based (Build)Requires or directly use
%{name}-devel.
- Drop suitesparse-rpmlintrc and make -doc packages noarch.
-------------------------------------------------------------------
Tue Jan 16 11:25:21 UTC 2024 - Soc Virnyl Estela <uncomfy+openbuildservice@uncomfyhalomacro.pl>
- Update to version 7.5.1 (boo#1208165):
* SuiteSparse_config: bug fix to SUITESPARSE__VERCODE macro.
* Example 1.6.1: add tests for *__VERSION macros.
- Changes introduced since 7.5.0:
* Suitesparse_config: 7.5.0, to reflect the addition of
GraphBLAS 9.0.0.
* Minor updates to build system, including bug fixes when
specifying a specific BLAS/LAPACK library, and configuration
of *.pc files.
* GraphBLAS 9.0.0: supporting the v2.1 C API; see
https://github.com/GraphBLAS/graphblas-api-c
* Example 1.6.0: using GraphBLAS 9.0.0 and SuiteSparse_config
7.5.0,
* Remove explicit dependencies on OpenMP, libm, GMP, and MPFR.
* Add programs to test the *Config.cmake of each package.
* All other packages (except CSparse): minor updates to build
system.
* Package versions in this release:
- SuiteSparse_config 7.5.0
- AMD 3.3.1
- BTF 2.3.1
- CAMD 3.3.1
- CCOLAMD 3.3.1
- CHOLMOD 5.1.1
- COLAMD 3.3.1
- CSparse 4.3.0 (unchanged from SuiteSparse 7.4.0)
- CXSparse 4.3.1
- Example 1.6.0
- GraphBLAS 9.0.0
- KLU 2.3.1
- LDL 3.3.1
- LAGraph 1.1.1
- SuiteSparse_Mongoose 3.3.1
- ParU 0.1.1
- RBio 4.3.1
- SPEX 2.3.1
- SPQR 4.3.1
- UMFPACK 6.3.1
- Changes introduced since 7.4.0:
* Major change to build system:
- Includes a top-level CMakeLists.txt that builds all
packages.
- Support for pkg-config.
* LAGraph 1.1.0: new package: graph algorithms based on
GraphBLAS
* ParU 0.1.0: new package: parallel unsymmetric multifrontal
method.
* CHOLMOD 5.1.0: full support for sparse single precision
matrices, bug fixes in the GPU Module.
* AMD 3.3.0: minor change for CHOLMOD 5.1.0 tests
* CAMD 3.3.0: minor change for CHOLMOD 5.1.0 tests
* SuiteSparse_config 7.4.0: added wrappers for single-precision
BLAS/LAPACK, added SUITESPARSE_TIME macro.
* *_version: added methods to all package that didn't have them:
AMD, CAMD, COLAMD, CCOLAMD, BTF, CSparse, CXSparse, KLU, BTF,
RBio, SPEX, SPQR, and UMFPACK.
- Add new subpackage suitesparse_mongoose, an executable for
Mongoose.
- Specfile now runs patchelf for broken RPATHs.
- Add keep-mongoose-test-sources.patch. This avoids test sources
getting deleted.
- Remove not needed patchsets:
* build_csparse_shared.patch
* bnc775418-enable-SuiteSparse_time-symbol.patch
- Use BLAS environment variable when choosing over -lopenblas
and -lblas
- Add list-mongoose-test-sources.py: a helper script to list
matrix ids mentioned in the test step of the build of Mongoose's
CMakeLists.txt
- Add new test tarballs for mongoose from
list-mongoose-test-sources.py:
* 1138_bus.tar.gz
* 494_bus.tar.gz
* 662_bus.tar.gz
* 685_bus.tar.gz
* arc130.tar.gz
* ash292.tar.gz
* ash85.tar.gz
* bcspwr01.tar.gz
* bcspwr02.tar.gz
* bcspwr03.tar.gz
* bcspwr09.tar.gz
* bcsstk17.tar.gz
* bcsstm02.tar.gz
* jagmesh7.tar.gz
* lnsp3937.tar.gz
* lshp3466.tar.gz
* sherman1.tar.gz
* sstmodel.tar.gz
* crystm01.tar.gz
* msc04515.tar.gz
* G42.tar.gz
* nasa4704.tar.gz
* fxm3_6.tar.gz
* net25.tar.gz
* LF10000.tar.gz
* Erdos992.tar.gz
* USpowerGrid.tar.gz
* yeast.tar.gz
* c-38.tar.gz
* c-43.tar.gz
* minnesota.tar.gz
* netscience.tar.gz
* netz4504.tar.gz
* delaunay_n13.tar.gz
* tx2010.tar.gz
- _constraints: Increase disk size to 40G
- Add README-suse-maintenance.md
-------------------------------------------------------------------
Wed Apr 26 15:00:16 UTC 2023 - David Anes <david.anes@suse.com>

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