Merge pull request #867 from DrTimothyAldenDavis/dev

SuiteSparse 7.8.2
DrTimothyAldenDavis · Aug 24, 2024 · c8c3a9d · c8c3a9d
2 parents 05710d0 + 09cfee7
commit c8c3a9d
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Showing 31 changed files with 615 additions and 99 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -111,7 +111,7 @@ include ( SuiteSparsePolicy )
 
 if ( SUITESPARSE_USE_SYSTEM_GRAPHBLAS )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "graphblas" )
-    find_package ( GraphBLAS 9.3.0 REQUIRED )
+    find_package ( GraphBLAS 9.3.1 REQUIRED )
 else ( )
     if ( "lagraph" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
         # LAGraph requires GraphBLAS.
@@ -137,7 +137,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_UMFPACK )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "umfpack" )
-    find_package ( UMFPACK 6.3.3 REQUIRED )
+    find_package ( UMFPACK 6.3.4 REQUIRED )
 else ( )
     if ( "paru" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
         # ParU requires UMFPACK.
@@ -168,7 +168,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_AMD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "amd" )
-    find_package ( AMD 3.3.2 REQUIRED )
+    find_package ( AMD 3.3.3 REQUIRED )
 else ( )
     if ( "cholmod" IN_LIST SUITESPARSE_ENABLE_PROJECTS
             OR "ldl" IN_LIST SUITESPARSE_ENABLE_PROJECTS
@@ -184,7 +184,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_COLAMD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "colamd" )
-    find_package ( COLAMD 3.3.3 REQUIRED )
+    find_package ( COLAMD 3.3.4 REQUIRED )
 else ( )
     if ( "cholmod" IN_LIST SUITESPARSE_ENABLE_PROJECTS
             OR "spex" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
@@ -198,7 +198,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_CAMD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "camd" )
-    find_package ( CAMD 3.3.2 REQUIRED )
+    find_package ( CAMD 3.3.3 REQUIRED )
 else ( )
     if ( CHOLMOD_CAMD AND "cholmod" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
         # CHOLMOD can optionally use CAMD.
@@ -211,7 +211,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_CCOLAMD )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "ccolamd" )
-    find_package ( CCOLAMD 3.3.3 REQUIRED )
+    find_package ( CCOLAMD 3.3.4 REQUIRED )
 else ( )
     if ( CHOLMOD_CAMD AND "cholmod" IN_LIST SUITESPARSE_ENABLE_PROJECTS )
         # CHOLMOD can optionally use CCOLAMD.
@@ -224,7 +224,7 @@ endif ( )
 
 if ( SUITESPARSE_USE_SYSTEM_SUITESPARSE_CONFIG )
     list ( REMOVE_ITEM SUITESPARSE_ENABLE_PROJECTS "suitesparse_config" )
-    find_package ( SuiteSparse_config 7.8.0 REQUIRED )
+    find_package ( SuiteSparse_config 7.8.2 REQUIRED )
 else ( )
     if ( "mongoose" IN_LIST SUITESPARSE_ENABLE_PROJECTS
             OR "amd" IN_LIST SUITESPARSE_ENABLE_PROJECTS

diff --git a/ChangeLog b/ChangeLog
@@ -1,3 +1,32 @@
+Aug 20, 2024: version 7.8.2
+
+    * LAGraph 1.1.4: bug fix for LAGraph_MMWrite when matrix is dense
+    * SPEX 3.2.1: release date revised, sync with primary SPEX repo
+    * SuiteSparse_config, Example: modified to reflect the release of
+        LAGraph 1.1.4 and SPEX 3.2.1
+    * ParU 0.3.0: added parameter to ParU_Get
+    * Package versions in this release: (* denotes a new version)
+        SuiteSparse_config 7.8.2    *
+        AMD 3.3.3
+        BTF 2.3.2
+        CAMD 3.3.3
+        CCOLAMD 3.3.4
+        CHOLMOD 5.3.0
+        COLAMD 3.3.4
+        CSparse 4.3.2
+        CXSparse 4.4.1
+        Example 1.8.2               *
+        GraphBLAS 9.3.1
+        KLU 2.3.4
+        LDL 3.3.2
+        LAGraph 1.1.4               *
+        SuiteSparse_Mongoose 3.3.4
+        ParU 0.3.0                  *
+        RBio 4.3.3
+        SPEX 3.2.1                  *
+        SPQR 4.3.4
+        UMFPACK 6.3.4
+
 Aug 12, 2024: version 7.8.1
 
     * GraphBLAS 9.3.1: bug fix in creation of JIT package

diff --git a/Example/CMakeLists.txt b/Example/CMakeLists.txt
@@ -53,10 +53,10 @@ message ( STATUS "MY prefix path:    ${CMAKE_PREFIX_PATH}" )
 #-------------------------------------------------------------------------------
 
 # cmake inserts the date and version number into Include/my.h:
-set ( MY_DATE "Aug 12, 2024" )
+set ( MY_DATE "Aug 20, 2024" )
 set ( MY_VERSION_MAJOR 1 )
 set ( MY_VERSION_MINOR 8 )
-set ( MY_VERSION_PATCH 1 )
+set ( MY_VERSION_PATCH 2 )
 
 message ( STATUS "Building MY library version: v"
     ${MY_VERSION_MAJOR}.
@@ -87,7 +87,7 @@ project ( my
 #-------------------------------------------------------------------------------
 
 # look for all SuiteSparse packages:
-find_package ( SuiteSparse_config 7.8.1 REQUIRED )
+find_package ( SuiteSparse_config 7.8.2 REQUIRED )
 find_package ( AMD 3.3.3 REQUIRED )
 find_package ( BTF 2.3.2 REQUIRED )
 find_package ( CAMD 3.3.3 REQUIRED )
@@ -99,11 +99,11 @@ find_package ( GraphBLAS 9.3.1 )
 find_package ( KLU 2.3.4 REQUIRED )
 find_package ( KLU_CHOLMOD 2.3.4 REQUIRED )
 find_package ( LDL 3.3.2 REQUIRED )
-find_package ( LAGraph 1.1.3 )
+find_package ( LAGraph 1.1.4 )
 find_package ( SuiteSparse_Mongoose 3.3.4 REQUIRED )
-find_package ( ParU 0.2.0 REQUIRED )
+find_package ( ParU 0.3.0 REQUIRED )
 find_package ( RBio 4.3.3 REQUIRED )
-find_package ( SPEX 3.2.0 REQUIRED )    # requires GMP and MPFR
+find_package ( SPEX 3.2.1 REQUIRED )    # requires GMP and MPFR
 find_package ( SPQR 4.3.4 REQUIRED )
 find_package ( UMFPACK 6.3.4 REQUIRED )
 

diff --git a/Example/Include/my.h b/Example/Include/my.h
@@ -11,10 +11,10 @@
 // file, since it is constructed from Config/my.h.in by cmake.
 
 // version and date for example user library
-#define MY_DATE "Aug 12, 2024"
+#define MY_DATE "Aug 20, 2024"
 #define MY_MAJOR_VERSION 1
 #define MY_MINOR_VERSION 8
-#define MY_PATCH_VERSION 1
+#define MY_PATCH_VERSION 2
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/Example/Include/my_internal.h b/Example/Include/my_internal.h
@@ -14,8 +14,8 @@
 
 // SuiteSparse include files for C/C++:
 #include "SuiteSparse_config.h"
-#if !defined (SUITESPARSE__VERSION) || SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,8,1)
-#error "This library requires SuiteSparse_config 7.8.1 or later"
+#if !defined (SUITESPARSE__VERSION) || SUITESPARSE__VERSION < SUITESPARSE__VERCODE(7,8,2)
+#error "This library requires SuiteSparse_config 7.8.2 or later"
 #endif
 
 #include "amd.h"
@@ -63,8 +63,8 @@
 
 #if ! defined (NO_LAGRAPH)
     #include "LAGraph.h"
-    #if SUITESPARSE__VERCODE(LAGRAPH_VERSION_MAJOR,LAGRAPH_VERSION_MINOR,LAGRAPH_VERSION_UPDATE) < SUITESPARSE__VERCODE(1,1,3)
-    #error "This library requires LAGraph 1.1.3 or later"
+    #if SUITESPARSE__VERCODE(LAGRAPH_VERSION_MAJOR,LAGRAPH_VERSION_MINOR,LAGRAPH_VERSION_UPDATE) < SUITESPARSE__VERCODE(1,1,4)
+    #error "This library requires LAGraph 1.1.4 or later"
     #endif
 #endif
 
@@ -84,8 +84,8 @@
 #endif
 
 #include "SPEX.h"
-#if !defined (SPEX__VERSION) || SPEX__VERSION < SUITESPARSE__VERCODE(3,2,0)
-#error "This library requires SPEX 3.2.0 or later"
+#if !defined (SPEX__VERSION) || SPEX__VERSION < SUITESPARSE__VERCODE(3,2,1)
+#error "This library requires SPEX 3.2.1 or later"
 #endif
 
 #include "SuiteSparseQR_C.h"

diff --git a/LAGraph/CMakeLists.txt b/LAGraph/CMakeLists.txt
@@ -39,10 +39,10 @@
 cmake_minimum_required ( VERSION 3.20 ) # LAGraph can be built stand-alone
 
 # version of LAGraph
-set ( LAGraph_DATE "Mar 22, 2024" )
+set ( LAGraph_DATE "Aug 20, 2024" )
 set ( LAGraph_VERSION_MAJOR 1 CACHE STRING "" FORCE )
 set ( LAGraph_VERSION_MINOR 1 CACHE STRING "" FORCE )
-set ( LAGraph_VERSION_SUB   3 CACHE STRING "" FORCE )
+set ( LAGraph_VERSION_SUB   4 CACHE STRING "" FORCE )
 
 message ( STATUS "Building LAGraph version: v"
     ${LAGraph_VERSION_MAJOR}.

diff --git a/LAGraph/ChangeLog b/LAGraph/ChangeLog
@@ -1,3 +1,7 @@
+Aug 20, 2024: version 1.1.4
+
+    * fix MMWrite when matrix is dense
+
 Mar 22, 2024: version 1.1.3
 
     * minor updates to build system

diff --git a/LAGraph/data/comments_full.mtx b/LAGraph/data/comments_full.mtx
@@ -2,7 +2,7 @@
 %%GraphBLAS type double
 % comments for full.mtx
 % this file was created by test_MMRead.c
-3 3 9
+3 3
 .646
 .709
 .754

diff --git a/LAGraph/experimental/test/test_BF.c b/LAGraph/experimental/test/test_BF.c
@@ -396,8 +396,6 @@ void test_BF (void)
                     // since d5 is a dense vector filled with infinity, we have
                     // to compare it against d seperaterly
                     OK (GrB_Vector_extractElement (&di, d5, i)) ;
-                    printf ("di %g d[i] %g difference %g\n",
-                        di, d [i], di - d [i]) ;
                     TEST_CHECK (di == d[i]) ;
 
                     // since d5a is a dense vector filled with infinity, we

diff --git a/LAGraph/github_workflows/workflows/build.yml b/LAGraph/github_workflows/workflows/build.yml
@@ -1,4 +1,4 @@
-name: LAGraph CI
+name: LAGraph CI with Builtin GraphBLAS
 
 on:
   workflow_dispatch:
@@ -13,38 +13,34 @@ jobs:
     strategy:
       matrix:
         config:
-         - {grb_version: 7.1.0, conda_grb_package_hash: h27087fc, conda_extension: tar.bz2}
-         - {grb_version: 7.3.0, conda_grb_package_hash: h27087fc, conda_extension: tar.bz2}
-         - {grb_version: 7.4.1, conda_grb_package_hash: hcb278e6, conda_extension: conda}
+        # if there are multiple items in this list, only use should
+        # deployit=true for just one of them.
+         - {grb_version: 9.3.1, deployit: true}
     steps:
     - name: Checkout
       uses: actions/[email protected]
     - name: Install tools for build
       run: |
         sudo apt install -y lcov
-    - name: Get GraphBLAS binaries
+    - name: Build GraphBLAS
       run: |
-        mkdir graphblas-binaries
-        cd graphblas-binaries
-        wget --quiet https://anaconda.org/conda-forge/graphblas/${{ matrix.config.grb_version }}/download/linux-64/graphblas-${{ matrix.config.grb_version }}-${{ matrix.config.conda_grb_package_hash }}_0.${{ matrix.config.conda_extension }}
-        if [ ${{ matrix.config.conda_extension }} == "tar.bz2" ]; then
-          tar xf graphblas-${{ matrix.config.grb_version }}-${{ matrix.config.conda_grb_package_hash }}_0.${{ matrix.config.conda_extension }}
-        else
-          unzip graphblas-${{ matrix.config.grb_version }}-${{ matrix.config.conda_grb_package_hash }}_0.${{ matrix.config.conda_extension }}
-          tar xf pkg-graphblas-${{ matrix.config.grb_version }}-${{ matrix.config.conda_grb_package_hash }}_0.tar.zst
-        fi
+        git clone https://github.com/DrTimothyAldenDavis/GraphBLAS.git
+        cd GraphBLAS
+        git checkout tags/v${{ matrix.config.grb_version }}
+        make compact
+        sudo make install
         cd ..
     - name: Build project
       run: |
-        export GRAPHBLAS_INCLUDE_DIR=`pwd`/graphblas-binaries/include
-        export GRAPHBLAS_LIBRARY=`pwd`/graphblas-binaries/lib/libgraphblas.so
+        export GRAPHBLAS_INCLUDE_DIR=`pwd`/GraphBLAS/include/suitesparse
+        export GRAPHBLAS_LIBRARY=`pwd`/GraphBLAS/lib/libgraphblas.so
         cd build
         cmake .. -DCOVERAGE=1 -DGRAPHBLAS_INCLUDE_DIR=${GRAPHBLAS_INCLUDE_DIR} -DGRAPHBLAS_LIBRARY=${GRAPHBLAS_LIBRARY}
         JOBS=2 make
         make test_coverage
     - name: Deploy
       uses: JamesIves/[email protected]
-      if: matrix.config.grb_version == '7.4.1' && github.event_name == 'push' && github.ref == 'refs/heads/stable'
+      if: matrix.config.deployit && github.event_name == 'push' && github.ref == 'refs/heads/stable'
       with:
         branch: gh-pages
         folder: build/test_coverage/
@@ -59,9 +55,7 @@ jobs:
     strategy:
       matrix:
         config:
-         - {grb_version: 7.1.0, conda_grb_package_hash: h7881ed4, conda_extension: tar.bz2}
-         - {grb_version: 7.3.0, conda_grb_package_hash: ha894c9a, conda_extension: tar.bz2}
-         - {grb_version: 7.4.1, conda_grb_package_hash: ha894c9a, conda_extension: conda}
+         - {grb_version: 9.3.1}
     steps:
     - name: Checkout
       uses: actions/[email protected]
@@ -70,22 +64,18 @@ jobs:
         brew tap-new libomp/cask
         brew extract --version=14.0.6 libomp libomp/cask
         brew install [email protected]
-    - name: Get GraphBLAS binaries
+    - name: Build GraphBLAS
       run: |
-        mkdir graphblas-binaries
-        cd graphblas-binaries
-        wget --quiet https://anaconda.org/conda-forge/graphblas/${{ matrix.config.grb_version }}/download/osx-64/graphblas-${{ matrix.config.grb_version }}-${{ matrix.config.conda_grb_package_hash }}_0.${{ matrix.config.conda_extension }}
-        if [ ${{ matrix.config.conda_extension }} == "tar.bz2" ]; then
-          tar xf graphblas-${{ matrix.config.grb_version }}-${{ matrix.config.conda_grb_package_hash }}_0.${{ matrix.config.conda_extension }}
-        else
-          unzip graphblas-${{ matrix.config.grb_version }}-${{ matrix.config.conda_grb_package_hash }}_0.${{ matrix.config.conda_extension }}
-          tar xf pkg-graphblas-${{ matrix.config.grb_version }}-${{ matrix.config.conda_grb_package_hash }}_0.tar.zst
-        fi
+        git clone https://github.com/DrTimothyAldenDavis/GraphBLAS.git
+        cd GraphBLAS
+        git checkout tags/v${{ matrix.config.grb_version }}
+        make compact
+        sudo make install
         cd ..
     - name: Build project
       run: |
-        export GRAPHBLAS_INCLUDE_DIR=`pwd`/graphblas-binaries/include
-        export GRAPHBLAS_LIBRARY=`pwd`/graphblas-binaries/lib/libgraphblas.dylib
+        export GRAPHBLAS_INCLUDE_DIR=`pwd`/GraphBLAS/include/suitesparse
+        export GRAPHBLAS_LIBRARY=`pwd`/GraphBLAS/lib/libgraphblas.dylib
         # adding an extra line to the CMakeLists.txt file to locate the libomp instance installed by brew
         echo 'include_directories("/usr/local/opt/libomp/include")' | cat - CMakeLists.txt
         cd build

diff --git a/LAGraph/include/LAGraph.h b/LAGraph/include/LAGraph.h
@@ -37,10 +37,10 @@
 // See also the LAGraph_Version utility method, which returns these values.
 // These definitions are derived from LAGraph/CMakeLists.txt.
 
-#define LAGRAPH_DATE "Mar 22, 2024"
+#define LAGRAPH_DATE "Aug 20, 2024"
 #define LAGRAPH_VERSION_MAJOR  1
 #define LAGRAPH_VERSION_MINOR  1
-#define LAGRAPH_VERSION_UPDATE 3
+#define LAGRAPH_VERSION_UPDATE 4
 
 //==============================================================================
 // include files and helper macros

diff --git a/LAGraph/src/utility/LAGraph_MMWrite.c b/LAGraph/src/utility/LAGraph_MMWrite.c
@@ -459,8 +459,18 @@ int LAGraph_MMWrite
         nvals_to_print = nself_edges + (nvals - nself_edges) / 2 ;
     }
 
-    FPRINTF (f, "%" PRIu64 " %" PRIu64 " %" PRIu64 "\n",
-        nrows, ncols, nvals_to_print) ;
+    if (MM_fmt == MM_array)
+    {
+        // write `nrows ncols` if the array format is used
+        FPRINTF (f, "%" PRIu64 " %" PRIu64 "\n",
+            nrows, ncols) ;
+    }
+    else
+    {
+        // otherwise write `nrows ncols nvals` for the coordinate format
+        FPRINTF (f, "%" PRIu64 " %" PRIu64 " %" PRIu64 "\n",
+            nrows, ncols, nvals_to_print) ;
+    }
 
     if (nvals_to_print == 0)
     {

diff --git a/ParU/CMakeLists.txt b/ParU/CMakeLists.txt
@@ -13,9 +13,9 @@
 # cmake 3.22 is required to find the BLAS in SuiteSparse_config
 cmake_minimum_required ( VERSION 3.22 )
 
-set ( PARU_DATE "Aug 2, 2024" )
+set ( PARU_DATE "Aug 20, 2024" )
 set ( PARU_VERSION_MAJOR  0 CACHE STRING "" FORCE )
-set ( PARU_VERSION_MINOR  2 CACHE STRING "" FORCE )
+set ( PARU_VERSION_MINOR  3 CACHE STRING "" FORCE )
 set ( PARU_VERSION_UPDATE 0 CACHE STRING "" FORCE )
 
 message ( STATUS "Building PARU version: v"
@@ -423,14 +423,20 @@ if ( SUITESPARSE_DEMOS )
 
     if ( PARU_HAS_OPENMP )
         add_executable ( paru_demo "Demo/paru_demo.cpp" )
+        add_executable ( paru_benchmark "Demo/paru_benchmark.cpp" )
         if ( BUILD_SHARED_LIBS )
             target_link_libraries ( paru_demo PUBLIC ParU )
+            target_link_libraries ( paru_benchmark PUBLIC ParU )
         else ( )
             target_link_libraries ( paru_demo PUBLIC ParU_static )
+            target_link_libraries ( paru_benchmark PUBLIC ParU_static )
         endif ( )
         target_link_libraries ( paru_demo
             PUBLIC SuiteSparse::CHOLMOD SuiteSparse::UMFPACK
             SuiteSparse::SuiteSparseConfig OpenMP::OpenMP_CXX )
+        target_link_libraries ( paru_benchmark
+            PUBLIC SuiteSparse::CHOLMOD SuiteSparse::UMFPACK
+            SuiteSparse::SuiteSparseConfig OpenMP::OpenMP_CXX )
 
         add_executable ( paru_democ "Demo/paru_democ.c" )
         if ( BUILD_SHARED_LIBS )

diff --git a/ParU/Config/ParU.h.in b/ParU/Config/ParU.h.in
@@ -139,6 +139,7 @@ typedef enum
     // int64_t parameter, for ParU_Get only:
     PARU_CONTROL_OPENMP = 1013,               // if ParU compiled with OpenMP;
                                               // (for ParU_Get only, not set)
+    PARU_CONTROL_NUM_THREADS = 1014,          // actual number of threads used
 
     // double parameters for ParU_Set and ParU_Get:
     PARU_CONTROL_PIVOT_TOLERANCE = 2001,      // pivot tolerance

diff --git a/ParU/Demo/.gitignore b/ParU/Demo/.gitignore
@@ -0,0 +1,3 @@
+# Ignore the following:
+Res
+!.gitignore