Merge pull request #2 from DrTimothyAldenDavis/master

v3.2.1

CMakeLists.txt

@@ -57,10 +57,10 @@ if ( CMAKE_VERSION VERSION_GREATER "3.0" )
 endif ( )
 
 # version of SuiteSparse:GraphBLAS
-set ( GraphBLAS_DATE "Feb 20, 2020" )
+set ( GraphBLAS_DATE "Mar 10, 2020" )
 set ( GraphBLAS_VERSION_MAJOR 3 )
 set ( GraphBLAS_VERSION_MINOR 2 )
-set ( GraphBLAS_VERSION_SUB   0 )
+set ( GraphBLAS_VERSION_SUB   1 )
 
 # GraphBLAS C API Specification version, at graphblas.org
 set ( GraphBLAS_API_DATE "May 18, 2018" )
@@ -107,6 +107,10 @@ if ( GB_BURBLE )
     set ( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DGB_BURBLE=1 " )
 endif ( )
 
+if ( GBCOMPACT )
+    set ( CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} -DGBCOMPACT=1 " )
+endif ( )
+
 #-------------------------------------------------------------------------------
 # configure GraphBLAS
 #-------------------------------------------------------------------------------

Demo/Include/simple_timer.h

@@ -36,19 +36,35 @@
 
 #include <time.h>
 
-#if defined ( __linux__ )
-#include <sys/time.h>
-#endif
+/* -------------------------------------------------------------------------- */
+/* decide which timer to use */
+/* -------------------------------------------------------------------------- */
 
 #if defined ( _OPENMP )
-#include <omp.h>
-#endif
 
-#if defined ( __MACH__ )
-#include <mach/clock.h>
-#include <mach/mach.h>
+    /* if OpenMP is available, use omp_get_wtime */
+    #include <omp.h>
+
+#elif defined ( __linux__ ) || defined ( __GNU__ )
+
+    /* otherwise, on Linux/GNU, use clock_gettime. May require -lrt */
+    #include <sys/time.h>
+
+#elif defined ( __MACH__ ) && defined ( __APPLE__ )
+
+    /* otherwise, on the Mac, use the MACH timer */
+    #include <mach/clock.h>
+    #include <mach/mach.h>
+
+#else
+
+    /* Finally, the ANSI C11 clock() function is used if no other timer
+       is available. */
+
 #endif
 
+/* -------------------------------------------------------------------------- */
+
 void simple_tic         /* returns current time in seconds and nanoseconds */
 (
     double tic [2]      /* tic [0]: seconds, tic [1]: nanoseconds */

Demo/Source/simple_timer.c

@@ -27,7 +27,7 @@ void simple_tic         /* returns current time in seconds and nanoseconds */
         tic [0] = omp_get_wtime ( ) ;
         tic [1] = 0 ;
 
-    #elif defined ( __linux__ )
+    #elif defined ( __linux__ ) || defined ( __GNU__ )
 
         /* Linux has a very low resolution clock() function, so use the high
            resolution clock_gettime instead.  May require -lrt */
@@ -36,8 +36,9 @@ void simple_tic         /* returns current time in seconds and nanoseconds */
         tic [0] = (double) t.tv_sec ;
         tic [1] = (double) t.tv_nsec ;
 
-    #elif defined ( __MACH__ )
+    #elif defined ( __MACH__ ) && defined ( __APPLE__ )
 
+        /* otherwise, on the Mac, use the MACH timer */
         clock_serv_t cclock ;
         mach_timespec_t t ;
         host_get_clock_service (mach_host_self ( ), SYSTEM_CLOCK, &cclock) ;

Doc/ChangeLog

@@ -1,3 +1,16 @@
+Version 3.2.1, Mar 10, 2020
+
+    * GAP benchmarks in MATLAB: in GraphBLAS/GraphBLAS/GAP (all but CC).
+    * atomic read/write: faster atomics for icc (see Source/GB_atomics.h)
+    * install name for Mac: in alternative/Makefile and Tcov/Makefile
+    * enable -DGBCOMPACT from CMake: for faster Travis builds
+    * MATLAB interface: better error message in GrB.reduce
+    * MATLAB triangle count: added sorting heuristic in GrB.tricount.
+    * bug fix for GraphBLAS/Demo/simple_timer: better selection of which
+        timer to use; simple_timer.[ch] made consistent.
+    * no bug fixes needed in primary GraphBLAS library: just in Demo, test,
+        and alternative/Makefile.
+
 Version 3.2.0, Feb 20, 2020
 
     * GxB_*_define for user-defined compile-time objects: removed.  Not
@@ -19,6 +32,7 @@ Version 3.2.0, Feb 20, 2020
         subset of "#pragma omp atomic" statements.  This will be resolved in a
         future version; in the meantime, use v3.1.2 with MS Visual Studio
         instead of v3.2.0.
+    * no bug fixes
 
 Version 3.1.2, Dec 16, 2019
 

Doc/GraphBLAS_version.tex

@@ -1,5 +1,5 @@
 % version of SuiteSparse:GraphBLAS
 \date{VERSION
-3.2.0,
-Feb 20, 2020}
+3.2.1,
+Mar 10, 2020}
 

GraphBLAS/@GrB/private/mexfunctions/gbvreduce.c

@@ -81,6 +81,9 @@ void mexFunction
     OK (GxB_Matrix_type (&atype, A)) ;
     if (C != NULL)
     { 
+        CHECK_ERROR (C->is_hyper, "Cin cannot be hypersparse") ;
+        CHECK_ERROR (!(C->is_csc), "Cin must be stored by column") ;
+        CHECK_ERROR (!GB_VECTOR_OK (C), "Cin must be a column vector") ;
         OK (GxB_Matrix_type (&ctype, C)) ;
     }
 

GraphBLAS/@GrB/tricount.m

@@ -1,4 +1,4 @@
-function s = tricount (A, check)
+function s = tricount (A, arg2, arg3)
 %GRB.TRICOUNT count triangles in a matrix.
 % s = GrB.tricount (A) counts the number of triangles in the matrix A.
 % spones (A) must be symmetric; results are undefined if spones (A) is
@@ -7,22 +7,75 @@
 % To check the input matrix A, use GrB.tricount (A, 'check').  This check
 % takes additional time so by default the input is not checked.
 %
-% See also GrB.ktruss.
+% If d is a vector of length n with d(i) equal to the degree of node i,
+% then s = tricount (A, d) can be used.  Otherwise, tricount must compute
+% the degrees first.
+%
+% See also GrB.ktruss, GrB.entries.
+%
+% ADDED: sort if warranted.  See LAGraph_tricount.
 
 [m, n] = size (A) ;
 if (m ~= n)
     gb_error ('A must be square') ;
 end
-if (nargin < 2)
-    check = false ;
-else
-    check = isequal (check, 'check') ;
+
+d = [ ] ;
+check = false ;
+
+if (nargin == 2)
+    if (ischar (arg2))
+        % s = tricount (A, 'check')
+        check = isequal (arg2, 'check') ;
+    else
+        % s = tricount (A, d)
+        d = arg2 ;
+    end
+elseif (nargin == 3)
+    if (ischar (arg2))
+        % s = tricount (A, 'check', d)
+        check = isequal (arg2, 'check') ;
+        d = arg3 ;
+    else
+        % s = tricount (A, d, 'check')
+        d = arg2 ;
+        check = isequal (arg3, 'check') ;
+    end
 end
 
 if (check && ~issymmetric (spones (A)))
     gb_error ('pattern of A must be symmetric') ;
 end
 
+if (isequal (class (d), 'GrB'))
+    d = double (d) ;
+end
+
+% determine if A should be sorted first
+if (n > 1000 && GrB.entries (A) >= 10*n)
+    if (isempty (d))
+        % compute the degree of each node, if not provided on input
+        if (GrB.isbyrow (A))
+            d = double (GrB.entries (A, 'row', 'degree')) ;
+        else
+            d = double (GrB.entries (A, 'col', 'degree')) ;
+        end
+    end
+    % sample the degree
+    p = randperm (n, 1000) ;
+    sample = d (randperm (n, 1000)) ;
+    dmean = full (mean (sample)) ;
+    dmed  = full (median (sample)) ;
+    % fprintf ('mean degree: %g median: %g\n', dmean, dmed) ;
+    if (dmean > 4 * dmed)
+        % sort if the average degree is very high compared to the median
+        % fprintf ('sorting A first\n') ;
+        [~, p] = sort (d, 'descend') ;
+        A = A (p,p) ;
+        clear p
+    end
+end
+
 % C, L, and U will have the same format as A
 C = GrB (n, n, 'int64', GrB.format (A)) ;
 L = tril (A, -1) ;

GraphBLAS/GAP/Contents.m

@@ -1,13 +1,17 @@
 % GAP: GAP benchmark methods in MATLAB (in progress)
 %
-% Files
-%   gap          - run GAP benchmarks
-%   gap_bfs      - run bfs for the GAP benchmark
-%   gap_pagerank - PageRank of a graph (GAP benchmark algorithm)
-%   gap_pr       - run pagerank for the GAP benchmark
-%   gap_tc       - run tricount for the GAP benchmark
-%   tric         - triangle countting tests
-%   ttest        - run triangle counting tests
+%   gap            - run 5 GAP benchmarks (BFS, PR, BC, TC, SSSP; not CC)
+%   gap_bfs        - run bfs for the GAP benchmark
+%   gap_pr         - run pagerank for the GAP benchmark
+%   gap_pagerank   - PageRank of a graph (GAP benchmark algorithm)
+%   gap_tc         - run tricount for the GAP benchmark
+%   tric           - triangle counting tests
+%   ttest          - run triangle counting tests
+%   gap_bc         - run centrality for the GAP benchmark
+%   gap_centrality - batch betweenness centrality of a graph, via GraphBLAS
+%   gap_sssp12c    - single source shortest path, via delta stepping, for GAP
+%   gap_sssp12     - single source shortest path, via delta stepping, for GAP
+%   gap_sssp       - run SSSP for the GAP benchmark
 
 % SuiteSparse:GraphBLAS, Timothy A. Davis, (c) 2017-2020, All Rights Reserved.
 % http://suitesparse.com   See GraphBLAS/Doc/License.txt for license.

GraphBLAS/GAP/bctest.m

@@ -0,0 +1,8 @@
+
+s = [20 34 14 51] ;
+Prob = ssget ('HB/west0067') ;
+A = GrB (Prob.A, 'by row') ;
+A = GrB (A, 'logical')
+
+c = gap_centrality (s, A)
+

GraphBLAS/GAP/cover.mtx

@@ -0,0 +1,17 @@
+%%MatrixMarket matrix coordinate real general
+%%GraphBLAS GrB_INT32
+% Matrix from the cover of "Graph Algorithms in the Language of Linear
+% Algebra", Kepner and Gilbert.  Note that cover shows A'.  This is A.
+7 7 12
+4 1 4
+1 2 2
+4 3 1
+6 3 5
+7 3 9
+1 4 7
+7 4 1
+2 5 5
+7 5 1
+3 6 1
+5 6 7
+2 7 8