01/04: gnu: Add Combinatorial BLAS.

[guix-commits]

bavier pushed a commit to branch master
in repository guix.

commit a6b9ebc2fc92a72ca8a1e61e2d321804eec9d738
Author: Eric Bavier <address@hidden>
Date:   Tue Oct 23 16:50:50 2018 -0500

    gnu: Add Combinatorial BLAS.
    
    * gnu/packages/maths.scm (combinatorial-blas): New variable.
    * gnu/packages/patches/combinatorial-blas-awpm.patch,
    gnu/packages/patches/combinatorial-blas-io-fix.patch: New files
    * gnu/local.mk(dist_patch_DATA): Add them.
---
 gnu/local.mk                                       |  2 +
 gnu/packages/maths.scm                             | 51 ++++++++++++++++
 gnu/packages/patches/combinatorial-blas-awpm.patch | 67 ++++++++++++++++++++++
 .../patches/combinatorial-blas-io-fix.patch        | 14 +++++
 4 files changed, 134 insertions(+)

diff --git a/gnu/local.mk b/gnu/local.mk
index 7500571..fb19c1a 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -692,6 +692,8 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/clucene-pkgconfig.patch                 \
   %D%/packages/patches/clx-remove-demo.patch                   \
   %D%/packages/patches/coda-use-system-libs.patch              \
+  %D%/packages/patches/combinatorial-blas-awpm.patch           \
+  %D%/packages/patches/combinatorial-blas-io-fix.patch         \
   %D%/packages/patches/cool-retro-term-dont-check-uninit-member.patch  \
   %D%/packages/patches/cool-retro-term-fix-array-size.patch    \
   %D%/packages/patches/cool-retro-term-memory-leak-1.patch     \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 2f52b4a..b53fa7f 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -48,6 +48,7 @@
 
 (define-module (gnu packages maths)
   #:use-module (ice-9 regex)
+  #:use-module (ice-9 match)
   #:use-module (gnu packages)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -4215,3 +4216,53 @@ easily be incorporated into existing simulation codes.")
            (add-before 'check 'mpi-setup
             ,%openmpi-setup)))))
     (synopsis "SUNDIALS with OpenMPI support")))
+
+(define-public combinatorial-blas
+  (package
+    (name "combinatorial-blas")
+    (version "1.6.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://eecs.berkeley.edu/~aydin/CombBLAS_FILES/";
+                           "CombBLAS_beta_"
+                           (match (string-split version #\.)
+                            ((major minor patch)
+                             (string-append major minor "_" patch))) ;e.g. 
"16_2"
+                           ".tgz"))
+       (sha256
+        (base32
+         "1a9wbgdqyy1whhfc0yl0yqkax3amnqa6iihhq48d063gc0jwfd9a"))
+       (patches (search-patches "combinatorial-blas-awpm.patch"
+                                "combinatorial-blas-io-fix.patch"))))
+    (build-system cmake-build-system)
+    (inputs
+     `(("mpi" ,openmpi)
+       ("test-data" ,(origin
+                       (method url-fetch)
+                       (uri (string-append 
"https://people.eecs.berkeley.edu/~aydin/";
+                                           
"CombBLAS_FILES/testdata_combblas1.6.1.tgz"))
+                       (sha256
+                        (base32
+                         
"01y2781cy3fww7znmidrp85mf8zx0c905w5vzvk1mgrmhhynim87"))))))
+    (arguments
+     `(#:configure-flags '("-DBUILD_SHARED_LIBS:BOOL=YES"
+                           "-DCMAKE_CXX_FLAGS=-DUSE_FUNNEL")
+       #:parallel-tests? #f             ;tests use 'mpiexec -n4'
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'mpi-setup
+           ,%openmpi-setup)
+         (add-before 'check 'test-setup
+           (lambda* (#:key inputs #:allow-other-keys)
+             (setenv "OMP_NUM_THREADS" "2")
+             (invoke "tar" "xf" (assoc-ref inputs "test-data")))))))
+    (home-page "https://people.eecs.berkeley.edu/~aydin/CombBLAS/html/";)
+    (synopsis "Linear algebra primitives for graph analytics")
+    (description "The Combinatorial BLAS (CombBLAS) is an extensible
+distributed-memory parallel graph library offering a small but powerful set of
+linear algebra primitives specifically targeting graph analytics.")
+    (license (list
+              license:gpl2+             ;include/psort/(funnel|sort)*.h
+              license:x11               ;usort and psort
+              license:bsd-3))))         ;CombBLAS and MersenneTwister.h
diff --git a/gnu/packages/patches/combinatorial-blas-awpm.patch 
b/gnu/packages/patches/combinatorial-blas-awpm.patch
new file mode 100644
index 0000000..86d4ab2
--- /dev/null
+++ b/gnu/packages/patches/combinatorial-blas-awpm.patch
@@ -0,0 +1,67 @@
+Install BipartiteMatchings headers for SuperLU_DIST.
+
+--- a/BipartiteMatchings/ApproxWeightPerfectMatching.h
++++ b/BipartiteMatchings/ApproxWeightPerfectMatching.h
+@@ -9,7 +9,7 @@
+ #ifndef ApproxWeightPerfectMatching_h
+ #define ApproxWeightPerfectMatching_h
+ 
+-#include "../CombBLAS.h"
++#include "CombBLAS.h"
+ #include "BPMaximalMatching.h"
+ #include "BPMaximumMatching.h"
+ #include <parallel/algorithm>
+--- a/BipartiteMatchings/BPMaximalMatching.h
++++ b/BipartiteMatchings/BPMaximalMatching.h
+@@ -1,7 +1,7 @@
+ #ifndef BP_MAXIMAL_MATCHING_H
+ #define BP_MAXIMAL_MATCHING_H
+ 
+-#include "../CombBLAS.h"
++#include "CombBLAS.h"
+ #include <iostream>
+ #include <functional>
+ #include <algorithm>
+--- a/BipartiteMatchings/BPMaximumMatching.h
++++ b/BipartiteMatchings/BPMaximumMatching.h
+@@ -1,7 +1,7 @@
+ #ifndef BP_MAXIMUM_MATCHING_H
+ #define BP_MAXIMUM_MATCHING_H
+ 
+-#include "../CombBLAS.h"
++#include "CombBLAS.h"
+ #include <mpi.h>
+ #include <sys/time.h>
+ #include <iostream>
+--- a/BipartiteMatchings/MatchingDefs.h
++++ b/BipartiteMatchings/MatchingDefs.h
+@@ -9,7 +9,7 @@
+ #ifndef MatchingDefs_h
+ #define MatchingDefs_h
+ 
+-#include "../CombBLAS.h"
++#include "CombBLAS.h"
+ #include <iostream>
+ 
+ namespace combblas {
+--- a/BipartiteMatchings/Utility.h
++++ b/BipartiteMatchings/Utility.h
+@@ -1,7 +1,7 @@
+ #ifndef BP_UTILITY_H
+ #define BP_UTILITY_H
+ 
+-#include "../CombBLAS.h"
++#include "CombBLAS.h"
+ 
+ namespace combblas {
+ 
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -68,6 +68,7 @@ set_property(TARGET CombBLAS PROPERTY VERSION 
${CombBLAS_VERSION})
+ # installation
+ install(DIRECTORY include/ DESTINATION include)
+ install(DIRECTORY psort-1.0/include/ DESTINATION include)
++install(DIRECTORY BipartiteMatchings DESTINATION include FILES_MATCHING 
PATTERN "*.h")
+ install(TARGETS CombBLAS EXPORT CombBLASTargets
+   LIBRARY DESTINATION lib
+   ARCHIVE DESTINATION lib
diff --git a/gnu/packages/patches/combinatorial-blas-io-fix.patch 
b/gnu/packages/patches/combinatorial-blas-io-fix.patch
new file mode 100644
index 0000000..0ad28e5
--- /dev/null
+++ b/gnu/packages/patches/combinatorial-blas-io-fix.patch
@@ -0,0 +1,14 @@
+IO not appropriate in the context of a sorting routine, and in any case the
+proper headers are not included, so gcc emits an undefined symbol error.
+Remove the "printf" statement.
+
+--- CombBLAS_beta_16_2/usort/include/usort/seqUtils.tcc
++++ CombBLAS_beta_16_2/usort/include/usort/seqUtils.tcc
+@@ -142,7 +142,6 @@
+       }
+         if ( (a[nmax]==a[nmin]) && (ctr==0) )
+         {
+-          printf("All the numbers are identical, the list is sorted\n");
+           return;
+         }
+