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gnu: Add Combinatorial BLAS.

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* 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.
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Eric Bavier 2018-10-23 16:50:50 -05:00 committed by Eric Bavier
parent 519be98c35
commit a6b9ebc2fc
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4 changed files with 134 additions and 0 deletions
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2
gnu/local.mk
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@ -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 \

51
gnu/packages/maths.scm
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@ -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 @@ (define-public sundials-openmpi
(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

67
gnu/packages/patches/combinatorial-blas-awpm.patch Normal file
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@ -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

14
gnu/packages/patches/combinatorial-blas-io-fix.patch Normal file
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@ -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;
}