superlu-dist: Upgrade to 6.1.0.

* gnu/packages/patches/superlu-dist-awpm-grid.patch: New file.
* gnu/packages/maths.scm (superlu-dist)[source]: Upgrade to 6.0.0.  Remove
extraneous 'use-modules' in snippet.
[build-system]: Change to cmake-build-system.
[propagated-inputs]:   Replace pt-scotch with pt-scotch32 to match integer
sizes.  Add "parmetis" input, from pt-scotch32.  Move lapack to ...
[inputs]: ...here.  Add openblas and combinatorial-blas.
[arguments]: Replace 'configure' phase with #:configure-flags.  Add
'set-c++-standard' and 'omp-setup' phases.  Remove
'create-install-directories, 'check', and 'install' phases, which are now
handled by cmake.
* gnu/local.mk (dist_patch_DATA): Add patch.
master
Eric Bavier 2018-10-31 14:58:51 -05:00 committed by Eric Bavier
parent fd3733432b
commit 6161141e91
No known key found for this signature in database
GPG Key ID: FD73CAC719D32566
3 changed files with 79 additions and 79 deletions

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@ -1238,6 +1238,7 @@ dist_patch_DATA = \
%D%/packages/patches/soundtouch-CVE-2018-1000223.patch \
%D%/packages/patches/steghide-fixes.patch \
%D%/packages/patches/streamlink-update-test.patch \
%D%/packages/patches/superlu-dist-awpm-grid.patch \
%D%/packages/patches/superlu-dist-scotchmetis.patch \
%D%/packages/patches/swig-guile-gc.patch \
%D%/packages/patches/swish-e-search.patch \

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@ -2298,20 +2298,18 @@ also provides threshold-based ILU factorization preconditioners.")
(define-public superlu-dist
(package
(name "superlu-dist")
(version "5.3.0")
(version "6.1.0")
(source
(origin
(method url-fetch)
(uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/"
"superlu_dist_" version ".tar.gz"))
(sha256
(base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y"))
(base32 "0pqgcgh1yxhfzs99fas3mggajzd5wca3nbyp878rziy74gfk03dl"))
(modules '((guix build utils)))
(snippet
;; Replace the non-free implementation of MC64 with a stub
'(begin
(use-modules (ice-9 regex)
(ice-9 rdelim))
(call-with-output-file "SRC/mc64ad_dist.c"
(lambda (port)
(display "
@ -2327,92 +2325,57 @@ void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g,
abort ();
}\n" port)))
(substitute* "SRC/util.c" ;adjust default algorithm
(("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag")
"RowPerm = NOROWPERM"))
(("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag_MC64;")
;; TODO: set to "LargeDiag_AWPM" once combinatorial-blas has
;; general (i.e. non-square) processor-grid support.
"RowPerm = NOROWPERM;"))
#t))
(patches (search-patches "superlu-dist-scotchmetis.patch"))))
(build-system gnu-build-system)
(patches (search-patches "superlu-dist-scotchmetis.patch"
"superlu-dist-awpm-grid.patch"))))
(build-system cmake-build-system)
(native-inputs
`(("tcsh" ,tcsh)))
(inputs
`(("gfortran" ,gfortran)))
`(("gfortran" ,gfortran)
("blas" ,openblas)
("lapack" ,lapack)
("combblas" ,combinatorial-blas)))
(propagated-inputs
`(("openmpi" ,openmpi) ;headers include MPI heades
("lapack" ,lapack) ;required to link with output library
("pt-scotch" ,pt-scotch))) ;same
`(("mpi" ,openmpi) ;headers include MPI heades
("parmetis" ,pt-scotch32 "metis")
("pt-scotch" ,pt-scotch32)))
(arguments
`(#:parallel-build? #f ;race conditions using ar
`(#:parallel-tests? #f ;tests use MPI and OpenMP
#:configure-flags (list "-DBUILD_SHARED_LIBS:BOOL=YES"
"-DTPL_ENABLE_COMBBLASLIB=YES"
"-DTPL_BLAS_LIBRARIES=-lopenblas"
"-DTPL_LAPACK_LIBRARIES=-llapack"
(string-append "-DTPL_PARMETIS_LIBRARIES="
(string-join
'("ptscotchparmetis" "ptscotch" "ptscotcherr"
"scotchmetis" "scotch" "scotcherr")
";"))
(string-append "-DTPL_PARMETIS_INCLUDE_DIRS="
(assoc-ref %build-inputs "parmetis")
"/include")
"-DTPL_ENABLE_COMBBLASLIB=ON"
(string-append "-DTPL_COMBBLAS_INCLUDE_DIRS="
(assoc-ref %build-inputs "combblas")
"/include/CombBLAS;"
(assoc-ref %build-inputs "combblas")
"/include/BipartiteMatchings")
"-DTPL_COMBBLAS_LIBRARIES=CombBLAS")
#:phases
(modify-phases %standard-phases
(replace 'configure
(lambda* (#:key inputs outputs #:allow-other-keys)
(call-with-output-file "make.inc"
(lambda (port)
(format port "
PLAT =
DSuperLUroot = ~a
DSUPERLULIB = ~a/lib/libsuperlu_dist.a
BLASDEF = -DUSE_VENDOR_BLAS
BLASLIB = -L~a/lib -lblas
PARMETISLIB = -L~a/lib \
-lptscotchparmetis -lptscotch -lptscotcherr -lptscotcherrexit \
-lscotch -lscotcherr -lscotcherrexit
METISLIB = -L~:*~a/lib \
-lscotchmetis -lscotch -lscotcherr -lscotcherrexit
LIBS = $(DSUPERLULIB) $(PARMETISLIB) $(METISLIB) $(BLASLIB)
ARCH = ar
ARCHFLAGS = cr
RANLIB = ranlib
CC = mpicc
PIC = -fPIC
CFLAGS = -O3 -g -DPRNTlevel=0 $(PIC)
NOOPTS = -O0 -g $(PIC)
FORTRAN = mpifort
FFLAGS = -O2 -g $(PIC)
LOADER = $(CC)
CDEFS = -DAdd_"
(getcwd)
(assoc-ref outputs "out")
(assoc-ref inputs "lapack")
(assoc-ref inputs "pt-scotch"))))
#t))
(add-after 'unpack 'remove-broken-symlinks
(add-before 'configure 'set-c++-standard
(lambda _
(for-each delete-file
(find-files "MAKE_INC" "\\.#make\\..*"))
#t))
(add-before 'build 'create-install-directories
(lambda* (#:key outputs #:allow-other-keys)
(for-each
(lambda (dir)
(mkdir-p (string-append (assoc-ref outputs "out")
"/" dir)))
'("lib" "include"))
#t))
(substitute* "CMakeLists.txt"
;; AWPM headers require C++14
(("CMAKE_CXX_STANDARD 11") "CMAKE_CXX_STANDARD 14"))))
(add-before 'check 'mpi-setup
,%openmpi-setup)
(replace 'check
(lambda _
(with-directory-excursion "EXAMPLE"
(invoke "mpirun" "-n" "2"
"./pddrive" "-r" "1" "-c" "2" "g20.rua")
(invoke "mpirun" "-n" "2"
"./pzdrive" "-r" "1" "-c" "2" "cg20.cua"))
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
;; Library is placed in lib during the build phase. Copy over
;; headers to include.
(let* ((out (assoc-ref outputs "out"))
(incdir (string-append out "/include")))
(for-each (lambda (file)
(let ((base (basename file)))
(format #t "installing `~a' to `~a'~%"
base incdir)
(copy-file file
(string-append incdir "/" base))))
(find-files "SRC" ".*\\.h$")))
#t)))))
(add-before 'check 'omp-setup
(lambda _ (setenv "OMP_NUM_THREADS" "1") #t)))))
(home-page (package-home-page superlu))
(synopsis "Parallel supernodal direct solver")
(description

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@ -0,0 +1,36 @@
Create the CombBLAS::SpParMat with the MPI_Comm from the input 'gridinfo_t'.
This prevents a warning/error from CombBLAS about using MPI_COMM_WORLD.
--- a/SRC/AWPM_CombBLAS.hpp
+++ b/SRC/AWPM_CombBLAS.hpp
@@ -52,7 +52,7 @@
{
printf("AWPM only supports square process grid. Retuning without a permutation.\n");
}
- combblas::SpParMat < int_t, double, combblas::SpDCCols<int_t,double> > Adcsc;
+ combblas::SpParMat < int_t, double, combblas::SpDCCols<int_t,double> > Adcsc(grid->comm);
std::vector< std::vector < std::tuple<int_t,int_t,double> > > data(procs);
/* ------------------------------------------------------------
@@ -100,11 +100,10 @@
combblas::AWPM(Adcsc, mateRow2Col, mateCol2Row,true);
// now gather the matching vector
- MPI_Comm World = mateRow2Col.getcommgrid()->GetWorld();
int * rdispls = new int[procs];
int sendcnt = mateRow2Col.LocArrSize();
int * recvcnt = new int[procs];
- MPI_Allgather(&sendcnt, 1, MPI_INT, recvcnt, 1, MPI_INT, World);
+ MPI_Allgather(&sendcnt, 1, MPI_INT, recvcnt, 1, MPI_INT, grid->comm);
rdispls[0] = 0;
for(int i=0; i<procs-1; ++i)
{
@@ -112,7 +111,7 @@
}
int_t *senddata = (int_t *)mateRow2Col.GetLocArr();
- MPI_Allgatherv(senddata, sendcnt, combblas::MPIType<int_t>(), ScalePermstruct->perm_r, recvcnt, rdispls, combblas::MPIType<int_t>(), World);
+ MPI_Allgatherv(senddata, sendcnt, combblas::MPIType<int_t>(), ScalePermstruct->perm_r, recvcnt, rdispls, combblas::MPIType<int_t>(), grid->comm);
delete[] rdispls;
delete[] recvcnt;