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03/04: superlu-dist: Upgrade to 6.1.0.
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From: |
guix-commits |
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Subject: |
03/04: superlu-dist: Upgrade to 6.1.0. |
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Date: |
Fri, 25 Jan 2019 14:10:12 -0500 (EST) |
bavier pushed a commit to branch master
in repository guix.
commit 6161141e9181ca82f151779f8048b28e093a025f
Author: Eric Bavier <address@hidden>
Date: Wed Oct 31 14:58:51 2018 -0500
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.
---
gnu/local.mk | 1 +
gnu/packages/maths.scm | 121 ++++++++--------------
gnu/packages/patches/superlu-dist-awpm-grid.patch | 36 +++++++
3 files changed, 79 insertions(+), 79 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index d3b40b3..c76653b 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -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 \
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 648cbfb..e2f3d84 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -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
diff --git a/gnu/packages/patches/superlu-dist-awpm-grid.patch
b/gnu/packages/patches/superlu-dist-awpm-grid.patch
new file mode 100644
index 0000000..d6cb8e5
--- /dev/null
+++ b/gnu/packages/patches/superlu-dist-awpm-grid.patch
@@ -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;