diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 237 |
1 files changed, 133 insertions, 104 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index cccc3636a4..871b4a5a3f 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) @@ -2297,20 +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 " @@ -2326,92 +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 @@ -2423,25 +2387,25 @@ implemented in ANSI C, and MPI for communications.") (define-public scotch (package (name "scotch") - (version "6.0.5a") + (version "6.0.6") (source (origin (method url-fetch) (uri (string-append "https://gforge.inria.fr/frs/download.php/" "latestfile/298/scotch_" version ".tar.gz")) (sha256 - (base32 "0vsmgjz8qv80di3ljmc7hbdsizxxxwy2b9rgd2fl1mdc6dgbj8av")) - (patches (search-patches "scotch-test-threading.patch" - "scotch-build-parallelism.patch" - "scotch-graph-induce-type-64.patch" - "scotch-graph-diam-64.patch")))) + (base32 "1ky4k9r6jvajhqaqnnx6h8fkmds2yxgp70dpr1qzwcyhi2nhqvv8")) + (patches (search-patches "scotch-build-parallelism.patch" + "scotch-integer-declarations.patch")))) (build-system gnu-build-system) (inputs `(("zlib" ,zlib) ("flex" ,flex) ("bison" ,bison))) + (outputs '("out" "metis")) (arguments - `(#:phases + `(#:make-flags (list (string-append "prefix=" %output)) + #:phases (modify-phases %standard-phases (add-after 'unpack 'chdir-to-src @@ -2476,7 +2440,7 @@ YACC = bison -pscotchyy -y -b y '("COMMON_FILE_COMPRESS_GZ" "COMMON_PTHREAD" "COMMON_RANDOM_FIXED_SEED" - "INTSIZE64" ;use 'long' instead of 'int' + "INTSIZE64" ;use 'int64_t' ;; Prevents symbolc clashes with libesmumps "SCOTCH_RENAME" ;; XXX: Causes invalid frees in superlu-dist tests @@ -2489,22 +2453,21 @@ YACC = bison -pscotchyy -y -b y (invoke "make" (format #f "-j~a" (parallel-job-count)) "esmumps"))) - (replace - 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (mkdir out) - (invoke "make" - (string-append "prefix=" out) - "install") - ;; esmumps files are not installed with the above - (for-each (lambda (f) - (copy-file f (string-append out "/include/" f))) - (find-files "../include" ".*esmumps.h$")) - (for-each (lambda (f) - (copy-file f (string-append out "/lib/" f))) - (find-files "../lib" "^lib.*esmumps.*")) - #t)))))) + (add-before 'install 'make-install-dirs + (lambda* (#:key outputs #:allow-other-keys) + (mkdir (assoc-ref outputs "out")))) + (add-after 'install 'install-metis + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "metis"))) + (mkdir out) + ;; metis files are not installed with 'make install' + (for-each (lambda (f) + (install-file f (string-append out "/include"))) + (find-files "../include/" ".*metis\\.h")) + (for-each (lambda (f) + (install-file f (string-append out "/lib"))) + (find-files "../lib/" ".*metis\\..*")) + #t)))))) (home-page "http://www.labri.fr/perso/pelegrin/scotch/") (synopsis "Programs and libraries for graph algorithms") (description "SCOTCH is a set of programs and libraries which implement @@ -2742,6 +2705,7 @@ to BMP, JPEG or PNG image formats.") (inputs `(("gcl" ,gcl) ("gnuplot" ,gnuplot) ;for plots + ("sed" ,sed) ("tk" ,tk))) ;Tcl/Tk is used by 'xmaxima' (native-inputs `(("texinfo" ,texinfo) @@ -2764,6 +2728,17 @@ to BMP, JPEG or PNG image formats.") #:make-flags (list "TMPDIR=/tmp") #:phases (modify-phases %standard-phases + (add-after 'unpack 'patch-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ((sed (string-append (assoc-ref inputs "sed") "/bin/sed")) + (coreutils (assoc-ref inputs "coreutils")) + (dirname (string-append coreutils "/bin/dirname")) + (head (string-append coreutils "/bin/head"))) + (substitute* "src/maxima.in" + (("sed ") (string-append sed " ")) + (("dirname") dirname) + (("head") head)) + #t))) (add-before 'check 'pre-check (lambda _ (chmod "src/maxima" #o555) @@ -3531,7 +3506,11 @@ in finite element programs.") ``("-DMPI_C_COMPILER=mpicc" "-DMPI_CXX_COMPILER=mpicxx" "-DMPI_Fortran_COMPILER=mpifort" - ,@,cf)))) + ,@,cf)) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'mpi-setup + ,%openmpi-setup))))) (synopsis "Finite element library (with MPI support)"))) (define-public flann @@ -4215,3 +4194,53 @@ 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 |