diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 263 |
1 files changed, 256 insertions, 7 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 1d9cadf044..962bcd8278 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -11,7 +11,7 @@ ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2015 Fabian Harfert <fhmgufs@web.de> ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> -;;; Copyright © 2016 Kei Kebreau <kei@openmailbox.org> +;;; Copyright © 2016 Kei Kebreau <kkebreau@posteo.net> ;;; Copyright © 2016, 2017 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016 Thomas Danckaert <post@thomasdanckaert.be> @@ -149,14 +149,14 @@ interactive dialogs to guide them.") (define-public coda (package (name "coda") - (version "2.18") + (version "2.18.2") (source (origin (method url-fetch) (uri (string-append "https://github.com/stcorp/coda/releases/download/" version "/coda-" version ".tar.gz")) (sha256 - (base32 "11asla1ap8vd73farqjlpb179sfiy0biydcwxjfcakrp9sf8v9bs")) + (base32 "01fnqcby9jijvf3jxr1fk4bny059lvvq5wbqm7ns60ilykfdnm6a")) (patches (search-patches "coda-use-system-libs.patch")) (modules '((guix build utils))) (snippet @@ -605,7 +605,18 @@ computations.") (("@HDF_BUILD_SHARED_TRUE@AM_LDFLAGS = \ -R\\$\\(abs_top_builddir\\)/mfhdf/libsrc/\\.libs \ -R\\$\\(abs_top_builddir\\)/hdf/src/\\.libs \\$\\(XDR_ADD\\)") "")) - #t))))) + #t)) + (add-after 'configure 'patch-settings + (lambda _ + ;; libhdf4.settings contains the full path of the + ;; compilers used, and its contents are included in + ;; .so-files. We truncate the hashes to avoid + ;; unnecessary store references to those compilers: + (substitute* "libhdf4.settings" + (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) + (string-append prefix (string-take hash 10) "..."))) + #t)) + ))) (home-page "https://www.hdfgroup.org/products/hdf4/") (synopsis "Library and multi-object file format for storing and managing data") @@ -648,16 +659,40 @@ incompatible with HDF5.") (build-system gnu-build-system) (inputs `(("zlib" ,zlib))) + (native-inputs + `(("gfortran" ,gfortran))) + (outputs '("out" ; core library + "fortran")) ; fortran interface (arguments `(;; Some of the users, notably Flann, need the C++ interface. - #:configure-flags '("--enable-cxx") + #:configure-flags '("--enable-cxx" + "--enable-fortran" + "--enable-fortran2003") #:phases (modify-phases %standard-phases (add-before 'configure 'patch-configure - (lambda _ + (lambda* (#:key outputs #:allow-other-keys) (substitute* "configure" (("/bin/mv") "mv")) + (substitute* "fortran/src/Makefile.in" + (("libhdf5_fortran_la_LDFLAGS =") + (string-append "libhdf5_fortran_la_LDFLAGS = -Wl-rpath=" + (assoc-ref outputs "fortran") "/lib"))) + (substitute* "hl/fortran/src/Makefile.in" + (("libhdf5hl_fortran_la_LDFLAGS =") + (string-append "libhdf5hl_fortran_la_LDFLAGS = -Wl,-rpath=" + (assoc-ref outputs "fortran") "/lib"))) + #t)) + (add-after 'configure 'patch-settings + (lambda _ + ;; libhdf5.settings contains the full path of the + ;; compilers used, and its contents are included in + ;; libhdf5.so. We truncate the hashes to avoid + ;; unnecessary store references to those compilers: + (substitute* "src/libhdf5.settings" + (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) + (string-append prefix (string-take hash 10) "..."))) #t)) (add-after 'install 'patch-references (lambda* (#:key inputs outputs #:allow-other-keys) @@ -666,7 +701,40 @@ incompatible with HDF5.") (substitute* (find-files bin "h5p?cc") (("-lz" lib) (string-append "-L" zlib "/lib " lib))) - #t)))))) + #t))) + (add-after 'install 'split + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Move all fortran-related files + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (lib (string-append out "/lib")) + (inc (string-append out "/include")) + (ex (string-append out "/share/hdf5_examples/fortran")) + (fort (assoc-ref outputs "fortran")) + (fbin (string-append fort "/bin")) + (flib (string-append fort "/lib")) + (finc (string-append fort "/include")) + (fex (string-append fort "/share/hdf5_examples/fortran"))) + (mkdir-p fbin) + (mkdir-p flib) + (mkdir-p finc) + (mkdir-p fex) + (rename-file (string-append bin "/h5fc") + (string-append fbin "/h5fc")) + (for-each (lambda (file) + (rename-file file + (string-append flib "/" (basename file)))) + (find-files lib ".*fortran.*")) + (for-each (lambda (file) + (rename-file file + (string-append finc "/" (basename file)))) + (find-files inc ".*mod")) + (for-each (lambda (file) + (rename-file file + (string-append fex "/" (basename file)))) + (find-files ex ".*")) + (delete-file-recursively ex)) + #t))))) (home-page "http://www.hdfgroup.org") (synopsis "Management suite for extremely large and complex data") (description "HDF5 is a suite that makes possible the management of @@ -850,6 +918,29 @@ similar to MATLAB, GNU Octave or SciPy.") ("libjpeg" ,libjpeg))) (arguments `(#:configure-flags '("--enable-doxygen" "--enable-dot" "--enable-hdf4") + + #:phases (modify-phases %standard-phases + (add-before 'configure 'fix-source-date + (lambda _ + ;; As we ${SOURCE_DATE_EPOCH} evaluates to "1" in the build + ;; environment, `date -u -d ${SOURCE_DATE_EPOCH}` will evaluate + ;; to '1st hour of the current day', and therefore makes the + ;; package not reproducible. + (substitute* "./configure" + (("date -u -d \"\\$\\{SOURCE_DATE_EPOCH\\}\"") + "date --date='@0'")) + #t)) + (add-after 'configure 'patch-settings + (lambda _ + ;; libnetcdf.settings contains the full filename of the compilers + ;; used to build the library. We truncate the hashes of those + ;; filenames to avoid unnecessary references to the corresponding + ;; store items. + (substitute* "libnetcdf.settings" + (("(/gnu/store/)([a-Z0-9]*)" all prefix hash) + (string-append prefix (string-take hash 10) "..."))) + #t))) + #:parallel-tests? #f)) ;various race conditions (home-page "http://www.unidata.ucar.edu/software/netcdf/") (synopsis "Library for scientific data") @@ -1946,6 +2037,55 @@ bio-chemistry.") ;; See LICENSE_en.txt (license license:cecill-c))) +(define-public scotch32 + ;; This is the 'INTSIZE32' variant, which uses 32-bit integers, as needed by + ;; some applications. + (package (inherit scotch) + (name "scotch32") + (arguments + (substitute-keyword-arguments (package-arguments scotch) + ((#:phases scotch-phases) + `(modify-phases ,scotch-phases + (replace + 'configure + (lambda _ + (call-with-output-file "Makefile.inc" + (lambda (port) + (format port " +EXE = +LIB = .a +OBJ = .o +MAKE = make +AR = ar +ARFLAGS = -ruv +CAT = cat +CCS = gcc +CCP = mpicc +CCD = gcc +CPPFLAGS =~{ -D~a~} +CFLAGS = -O2 -g -fPIC $(CPPFLAGS) +LDFLAGS = -lz -lm -lrt -lpthread +CP = cp +LEX = flex -Pscotchyy -olex.yy.c +LN = ln +MKDIR = mkdir +MV = mv +RANLIB = ranlib +YACC = bison -pscotchyy -y -b y +" + '("COMMON_FILE_COMPRESS_GZ" + "COMMON_PTHREAD" + "COMMON_RANDOM_FIXED_SEED" + "INTSIZE32" ;use 32-bit integers. See INSTALL.txt + ;; Prevents symbolc clashes with libesmumps + "SCOTCH_RENAME" + ;; XXX: Causes invalid frees in superlu-dist tests + ;; "SCOTCH_PTHREAD" + ;; "SCOTCH_PTHREAD_NUMBER=2" + "restrict=__restrict")))))))))) + (synopsis + "Programs and libraries for graph algorithms (32-bit integers)"))) + (define-public pt-scotch (package (inherit scotch) (name "pt-scotch") @@ -1969,6 +2109,29 @@ bio-chemistry.") (lambda _ (zero? (system* "make" "ptcheck")))))))) (synopsis "Programs and libraries for graph algorithms (with MPI)"))) +(define-public pt-scotch32 + (package (inherit scotch32) + (name "pt-scotch32") + (propagated-inputs + `(("openmpi" ,openmpi))) ;headers include MPI headers + (arguments + (substitute-keyword-arguments (package-arguments scotch32) + ((#:phases scotch32-phases) + `(modify-phases ,scotch32-phases + (replace 'build + (lambda _ + (and + (zero? (system* "make" + (format #f "-j~a" (parallel-job-count)) + "ptscotch" "ptesmumps")) + ;; Install the serial metis compatibility library + (zero? (system* "make" "-C" "libscotchmetis" "install"))))) + (replace 'check + (lambda _ + (zero? (system* "make" "ptcheck")))))))) + (synopsis + "Programs and libraries for graph algorithms (with MPI and 32-bit integers)"))) + (define-public metis (package (name "metis") @@ -2353,6 +2516,92 @@ parts of it.") "OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") (license license:bsd-3))) +(define* (make-blis implementation #:optional substitutable?) + "Return a BLIS package with the given IMPLEMENTATION (see config/ in the +source tree for a list of implementations.) + +SUBSTITUTABLE? determines whether the package is made available as a +substitute. + +Currently the specialization must be selected at configure-time, but work is +underway to allow BLIS to select the right optimized kernels at run time: +<https://github.com/flame/blis/issues/129>." + (package + (name (if (string=? implementation "reference") + "blis" + (string-append "blis-" implementation))) + (version "0.2.2") + (home-page "https://github.com/flame/blis") + (source (origin + (method git-fetch) + (uri (git-reference (url home-page) (commit version))) + (sha256 + (base32 + "1wr79a50nm4abhw8w3sn96nmwp5mrzifcigk7khw9qcgyyyqayfh")) + (file-name (git-file-name "blis" version)))) + (build-system gnu-build-system) + (arguments + `(#:test-target "test" + + #:substitutable? ,substitutable? + + #:phases (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + ;; This is a home-made 'configure' script. + (let ((out (assoc-ref outputs "out"))) + (zero? (system* "./configure" "-p" out + "-d" "opt" + "--disable-static" + "--enable-shared" + "--enable-threading=openmp" + + ,implementation))))) + (add-before 'check 'show-test-output + (lambda _ + ;; By default "make check" is silent. Make it verbose. + (system "tail -F output.testsuite &") + #t))))) + (synopsis "High-performance basic linear algebra (BLAS) routines") + (description + "BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries. The framework was designed to +isolate essential kernels of computation that, when optimized, immediately +enable optimized implementations of most of its commonly used and +computationally intensive operations. While BLIS exports a new BLAS-like API, +it also includes a BLAS compatibility layer which gives application developers +access to BLIS implementations via traditional BLAS routine calls.") + (license license:bsd-3))) + +(define-public blis + ;; This is the "reference" implementation, which is the non-optimized but + ;; portable variant (no assembly). + (make-blis "reference" #t)) + +(define ignorance blis) + +(define-syntax-rule (blis/x86_64 processor) + "Expand to a package specialized for PROCESSOR." + (package + (inherit (make-blis processor)) + (supported-systems '("x86_64-linux")))) + +(define-public blis-sandybridge + ;; BLIS specialized for Sandy Bridge processors (launched 2011): + ;; <http://ark.intel.com/products/codename/29900/Sandy-Bridge>. + (blis/x86_64 "sandybridge")) + +(define-public blis-haswell + ;; BLIS specialized for Haswell processors (launched 2013): + ;; <http://ark.intel.com/products/codename/42174/Haswell>. + (blis/x86_64 "haswell")) + +(define-public blis-knl + ;; BLIS specialized for Knights Landing processor (launched 2016): + ;; <http://ark.intel.com/products/series/92650/Intel-Xeon-Phi-x200-Product-Family>. + (blis/x86_64 "knl")) + + (define-public openlibm (package (name "openlibm") |