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-rw-r--r--gnu/packages/maths.scm263
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")
generated by cgit v1.2.3 (git 2.45.2) at 2024-07-03 22:23:28 +0000