diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 129 |
1 files changed, 114 insertions, 15 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 50c0a320e0..01bd03c600 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2016, 2017, 2018 Ludovic Courtès <ludo@gnu.org> ;;; Copyright © 2016 Leo Famulari <leo@famulari.name> ;;; Copyright © 2016, 2017 Thomas Danckaert <post@thomasdanckaert.be> -;;; Copyright © 2017 Paul Garlick <pgarlick@tourbillion-technology.com> +;;; Copyright © 2017, 2018 Paul Garlick <pgarlick@tourbillion-technology.com> ;;; Copyright © 2017 Nils Gillmann <ng0@n0.is> ;;; Copyright © 2017 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2017 Theodoros Foradis <theodoros@foradis.org> @@ -1580,7 +1580,7 @@ September 2004}") (define-public petsc (package (name "petsc") - (version "3.8.0") + (version "3.9.3") (source (origin (method url-fetch) @@ -1588,7 +1588,9 @@ September 2004}") (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" "petsc-lite-" version ".tar.gz")) (sha256 - (base32 "1lajbk3c29hnh83v6cbmm3a8wv6bdykh0p70kwrr4vrnizalk88s")))) + (base32 "1fwkbwv4g7zf2lc8fw865xd0bl9anb6jaczfis5dff7h449gwa48")))) + (outputs '("out" ;libraries and headers + "examples")) ;~30MiB of examples (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -1605,11 +1607,7 @@ September 2004}") #:configure-flags `("--with-mpi=0" "--with-openmp=1" - "--with-superlu=1" - ,(string-append "--with-superlu-include=" - (assoc-ref %build-inputs "superlu") "/include") - ,(string-append "--with-superlu-lib=" - (assoc-ref %build-inputs "superlu") "/lib/libsuperlu.a")) + "--with-superlu=1") #:make-flags ;; Honor (parallel-job-count) for build. Do not use --with-make-np, ;; whose value is dumped to $out/lib/petsc/conf/petscvariables. @@ -1662,6 +1660,15 @@ September 2004}") "PETScBuildInternal.cmake" ;; Once installed, should uninstall with Guix "uninstall.py")) + #t))) + (add-after 'install 'move-examples + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (examples (assoc-ref outputs "examples")) + (exdir (string-append out "/share/petsc/examples")) + (exdir' (string-append examples "/share/petsc/examples"))) + (copy-recursively exdir exdir') + (delete-file-recursively exdir) #t)))))) (home-page "http://www.mcs.anl.gov/petsc") (synopsis "Library to solve PDEs") @@ -1685,6 +1692,7 @@ scientific applications modeled by partial differential equations.") (name "petsc-openmpi") (inputs `(("openmpi" ,openmpi) + ("hdf5" ,hdf5-parallel-openmpi) ,@(package-inputs petsc))) (arguments (substitute-keyword-arguments (package-arguments petsc) @@ -1692,7 +1700,21 @@ scientific applications modeled by partial differential equations.") ``("--with-mpiexec=mpirun" ,(string-append "--with-mpi-dir=" (assoc-ref %build-inputs "openmpi")) - ,@(delete "--with-mpi=0" ,cf))))) + ,(string-append "--with-hdf5-include=" + (assoc-ref %build-inputs "hdf5") "/include") + ,(string-append "--with-hdf5-lib=" + (assoc-ref %build-inputs "hdf5") "/lib/libhdf5.a") + ,@(delete "--with-mpi=0" ,cf))) + ((#:phases phases) + `(modify-phases ,phases + (add-before 'check 'set-test-environment + (lambda _ + ;; By default, running the test suite would fail because 'ssh' + ;; could not be found in $PATH. Define this variable to + ;; placate Open MPI without adding a dependency on OpenSSH (the + ;; agent isn't used anyway.) + (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) + #t)))))) (synopsis "Library to solve PDEs (with MPI support)"))) (define-public petsc-complex-openmpi @@ -1738,7 +1760,7 @@ savings are consistently > 5x.") (define-public slepc (package (name "slepc") - (version "3.8.2") + (version "3.9.2") (source (origin (method url-fetch) @@ -1746,7 +1768,7 @@ savings are consistently > 5x.") version ".tar.gz")) (sha256 (base32 - "04zd48p43rnvg68p6cp28zll0px5whglc5v0sc3s6vdj1v920z8y")))) + "0gmhdqac8zm3jx43h935z7bflazjnpvqxjv4jh5za2y1z2rqax94")))) (build-system gnu-build-system) (native-inputs `(("python" ,python-2))) @@ -2824,8 +2846,8 @@ parts of it.") (source (origin (method url-fetch) - (uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v" - version)) + (uri (string-append "mirror://sourceforge/openblas/v" version "/OpenBLAS%20" + version "%20version.tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 @@ -3231,7 +3253,7 @@ Failure to do so will result in a library with poor performance.") (define-public glm (package (name "glm") - (version "0.9.9.0") + (version "0.9.9.1") (source (origin (method url-fetch) @@ -3239,7 +3261,7 @@ Failure to do so will result in a library with poor performance.") version "/glm-" version ".zip")) (sha256 (base32 - "0ihjadp2sb8w312a276skfjsljm3y41bjscbxf79wn23gi00giz1")))) + "042a23hmxfs429czkmlg5ixf28aikzfbw18780prj2gcd4flgw8h")))) (build-system cmake-build-system) (native-inputs `(("unzip" ,unzip))) @@ -4027,3 +4049,80 @@ terminal do calculations simply and quickly. The formula to be calculated can be fed to @command{tcalc} through the command line.") (home-page "https://sites.google.com/site/mohammedisam2000/tcalc") (license license:gpl3+))) + +(define-public sundials + (package + (name "sundials") + (version "3.1.1") + (source + (origin + (method url-fetch) + (uri (string-append "https://computation.llnl.gov/projects/sundials/download/" + "sundials-" version ".tar.gz")) + (sha256 + (base32 + "090s8ymhd0g1s1d44fa73r5yi32hb4biwahhbfi327zd64yn8kd2")))) + (build-system cmake-build-system) + (native-inputs + `(("python" ,python-2))) ;for tests; syntax incompatible with python 3 + (inputs + `(("fortran" ,gfortran) ;for fcmix + ("blas" ,openblas) + ("suitesparse" ,suitesparse))) ;TODO: Add hypre + (arguments + `(#:configure-flags `("-DEXAMPLES_ENABLE_C:BOOL=ON" + "-DEXAMPLES_ENABLE_CXX:BOOL=ON" + "-DEXAMPLES_ENABLE_F77:BOOL=ON" + "-DEXAMPLES_ENABLE_F90:BOOL=ON" + "-DEXAMPLES_INSTALL:BOOL=OFF" + + "-DFCMIX_ENABLE:BOOL=ON" + + "-DKLU_ENABLE:BOOL=ON" + ,(string-append "-DKLU_INCLUDE_DIR=" + (assoc-ref %build-inputs "suitesparse") + "/include") + ,(string-append "-DKLU_LIBRARY_DIR=" + (assoc-ref %build-inputs "suitesparse") + "/lib")))) + (home-page "https://computation.llnl.gov/projects/sundials") + (synopsis "Suite of nonlinear and differential/algebraic equation solvers") + (description "SUNDIALS is a family of software packages implemented with +the goal of providing robust time integrators and nonlinear solvers that can +easily be incorporated into existing simulation codes.") + (license license:bsd-3))) + +(define-public sundials-openmpi + (package (inherit sundials) + (name "sundials-openmpi") + (inputs + `(("mpi" ,openmpi) + ("petsc" ,petsc-openmpi) ;support in SUNDIALS requires MPI + ,@(package-inputs sundials))) + (arguments + (substitute-keyword-arguments (package-arguments sundials) + ((#:configure-flags flags '()) + `(cons* "-DMPI_ENABLE:BOOL=ON" + "-DPETSC_ENABLE:BOOL=ON" + (string-append "-DPETSC_INCLUDE_DIR=" + (assoc-ref %build-inputs "petsc") + "/include") + (string-append "-DPETSC_LIBRARY_DIR=" + (assoc-ref %build-inputs "petsc") + "/lib") + ,flags)) + ((#:phases phases '%standard-phases) + `(modify-phases ,phases + (add-before 'check 'set-test-environment + (lambda _ + ;; By default, running the test suite would fail because 'ssh' + ;; could not be found in $PATH. Define this variable to + ;; placate Open MPI without adding a dependency on OpenSSH (the + ;; agent isn't used anyway.) + (setenv "OMPI_MCA_plm_rsh_agent" (which "cat")) + ;; Allow oversubscription in case there are less + ;; physical cores available in the build environment + ;; than SUNDIALS wants while testing. + (setenv "OMPI_MCA_rmaps_base_oversubscribe" "yes") + #t)))))) + (synopsis "SUNDIALS with OpenMPI support"))) |