diff options
| -rw-r--r-- | gnu-system.am | 1 | ||||
| -rw-r--r-- | gnu/packages/maths.scm | 89 | ||||
| -rw-r--r-- | gnu/packages/patches/petsc-fix-threadcomm.patch | 15 |
3 files changed, 105 insertions, 0 deletions
diff --git a/gnu-system.am b/gnu-system.am index c18db0dc56..0bf3eece30 100644 --- a/gnu-system.am +++ b/gnu-system.am @@ -323,6 +323,7 @@ dist_patch_DATA = \ gnu/packages/patches/patchelf-page-size.patch \ gnu/packages/patches/patchutils-xfail-gendiff-tests.patch \ gnu/packages/patches/perl-no-sys-dirs.patch \ + gnu/packages/patches/petsc-fix-threadcomm.patch \ gnu/packages/patches/plotutils-libpng-jmpbuf.patch \ gnu/packages/patches/procps-make-3.82.patch \ gnu/packages/patches/python-fix-tests.patch \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 03f6be120b..8ac9e461a1 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -366,3 +366,92 @@ mesh, solver and post-processing. The specification of any input to these modules is done either interactively using the graphical user interface or in ASCII text files using Gmsh's own scripting language.") (license license:gpl2+))) + +(define-public petsc + (package + (name "petsc") + (version "3.4.4") + (source + (origin + (method url-fetch) + ;; The *-lite-* tarball does not contain the *large* documentation + (uri (string-append "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/" + "petsc-lite-" version ".tar.gz")) + (sha256 + (base32 "0v5dg6dhdjpi5ianvd4mm6hsvxzv1bsxwnh9f9myag0a0d9xk9iv")) + (patches + (list (search-patch "petsc-fix-threadcomm.patch"))))) + (build-system gnu-build-system) + (native-inputs + `(("python" ,python-2) + ("perl" ,perl))) + (inputs + `(("gfortran" ,gfortran-4.8) + ("lapack" ,lapack) + ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi + ;; leaving out opengl, as configuration seems to only be for mac + )) + (arguments + `(#:test-target "test" + #:parallel-build? #f + #:configure-flags + `("--with-mpi=0" + "--with-openmp=1") + #:phases + (alist-replace + 'configure + ;; PETSc's configure script is actually a python script, so we can't + ;; run it with bash. + (lambda* (#:key outputs (configure-flags '()) + #:allow-other-keys) + (let* ((prefix (assoc-ref outputs "out")) + (flags `(,(string-append "--prefix=" prefix) + ,@configure-flags))) + (format #t "build directory: ~s~%" (getcwd)) + (format #t "configure flags: ~s~%" flags) + (zero? (apply system* "./configure" flags)))) + (alist-cons-after + 'install 'clean-local-references + ;; Try to keep installed files from leaking build directory names. + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out")) + (fortran (assoc-ref inputs "gfortran"))) + (substitute* (map (lambda (file) + (string-append out "/" file)) + '("conf/petscvariables" + "conf/PETScConfig.cmake" + "include/petscconf.h" + "include/petscmachineinfo.h")) + (((getcwd)) out)) + ;; Make compiler references point to the store + (substitute* (string-append out "/conf/petscvariables") + (("= g(cc|\\+\\+|fortran)" _ suffix) + (string-append "= " fortran "/bin/g" suffix))) + ;; PETSc installs some build logs, which aren't necessary. + (for-each (lambda (file) + (delete-file (string-append out "/" file))) + '("conf/configure.log" + "conf/make.log" + "conf/test.log" + "conf/RDict.db" + ;; Once installed, should uninstall with Guix + "conf/uninstall.py")))) + %standard-phases)))) + (home-page "http://www.mcs.anl.gov/petsc") + (synopsis "Library to solve ODEs and algebraic equations") + (description "PETSc, pronounced PET-see (the S is silent), is a suite of +data structures and routines for the scalable (parallel) solution of +scientific applications modeled by partial differential equations.") + (license (license:bsd-style + "http://www.mcs.anl.gov/petsc/documentation/copyright.html")))) + +(define-public petsc-complex + (package (inherit petsc) + (name "petsc-complex") + (arguments + (substitute-keyword-arguments (package-arguments petsc) + ((#:configure-flags cf) + `(cons "--with-scalar-type=complex" ,cf)))) + (description + (string-append (package-description petsc) + " Complex scalar type version.")))) diff --git a/gnu/packages/patches/petsc-fix-threadcomm.patch b/gnu/packages/patches/petsc-fix-threadcomm.patch new file mode 100644 index 0000000000..3ef4f2d83d --- /dev/null +++ b/gnu/packages/patches/petsc-fix-threadcomm.patch @@ -0,0 +1,15 @@ +Fix "error: unknown type name 'cpu_set_t'". Patch submitted upstream +http://lists.mcs.anl.gov/pipermail/petsc-dev/2014-May/015345.html + +--- a/src/sys/threadcomm/impls/openmp/tcopenmp.c 2014-03-13 21:47:22.000000000 -0500 ++++ b/src/sys/threadcomm/impls/openmp/tcopenmp.c 2014-04-02 14:44:57.185170151 -0500 +@@ -1,6 +1,9 @@ + #define PETSC_DESIRE_FEATURE_TEST_MACROS + #include <../src/sys/threadcomm/impls/openmp/tcopenmpimpl.h> + #include <omp.h> ++#if defined(PETSC_HAVE_SCHED_CPU_SET_T) ++#include <sched.h> ++#endif + + PetscErrorCode PetscThreadCommGetRank_OpenMP(PetscInt *trank) + { |