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-rw-r--r--gnu-system.am1
-rw-r--r--gnu/packages/maths.scm89
-rw-r--r--gnu/packages/patches/petsc-fix-threadcomm.patch15
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)
+ {