diff options
Diffstat (limited to 'gnu/packages/maths.scm')
| -rw-r--r-- | gnu/packages/maths.scm | 87 |
1 files changed, 72 insertions, 15 deletions
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index aac042027b..09d2780ced 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -556,7 +556,16 @@ problems in numerical linear algebra.") ("fortran" ,gfortran) ("lapack" ,lapack))) ;for testing only (arguments - `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES"))) + `(#:configure-flags `("-DBUILD_SHARED_LIBS:BOOL=YES") + #:phases (modify-phases %standard-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))))) (home-page "http://www.netlib.org/scalapack/") (synopsis "Library for scalable numerical linear algebra") (description @@ -1793,6 +1802,18 @@ arising after the discretization of partial differential equations.") (define-public slepc-openmpi (package (inherit slepc) (name "slepc-openmpi") + (arguments + (substitute-keyword-arguments (package-arguments slepc) + ((#: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")) + #t)))))) (inputs `(("mpi" ,openmpi) ("arpack" ,arpack-ng-openmpi) @@ -1962,11 +1983,18 @@ sparse system of linear equations A x = b using Guassian elimination.") (substitute-keyword-arguments (package-arguments mumps) ((#:phases phases) `(modify-phases ,phases - (replace - 'check - (lambda _ - ((assoc-ref ,phases 'check) - #:exec-prefix '("mpirun" "-n" "2")))))))) + (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)) + (replace 'check + (lambda _ + ((assoc-ref ,phases 'check) + #:exec-prefix '("mpirun" "-n" "2")))))))) (synopsis "Multifrontal sparse direct solver (with MPI)"))) (define-public mumps-metis-openmpi @@ -2117,35 +2145,34 @@ also provides threshold-based ILU factorization preconditioners.") (define-public superlu-dist (package (name "superlu-dist") - (version "3.3") + (version "5.3.0") (source (origin (method url-fetch) (uri (string-append "http://crd-legacy.lbl.gov/~xiaoye/SuperLU/" "superlu_dist_" version ".tar.gz")) (sha256 - (base32 "1hnak09yxxp026blq8zhrl7685yip16svwngh1wysqxf8z48vzfj")) - (modules '((guix build utils))) + (base32 "0ja5ihqivkda1wd58y4lmzvmwssm9g91f70c5q0fzwhng6580h6y")) + (modules '((guix build utils))) (snippet ;; Replace the non-free implementation of MC64 with a stub '(begin (use-modules (ice-9 regex) (ice-9 rdelim)) - (call-with-output-file "SRC/mc64ad.c" + (call-with-output-file "SRC/mc64ad_dist.c" (lambda (port) (display " #include <stdio.h> #include <stdlib.h> -void mc64id_(int *a) { +void mc64id_dist(int *a) { fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); abort (); } -void mc64ad_ (int *a, int *b, int *c, int *d, int *e, double *f, int *g, +void mc64ad_dist (int *a, int *b, int *c, int *d, int *e, double *f, int *g, int *h, int *i, int *j, int *k, double *l, int *m, int *n) { fprintf (stderr, \"SuperLU_DIST: non-free MC64 not available. Aborting.\\n\"); abort (); }\n" port))) - (delete-file "SRC/mc64ad.f.bak") (substitute* "SRC/util.c" ;adjust default algorithm (("RowPerm[[:blank:]]*=[[:blank:]]*LargeDiag") "RowPerm = NOROWPERM")) @@ -2211,6 +2238,11 @@ CDEFS = -DAdd_" #t)) (replace 'check (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")) (with-directory-excursion "EXAMPLE" (and (zero? (system* "mpirun" "-n" "2" @@ -2305,6 +2337,12 @@ YACC = bison -pscotchyy -y -b y (add-after 'build 'build-esmumps (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")) + (zero? (system* "make" (format #f "-j~a" (parallel-job-count)) "esmumps")))) @@ -2484,7 +2522,16 @@ schemes.") " -lopenblas") ,(string-append "LAPACK_LIBS=-L" (assoc-ref %build-inputs "lapack") - " -llapack")))) + " -llapack")) + #:phases (modify-phases %standard-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))))) (home-page "http://www.p4est.org") (synopsis "Adaptive mesh refinement on forests of octrees") (description @@ -3547,7 +3594,17 @@ problems.") (substitute-keyword-arguments (package-arguments hypre) ((#:configure-flags flags) ``("--with-MPI" - ,@(delete "--without-MPI" ,flags))))) + ,@(delete "--without-MPI" ,flags))) + ((#: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 "Parallel solvers and preconditioners for linear equations") (description "HYPRE is a software library of high performance preconditioners and |