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-rw-r--r--gnu/packages/maths.scm87
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
generated by cgit v1.2.3 (git 2.25.4) at 2024-11-06 17:42:09 +0000