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03/05: gnu: openmpi: Update to 3.0.1.
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From: |
Ludovic Courtès |
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Subject: |
03/05: gnu: openmpi: Update to 3.0.1. |
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Date: |
Fri, 25 May 2018 07:43:19 -0400 (EDT) |
civodul pushed a commit to branch master
in repository guix.
commit 6df2a50ac4172b7109e4b86656ffd989e98184d7
Author: Ludovic Courtès <address@hidden>
Date: Sat May 12 17:53:54 2018 +0200
gnu: openmpi: Update to 3.0.1.
* gnu/packages/mpi.scm (openmpi): Update to 3.0.1.
[arguments]: In 'remove-absolute' phase, adjust romio file name.
* gnu/packages/maths.scm (scalapack)[arguments]: Add
'set-test-environment' phase.
(slepc-openmpi)[arguments]: Likewise.
(mumps-openmpi)[arguments]: Likewise.
(superlu-dist)[arguments]: In 'check' phase, set
'OMPI_MCA_plm_rsh_agent'.
(scotch)[arguments]: In 'build-esmumps', likewise.
(p4est)[arguments]: Add 'set-test-environment' phase.
(hypre-openmpi)[arguments]: Likewise.
---
gnu/packages/maths.scm | 74 ++++++++++++++++++++++++++++++++++++++++++++------
gnu/packages/mpi.scm | 8 +++---
2 files changed, 70 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 73c79c3..a36d233 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -554,7 +554,16 @@ 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
@@ -1786,6 +1795,18 @@ 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)
@@ -1955,11 +1976,18 @@ 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
@@ -2201,6 +2229,11 @@ 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"
@@ -2295,6 +2328,12 @@ 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"))))
@@ -2474,7 +2513,16 @@ 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
@@ -3531,7 +3579,17 @@ 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
diff --git a/gnu/packages/mpi.scm b/gnu/packages/mpi.scm
index 5dfb26a..5496ea9 100644
--- a/gnu/packages/mpi.scm
+++ b/gnu/packages/mpi.scm
@@ -153,7 +153,7 @@ bind processes, and much more.")
(define-public openmpi
(package
(name "openmpi")
- (version "1.10.7")
+ (version "3.0.1")
(source
(origin
(method url-fetch)
@@ -162,7 +162,7 @@ bind processes, and much more.")
"/downloads/openmpi-" version ".tar.bz2"))
(sha256
(base32
- "142s1vny9gllkq336yafxayjgcirj2jv0ddabj879jgya7hyr2d0"))))
+ "0pbqrm5faf57nasy1s81wqivl7zvxmv8lzjh8hvb0f3qxv8m0d36"))))
(build-system gnu-build-system)
(inputs
`(("hwloc" ,hwloc "lib")
@@ -205,8 +205,8 @@ bind processes, and much more.")
(("_ABSOLUTE") ""))
;; Avoid valgrind (which pulls in gdb etc.).
(substitute*
- '("./ompi/mca/io/romio/src/io_romio_component.c")
- (("MCA_io_romio_COMPLETE_CONFIGURE_FLAGS")
+
'("./ompi/mca/io/romio314/src/io_romio314_component.c")
+ (("MCA_io_romio314_COMPLETE_CONFIGURE_FLAGS")
"\"[elided to reduce closure]\""))
#t))
(add-before 'build 'scrub-timestamps ;reproducibility