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07/10: gnu: Add hdf5-openmpi.
From: |
Eric Bavier |
Subject: |
07/10: gnu: Add hdf5-openmpi. |
Date: |
Thu, 12 May 2016 20:02:43 +0000 (UTC) |
bavier pushed a commit to branch master
in repository guix.
commit c8378eea10fa57c207550978dcf2998f3fc6b81c
Author: Eric Bavier <address@hidden>
Date: Thu Mar 17 09:35:38 2016 -0500
gnu: Add hdf5-openmpi.
* gnu/packages/maths.scm (hdf5-openmpi): New variable.
---
gnu/packages/maths.scm | 28 +++++++++++++++++++++++++++-
1 file changed, 27 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index df21d5e..fce03ac 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -442,6 +442,33 @@ extremely large and complex data collections.")
(license (license:x11-style
"http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/COPYING"))))
+(define-public hdf5-parallel-openmpi
+ (package (inherit hdf5)
+ (name "hdf5-parallel-openmpi")
+ (inputs
+ `(("mpi" ,openmpi)
+ ,@(package-inputs hdf5)))
+ (arguments
+ (substitute-keyword-arguments `(#:configure-flags '("--enable-parallel")
+ ,@(package-arguments hdf5))
+ ((#:phases phases)
+ `(modify-phases ,phases
+ (add-before 'check 'patch-tests
+ (lambda _
+ ;; OpenMPI's mpirun will exit with non-zero status if it
+ ;; detects an "abnormal termination", i.e. any process not
+ ;; calling MPI_Finalize(). Since the test is explicitely
+ ;; avoiding MPI_Finalize so as not to have at_exit and thus
+ ;; H5C_flush_cache from being called, mpirun will always
+ ;; complain, so turn this test off.
+ (substitute* "testpar/Makefile"
+ (("(^TEST_PROG_PARA.*)t_pflush1(.*)" front back)
+ (string-append front back "\n")))
+ (substitute* "tools/h5diff/testph5diff.sh"
+ (("/bin/sh") (which "sh")))
+ #t))))))
+ (synopsis "Management suite for data with parallel IO support")))
+
(define-public nlopt
(package
(name "nlopt")
@@ -480,7 +507,6 @@ common interface for a number of different free
optimization routines available
online as well as original implementations of various other algorithms.")
(license license:lgpl2.1+)))
-
;; For a fully featured Octave, users are strongly recommended also to install
;; the following packages: texinfo, less, ghostscript, gnuplot.
(define-public octave
- branch master updated (f6292ba -> 889187a), Eric Bavier, 2016/05/12
- 05/10: gnu: hdf5: Patch output references to zlib., Eric Bavier, 2016/05/12
- 04/10: gnu: hdf5: Update to 1.8.17., Eric Bavier, 2016/05/12
- 07/10: gnu: Add hdf5-openmpi.,
Eric Bavier <=
- 09/10: gnu: Add Matio., Eric Bavier, 2016/05/12
- 06/10: gnu: hdf5: Have configure honor SOURCE_DATE_EPOCH., Eric Bavier, 2016/05/12
- 10/10: gnu: Add NetCDF., Eric Bavier, 2016/05/12
- 08/10: gnu: Add h5check., Eric Bavier, 2016/05/12
- 02/10: gnu: Add doc++., Eric Bavier, 2016/05/12
- 03/10: gnu: Add HYPRE., Eric Bavier, 2016/05/12
- 01/10: gnu: Move asciidoc and doxygen to new module., Eric Bavier, 2016/05/12