GNU bug report logs - #46830
[PATCH Added hdf5-1.12-parallel-openmpi] * gnu/packages/maths.scm (hdf5-1.12-parallel-openmpi): New package based on HDF5 1.12.0

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Gerd Heber <gerd.heber <at> gmail.com>
Subject: bug#46830: closed (Closing)
Date: Wed, 13 Sep 2023 09:30:02 +0000

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Your bug report

#46830: [PATCH Added hdf5-1.12-parallel-openmpi] * gnu/packages/maths.scm (hdf5-1.12-parallel-openmpi): New package based on HDF5 1.12.0

which was filed against the guix-patches package, has been closed.

The explanation is attached below, along with your original report.
If you require more details, please reply to 46830 <at> debbugs.gnu.org.

-- 
46830: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=46830
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Andreas Enge <andreas <at> enge.fr>
To: 46830-done <at> debbugs.gnu.org
Subject: Closing
Date: Wed, 13 Sep 2023 11:29:22 +0200

Hello,

thanks for your patch, that I only see just now (teams were not yet a thing
in 2021...). This version of hdf5 has been retired, so I am closing this issue.
It might be useful to add a parallel package to hdf5 <at> 1.14 instead.

Andreas

[Message part 3 (message/rfc822, inline)]

From: Gerd Heber <gerd.heber <at> gmail.com>
To: guix-patches <at> gnu.org
Cc: Gerd Heber <gheber <at> hdfgroup.org>
Subject: [PATCH Added hdf5-1.12-parallel-openmpi] * gnu/packages/maths.scm
 (hdf5-1.12-parallel-openmpi): New package based on HDF5 1.12.0
Date: Sun, 28 Feb 2021 07:33:14 -0600

---
 gnu/packages/maths.scm | 34 +++++++++++++++++++++++++++++++++-
 1 file changed, 33 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm
index 58433d4b0c..df101635ab 100644
--- a/gnu/packages/maths.scm
+++ b/gnu/packages/maths.scm
@@ -1451,7 +1451,7 @@ Swath).")
     (license (license:non-copyleft home-page))))
 
 (define-public hdf5-parallel-openmpi
-  (package/inherit hdf5-1.10                      ;use the latest
+  (package/inherit hdf5-1.10
     (name "hdf5-parallel-openmpi")
     (inputs
      `(("mpi" ,openmpi)
@@ -1482,6 +1482,38 @@ Swath).")
                #t))))))
     (synopsis "Management suite for data with parallel IO support")))
 
+(define-public hdf5-1.12-parallel-openmpi
+  (package/inherit hdf5-1.12
+    (name "hdf5-1.12-parallel-openmpi")
+    (inputs
+     `(("mpi" ,openmpi)
+       ,@(package-inputs hdf5)))
+    (arguments
+     (substitute-keyword-arguments (package-arguments hdf5)
+       ((#:configure-flags flags)
+        ``("--enable-parallel"
+           ,@(delete "--enable-cxx"
+                     (delete "--enable-threadsafe" ,flags))))
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'build 'mpi-setup
+             ,%openmpi-setup)
+           (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 explicitly
+               ;; 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/test/h5diff/testph5diff.sh"
+                 (("/bin/sh") (which "sh")))
+               #t))))))
+    (synopsis "Management suite for data with parallel IO support")))
+
 (define-public hdf5-blosc
   (package
     (name "hdf5-blosc")
-- 
2.30.1

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