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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Package: guix-patches; Reported by: Gerd Heber <gerd.heber@HIDDEN>; Keywords: patch; dated Sun, 28 Feb 2021 17:13:02 UTC; Maintainer for guix-patches is guix-patches@HIDDEN.

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From: Gerd Heber via web <issues.guix.gnu.org@HIDDEN>
To: 46830 <at> debbugs.gnu.org
Date: Sun, 28 Feb 2021 23:42:43 +0100
Message-ID: <7f9bd991d490.1956b6a559d1e5c4@HIDDEN>
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
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 Content preview: This needs to be a separate package since (as with all HDF5
 major releases) it's not 100% API compatible with HDF5 1.10. It would break
 other packages, e.g., `petsc-lite` 
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This needs to be a separate package since (as with all HDF5 major releases) it's not 100% API compatible with HDF5 1.10. It would break other packages, e.g., `petsc-lite`





Information forwarded to guix-patches@HIDDEN:
bug#46830; Package guix-patches. Full text available.

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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
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---
 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





Acknowledgement sent to Gerd Heber <gerd.heber@HIDDEN>:
New bug report received and forwarded. Copy sent to guix-patches@HIDDEN. Full text available.
Report forwarded to guix-patches@HIDDEN:
bug#46830; Package guix-patches. Full text available.
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