Your message dated Thu, 26 Mar 2026 15:18:47 +0000
with message-id <[email protected]>
and subject line Bug#1124933: fixed in xmds2 3.1.0+dfsg2-13
has caused the Debian Bug report #1124933,
regarding wscript: support cmake built HDF5 and fix HDF5+MPI detection
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1124933: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1124933
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: xmds2
Version: 3.1.0+dfsg2-11
Severity: normal
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hi,
While testing the build of xmds2 against cmake built HDF5 (1.14.6
currently in experimental) I noticed a couple if issues regarding HDF5
detection by the wscript tool.
Firstly, it extracts the HDF5 libpath from the full path of HDF5 static
library returned by 'h5cc -show -noshlib'. While it works currently,
it doesn't work with a cmake built HDF5 where the h5cc output comes
from pkg-config.
I propose to parse the -L link option from 'h5cc -show -shlib' instead
which works in both cases.
Secondly the HDF5 detection with MPI is not correct as is uses 'h5cc'
instead of 'h5pcc'.
Please see the attached patch proposal which should fix both issues. I've
tested it against autotools built HDF5 1.14.5 in unstable and cmake built
HDF5 1.14.6 in experimental.
Best,
_g.
- -- System Information:
Debian Release: 12.0
Architecture: amd64 (x86_64)
Kernel: Linux 6.1.0-34-amd64 (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
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diff -Nru xmds2-3.1.0+dfsg2/debian/changelog xmds2-3.1.0+dfsg2/debian/changelog
--- xmds2-3.1.0+dfsg2/debian/changelog 2025-09-26 15:19:18.000000000 +0200
+++ xmds2-3.1.0+dfsg2/debian/changelog 2026-01-07 10:38:44.000000000 +0100
@@ -1,3 +1,13 @@
+xmds2 (3.1.0+dfsg2-11.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * New patches for wscript:
+ - support for cmake built HDF5
+ - use the correct MPI HDF5 variant when building with MPI
+ * The last item above requires libhdf5-mpi-dev as build dependency
+
+ -- Gilles Filippini <[email protected]> Wed, 07 Jan 2026 10:38:44 +0100
+
xmds2 (3.1.0+dfsg2-11) unstable; urgency=medium
* d/control:
diff -Nru xmds2-3.1.0+dfsg2/debian/control xmds2-3.1.0+dfsg2/debian/control
--- xmds2-3.1.0+dfsg2/debian/control 2025-09-26 15:19:18.000000000 +0200
+++ xmds2-3.1.0+dfsg2/debian/control 2026-01-07 10:38:44.000000000 +0100
@@ -12,6 +12,7 @@
libfftw3-mpi-dev <!nocheck>,
libgsl-dev <!nocheck>,
libhdf5-dev <!nocheck>,
+ libhdf5-mpi-dev <!nocheck>,
libopenblas-dev | libblis-dev <!nocheck>,
mpi-default-bin <!nocheck>,
mpi-default-dev <!nocheck>,
diff -Nru xmds2-3.1.0+dfsg2/debian/patches/series
xmds2-3.1.0+dfsg2/debian/patches/series
--- xmds2-3.1.0+dfsg2/debian/patches/series 2025-09-26 15:19:18.000000000
+0200
+++ xmds2-3.1.0+dfsg2/debian/patches/series 2026-01-07 10:38:44.000000000
+0100
@@ -14,3 +14,5 @@
invalid-escape-sequences.patch
replace-deprecated-distutils.patch
auto-gitignore
+wscript-hdf5-cmake-support.patch
+wscript-hdf5-mpi-support.patch
diff -Nru xmds2-3.1.0+dfsg2/debian/patches/wscript-hdf5-cmake-support.patch
xmds2-3.1.0+dfsg2/debian/patches/wscript-hdf5-cmake-support.patch
--- xmds2-3.1.0+dfsg2/debian/patches/wscript-hdf5-cmake-support.patch
1970-01-01 01:00:00.000000000 +0100
+++ xmds2-3.1.0+dfsg2/debian/patches/wscript-hdf5-cmake-support.patch
2026-01-07 10:38:44.000000000 +0100
@@ -0,0 +1,19 @@
+Description: fix the weird way wscript has to find out the HDF5 libpath
+ It should relies on the standard -L link flag instead of the broken
+ way the autotools generated h5cc tool handles static linking.
+ .
+ BTW this fix adds support for the cmake built HDF5 1.14.6 currently in
+ experimental.
+Index: xmds2-3.1.0+dfsg2/xpdeint/support/wscript
+===================================================================
+--- xmds2-3.1.0+dfsg2.orig/xpdeint/support/wscript
++++ xmds2-3.1.0+dfsg2/xpdeint/support/wscript
+@@ -401,7 +401,7 @@ def configure(conf):
+ h5cc_shared_flags = conf.cmd_and_log([conf.env['H5CC'][0],
'-show', '-shlib'])
+ h5cc_static_flags = conf.cmd_and_log([conf.env['H5CC'][0],
'-show', '-noshlib'])
+
+- hdf5_libpath = re.search(r'(\S*)/libhdf5\.a',
h5cc_static_flags).group(1)
++ hdf5_libpath = re.search(r'\s-L(\S+)', h5cc_shared_flags).group(1)
+
+ conf.env.append_unique("LIBPATH_hdf5", hdf5_libpath)
+
diff -Nru xmds2-3.1.0+dfsg2/debian/patches/wscript-hdf5-mpi-support.patch
xmds2-3.1.0+dfsg2/debian/patches/wscript-hdf5-mpi-support.patch
--- xmds2-3.1.0+dfsg2/debian/patches/wscript-hdf5-mpi-support.patch
1970-01-01 01:00:00.000000000 +0100
+++ xmds2-3.1.0+dfsg2/debian/patches/wscript-hdf5-mpi-support.patch
2026-01-07 10:38:44.000000000 +0100
@@ -0,0 +1,27 @@
+Description: When building for the MPI variant of HDF5 the helper should
+ be 'h5pcc' ('p' for 'parallel') instead of 'h5cc' which relates to the
+ serial variant.
+Index: xmds2-3.1.0+dfsg2/xpdeint/support/wscript
+===================================================================
+--- xmds2-3.1.0+dfsg2.orig/xpdeint/support/wscript
++++ xmds2-3.1.0+dfsg2/xpdeint/support/wscript
+@@ -397,9 +397,16 @@ def configure(conf):
+ )
+
+ # Check for hdf5
+- if conf.find_program('h5cc', var='H5CC', mandatory = False):
+- h5cc_shared_flags = conf.cmd_and_log([conf.env['H5CC'][0],
'-show', '-shlib'])
+- h5cc_static_flags = conf.cmd_and_log([conf.env['H5CC'][0],
'-show', '-noshlib'])
++ if conf.env['ENVIRONMENT_NAME'] == 'default':
++ hdf5_helper = 'h5cc'
++ hdf5_helper_var = 'H5CC'
++ else:
++ hdf5_helper = 'h5pcc'
++ hdf5_helper_var = 'H5PCC'
++
++ if conf.find_program(f'{hdf5_helper}', var=hdf5_helper_var, mandatory
= False):
++ h5cc_shared_flags =
conf.cmd_and_log([conf.env[hdf5_helper_var][0], '-show', '-shlib'])
++ h5cc_static_flags =
conf.cmd_and_log([conf.env[hdf5_helper_var][0], '-show', '-noshlib'])
+
+ hdf5_libpath = re.search(r'\s-L(\S+)', h5cc_shared_flags).group(1)
+
--- End Message ---
--- Begin Message ---
Source: xmds2
Source-Version: 3.1.0+dfsg2-13
Done: Rafael Laboissière <[email protected]>
We believe that the bug you reported is fixed in the latest version of
xmds2, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Rafael Laboissière <[email protected]> (supplier of updated xmds2 package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Thu, 26 Mar 2026 12:48:46 +0000
Source: xmds2
Architecture: source
Version: 3.1.0+dfsg2-13
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Rafael Laboissière <[email protected]>
Closes: 1124933
Changes:
xmds2 (3.1.0+dfsg2-13) unstable; urgency=medium
.
* Upload to unstable
* d/copyright: Drop trailing slash in excluded path
* d/watch: Update Repacksuffix
.
xmds2 (3.1.0+dfsg2-12) experimental; urgency=medium
.
[ Gilles Filippini ]
* New patches for wscript:
- support for cmake built HDF5
- use the correct MPI HDF5 variant when building with MPI
* The last item above requires libhdf5-mpi-dev as build dependency
* These changes closes: #1124933
.
[ Rafael Laboissière ]
* d/control:
+ Drop the redundant Priority field, which defaults to optional now
+ Bump Standards-Version to 4.7.3 (no changes needed)
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