[From nobody Thu Mar 26 15:21:06 2026 Received: (at submit) by bugs.debian.org; 7 Jan 2026 14:05:57 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-10.9 required=4.0 tests=BAYES_00,FOURLA, FROMDEVELOPER,FVGT_m_MULTI_ODD,HEADER_FROM_DIFFERENT_DOMAINS, PGPSIGNATURE,RCVD_IN_VALIDITY_CERTIFIED_BLOCKED, RCVD_IN_VALIDITY_RPBL_BLOCKED,RCVD_IN_VALIDITY_SAFE_BLOCKED, SPF_HELO_NONE,SPF_PASS autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 94; hammy, 150; neutral, 227; spammy, 0. spammytokens: hammytokens:0.000-+--sk:taint_o, 0.000-+--sk:TAINT_O, 0.000-+--cmake, 0.000-+--sk:taint_u, 0.000-+--sk:TAINT_U Return-path: <SRS0=8Q8j=7M=debian.org=pini@bou-fi.net> Received: from mail.bou-fi.net ([51.255.91.82]:32914) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_X25519__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <SRS0=8Q8j=7M=debian.org=pini@bou-fi.net>) id 1vdUAe-002i0a-2M for submit@bugs.debian.org; Wed, 07 Jan 2026 14:05:57 +0000 Content-Type: multipart/mixed; boundary="===============1870307732897142776==" Authentication-Results: mail.bou-fi.net; auth=pass smtp.mailfrom=pini@debian.org MIME-Version: 1.0 From: Gilles Filippini <pini@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: wscript: support cmake built HDF5 and fix HDF5+MPI detection Message-ID: <176779006150.12523.16815149334613091188.reportbug@pinibrem14> Date: Wed, 07 Jan 2026 13:47:41 +0100 X-Spamd-Bar: -- X-Greylist: delayed 2399 seconds by postgrey-1.37 at buxtehude; Wed, 07 Jan 2026 14:05:56 UTC Delivered-To: submit@bugs.debian.org This is a multi-part MIME message sent by reportbug. --===============1870307732897142776== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline 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 -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEoJObzArDE05WtIyR7+hsbH/+z4MFAmleVeQACgkQ7+hsbH/+ z4MYGQgAiyGpyeFO+VQ4IsMiHEuemFRu+morkQQf+zdGPUP2oVacWtAjeEfv3mlf TM/XPsZSwb+ilY9YHWP4f9V+FY++m1n6bQM+zwSKIaR7CTwKPPcy8Ie36iDhokIp 1nDe6VrR4Ih9pn3PleKZts6Dzp5TEZT6m2ReUSMdXkk1FCg3dNPlBb57EXkhS7PU /P2MwaSVmIR0/pplczcVBilJMZTWzbhkZjgzBrGRt0evYTntHQrGkbB1iz/4ikpZ vpdQmWkzbR2CTYwu8PYf8ap23Tg/zQfKrtq2opYWm7lpBAz25/SNR0gCKCrJuGiZ dsNIQdEJH4nlCE6z+GrdvutGbJF9HQ== =EQzW -----END PGP SIGNATURE----- --===============1870307732897142776== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="xmds2.debdiff" 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 <pini@debian.org> 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) + --===============1870307732897142776==-- ]