Your message dated Sun, 13 Sep 2026 15:11:29 +0200
with message-id <[email protected]>
and subject line Re: Bug#1023446: libhdf5-openmpi-dev: h5pcc configured as
static build
has caused the Debian Bug report #1023446,
regarding libhdf5-openmpi-dev: h5pcc configured as static build
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1023446: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1023446
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--- Begin Message ---
Package: libhdf5-openmpi-dev
Version: 1.10.8+repack-1
Severity: important
Control: block 1020054 by -1
h5pcc is showing an unexpected default configuration:
$ h5pcc --showconfig
gcc -I/usr/include/hdf5/openmpi -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5_hl.a
/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.a -lcrypto -lcurl -lsz -lz -ldl
-lm -Wl,-rpath -Wl,/usr/lib/x86_64-linux-gnu/hdf5/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi
Note how it includes static linking to libhdf5_hl.a and libhdf5.a
I would expect the default configuration to use dynamic linking with
shared libraries, as in
$ h5pcc --showconfig -shlib
gcc -I/usr/include/hdf5/openmpi -L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
-lhdf5_hl -lhdf5 -lcrypto -lcurl -lsz -lz -ldl -lm -Wl,-rpath
-Wl,/usr/lib/x86_64-linux-gnu/hdf5/openmpi
As far as I can tell, the default static linking is causing the RC
Bug#1020054 reported against h5py.
Should the default configuration of h5pcc be changed to confirm with
the -shlib configuration?
-- System Information:
Debian Release: bookworm/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
merged-usr: no
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.0.0-2-amd64 (SMP w/8 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8),
LANGUAGE=en_AU:en
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages libhdf5-openmpi-dev depends on:
ii libaec-dev 1.0.6-1+b1
ii libcurl4-gnutls-dev [libcurl-dev] 7.86.0-1
ii libhdf5-openmpi-103-1 1.10.8+repack-1
ii libhdf5-openmpi-cpp-103-1 1.10.8+repack-1
ii libhdf5-openmpi-fortran-102 1.10.8+repack-1
ii libhdf5-openmpi-hl-100 1.10.8+repack-1
ii libhdf5-openmpi-hl-cpp-100 1.10.8+repack-1
ii libhdf5-openmpi-hl-fortran-100 1.10.8+repack-1
ii libjpeg-dev 1:2.1.2-1+b1
ii libjpeg62-turbo-dev [libjpeg-dev] 1:2.1.2-1+b1
ii libopenmpi-dev 4.1.4-3
ii libssl-dev 3.0.7-1
ii zlib1g-dev 1:1.2.11.dfsg-4.1
libhdf5-openmpi-dev recommends no packages.
Versions of packages libhdf5-openmpi-dev suggests:
pn libhdf5-doc <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
Version: 2.1.0+repack-1
Hi,
On Tue, 22 Nov 2022 23:28:12 +0100 Gilles Filippini <[email protected]> wrote:
Hi Drew,
Drew Parsons a écrit le 15/11/2022 à 16:28 :
> h5py is building fine against the shared libraries with
> HDF5_USE_SHLIB=yes, but leaves a question about rpath.
>
> Notice that `h5pcc --showconfig -shlib` includes
> "-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi -lhdf5_hl -lhdf5 -Wl,-rpath
> -Wl,/usr/lib/x86_64-linux-gnu/hdf5/openmpi"
>
> The h5py python extensions get linked with this, such the h5py .so files
> are generated with
> NEEDED libhdf5_openmpi.so.103
> RUNPATH /usr/lib/x86_64-linux-gnu/hdf5/openmpi
>
> In normal package policy we try to remove RUNPATH, and in the case of
> the hdf5 libraries libhdf5_openmpi.so.103 is available in the standard
> library path at /usr/lib/x86_64-linux-gnu/. In fact
> libhdf5_openmpi.so.103 is not even found in
> /usr/lib/x86_64-linux-gnu/hdf5/openmpi (instead libhdf5.so is found
> there as a symlink to ../../libhdf5_openmpi.so).
>
> As far as I can tell, the -rpath entry in the h5pcc configuration is
> redundant, possibly even wrong (since the linked library is
> libhdf5_openmpi.so.103, not the more general libhdf5.so)
>
> Should rpath be removed from the h5pcc shlib configuration?
I've just uploaded hdf5 1.10.8+repack-2 which should fix this issue.
Starting with release 2.1.0+repack-1, '-shlib' and '-norpath' are now
the default.
$ h5pcc -show
/usr/bin/mpicc.openmpi -I/usr/include/hdf5/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/lib/../../fortran/gfortran-mod-16/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -lhdf5_openmpi_hl
-lhdf5_openmpi -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08
-lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi
Best,
_g.
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