Your message dated Fri, 27 Mar 2020 19:00:11 +0000
with message-id <e1jhudd-0005ws...@fasolo.debian.org>
and subject line Bug#944769: fixed in h5py 2.10.0-3
has caused the Debian Bug report #944769,
regarding python3-h5py fails to import if offline due to apparent MPI failure
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.
(NB: If you are a system administrator and have no idea what this
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--
944769: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=944769
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: python3-h5py
Version: 2.10.0-2
Severity: serious
The latest version of h5py compiled against MPI completely fails to
import if there is no network connection:
servo:~ 0$ python3 -c 'import h5py; print("foo")'
--------------------------------------------------------------------------
No network interfaces were found for out-of-band communications. We require
at least one available network for out-of-band messaging.
--------------------------------------------------------------------------
[servo:32114] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on
the local node in file ess_singleton_module.c at line 532
[servo:32114] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a daemon on
the local node in file ess_singleton_module.c at line 166
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_init failed
--> Returned value Unable to start a daemon on the local node (-127)
instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: ompi_rte_init failed
--> Returned "Unable to start a daemon on the local node" (-127) instead of
"Success" (0)
--------------------------------------------------------------------------
*** An error occurred in MPI_Init_thread
*** on a NULL communicator
*** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort,
*** and potentially your MPI job)
[servo:32114] Local abort before MPI_INIT completed completed successfully, but
am not able to aggregate error messages, and not able to guarantee that all
other processes were killed!
servo:~ 1$
Note the return code and that the print command was not executed. The
import actually caused python to crash without throwing an exception.
This is obviously unacceptable and very major usability issue.
As mention in other similar reports, please drop the MPI support in
the default build!
jamie.
-- System Information:
Debian Release: bullseye/sid
APT prefers testing
APT policy: (600, 'testing'), (500, 'stable'), (200, 'unstable'), (101,
'experimental')
Architecture: amd64 (x86_64)
Kernel: Linux 5.2.0-3-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages python3-h5py depends on:
ii libc6 2.29-3
ii libhdf5-openmpi-103 1.10.4+repack-10
ii python3 3.7.5-1
ii python3-mpi4py 3.0.2-13
ii python3-numpy [python3-numpy-abi9] 1:1.16.5-1
ii python3-six 1.12.0-2
python3-h5py recommends no packages.
Versions of packages python3-h5py suggests:
pn python-h5py-doc <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: h5py
Source-Version: 2.10.0-3
Done: Drew Parsons <dpars...@debian.org>
We believe that the bug you reported is fixed in the latest version of
h5py, 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 944...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <dpars...@debian.org> (supplier of updated h5py 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Thu, 05 Mar 2020 19:22:27 +0800
Source: h5py
Binary: python-h5py-doc python3-h5py python3-h5py-mpi python3-h5py-mpi-dbg
python3-h5py-serial python3-h5py-serial-dbg
Architecture: source all amd64
Version: 2.10.0-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<debian-science-maintain...@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
python-h5py-doc - documentation for h5py
python3-h5py - general-purpose Python interface to hdf5
python3-h5py-mpi - general-purpose Python interface to hdf5 (Python 3)
python3-h5py-mpi-dbg - debug extensions for h5py (Python 3)
python3-h5py-serial - general-purpose Python interface to hdf5 (Python 3)
python3-h5py-serial-dbg - debug extensions for h5py (Python 3)
Closes: 944617 944769 946986
Changes:
h5py (2.10.0-3) unstable; urgency=medium
.
* Team upload.
.
[ Debian Janitor ]
* Use secure URI in Homepage field.
.
[ Drew Parsons ]
* provide separate serial and MPI builds in python3-h5py-serial and
python3-h5py-mpi. python3-h5py-serial provides a h5py.py loader
file to only import h5py-mpi for multiprocess jobs, otherwise
import h5py-serial. python3-h5py is a dummy package depending on
python3-h5py-serial or python3-h5py-mpi.
- provides generic h5py/__init__.py which imports h5py_serial or
h5py_mpi as required
- needs debian patches:
- hdf5_pkgconfig.patch allows pkg-config entry for HDF5 to be
specified (e.g. hdf5-serial)
- build_flavour.patch allows build flavour (_serial or _mpi) to be
specified for module path
- stop_circular_dep.patch stops circular dependency in _objects
- drop_deprecated_dtype_6a77b91.patch,
remove_deprecated_highlevel_module_2f41c78.patch,
file_default_read_5e71c49.patch for upstream commits 6a77b91,
2f41c78 and 5e71c49 and
drop_deprecation_tests.patch removes long-deprecated dtypes,
highlevel.py and tests/test_deprecation.py and use of
H5pyDeprecationWarning in tests (dropped upstream)
- tests_as_local_build.patch launches tests relative to the given
h5py build (i.e. don't hardcode "h5py")
- Closes: #944769, #944617, #946986.
* Standards-Version: 4.5.0
* Build-Depends: mpi-default-dev (need to know which mpi since there
is currently no hdf5-mpi.pc to invoke, only specific mpi versions)
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