FS#61764 - [openmpi] Removal of MPI-1 interfaces breaks packages
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Arch Linux
Opened by Christian Pfeiffer (ChrisTX) - Thursday, 14 February 2019, 16:22 GMT
Last edited by Levente Polyak (anthraxx) - Thursday, 10 October 2019, 21:18 GMT
Opened by Christian Pfeiffer (ChrisTX) - Thursday, 14 February 2019, 16:22 GMT
Last edited by Levente Polyak (anthraxx) - Thursday, 10 October 2019, 21:18 GMT
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Details
Description:
OpenMPI 4.0 removed some MPI-1 interfaces that were deprecated in MPI-2 and deleted in MPI-3 by default. The upgrade thus breaks dependent packages like hdf5-openmpi, which depend on these symbols. They can be enabled again by building with --enable-mpi1-compatibility . HDF5 in specific has a partial fix to replace them with their MPI-2 equivalents in the trunk, and it's staged to be fixed for release 1.10.5 - see https://forum.hdfgroup.org/t/hdf5-does-not-compile-with-openmpi-4-0-0/5110/3 for the upstream bug report. However, this most likely breaks other packages or softwares from AUR for the same reason. Additional info: * openmpi 4.0.0 * hdf5-openmpi 1.10.4 Steps to reproduce: Try to use hdf5-openmpi, get the following symbol errors: libhdf5.so: undefined reference to `MPI_Type_extent' libhdf5.so: undefined reference to `OMPI_C_MPI_NULL_COPY_FN' |
This task depends upon
Closed by Levente Polyak (anthraxx)
Thursday, 10 October 2019, 21:18 GMT
Reason for closing: Won't fix
Additional comments about closing: software must adjust, using something thats deprecated for 20 years is not acceptable and in my humble opinion not an issue at the distro but at upstream doing so
Thursday, 10 October 2019, 21:18 GMT
Reason for closing: Won't fix
Additional comments about closing: software must adjust, using something thats deprecated for 20 years is not acceptable and in my humble opinion not an issue at the distro but at upstream doing so
configure: WARNING: unrecognized options: --with-threads, --enable-mpi-thread-multiple, --enable-smp-locks
* https://bitbucket.org/mpi4py/mpi4py/issues/121/pip-install-error
* https://github.com/open-mpi/ompi/issues/6601
Yes, for the v4.0.x series, you do not need --with-threads, --enable-mpi-thread-multiple, --enable-smp-locks flags. These have all disappeared.
Additionally, Open MPI v4.0.x is moving towards removing legacy MPI constructs: APIs that were deprecated in 1996 (over 20 years ago) and deleted from the MPI specification in 2012.
That being said, some applications still use these legacy constructs. Hence, Open MPI v4.0.x is just continuing down the path of raising awareness (we started with legacy compilation warnings in the v3.0.x series) -- we haven't removed these legacy constructs yet. Please see https://www.open-mpi.org/faq/?category=mpi-removed for more detail.
Distros and packagers are encouraged to join the https://lists.open-mpi.org/mailman/listinfo/ompi-packagers mailing list to have a 2-way communication with the Open MPI developers, and be notified of these kinds of changes.
For the Open MPI v4.0.x series, you should probably configure Open MPI with --enable-mpi1-compatibility to restore legacy constructs to mpi.h (i.e., MPI's main header file for applications) so that legacy applications will continue to compile. Also please please please help us encourage MPI application developers to stop using these legacy constructs so that someday you can stop using the --enable-mpi1-compatibilty flag (which will also disappear in some future Open MPI release series).
Thank you!
So i very much respect your developer opinion provided but i try to continue the route of having legacy features not enabled. Thanks for reaching out, i have made a subscription request to that mailinglist (i was not yet approved).