I have now also tried release 3.1.0. Same thing (were I have replaced
/nix/store/glx60yay0hmmizhlxhqhnx9w3k4j9g1z-openmpi-3.1.0 with ....)
[orc-login2:107400] mca_base_component_repository_open: unable to open
mca_fcoll_individual: .../lib/openmpi/mca_fcoll_individual.so:
undefined symbol: mca_common_ompio_file_write (ignored)
[orc-login2:107400] mca_base_component_repository_open: unable to open
mca_fcoll_dynamic_gen2: .../lib/openmpi/mca_fcoll_dynamic_gen2.so:
undefined symbol: mca_common_ompio_register_print_entry (ignored)
[orc-login2:107400] mca_base_component_repository_open: unable to open
mca_fcoll_dynamic: .../lib/openmpi/mca_fcoll_dynamic.so: undefined
symbol: mca_common_ompio_register_print_entry (ignored)
[orc-login2:107400] mca_base_component_repository_open: unable to open
mca_fcoll_two_phase: .../lib/openmpi/mca_fcoll_two_phase.so: undefined
symbol: mca_common_ompio_register_print_entry (ignored)
[orc-login2:107400] mca_base_component_repository_open: unable to open
mca_fcoll_static: .../lib/openmpi/mca_fcoll_static.so: undefined
symbol: mca_common_ompio_register_print_entry (ignored)
Package: Open MPI nixbld@localhost Distribution
Open MPI: 3.1.0
Open MPI repo revision: v3.1.0
Open MPI release date: May 07, 2018
pppp Open RTE: 3.1.0
Open RTE repo revision: v3.1.0
Open RTE release date: May 07, 2018
OPAL: 3.1.0
OPAL repo revision: v3.1.0
OPAL release date: May 07, 2018
I straced the process, and, as far as I could tell, it was just mostly
opening the shared objects in alphabetical order. Would appreciate
any insight, such as whether this is normal behaviour I can ignore or
not?
Thanks! -Tyson
On Fri, 8 Jun 2018 at 17:37, Tyson Whitehead <twhiteh...@gmail.com> wrote:
>
> This email starts out talking about version 1.10.7 to give a complete
> picture. I tested 2.1.3 as well, it also exhibits this issue,
> although to a lesser extent though, and am asking for help on that
> release.
>
> I was compiling the OpenMPI 1.10.7 shipped with NixOS against a newer
> libibverbs with a large set of drivers and get some strange errors
> when when running opmi_info (I've replaced the common prefix
> /nix/store/9zm0pqsh67fw0xi5cpnybnd7hgzryffs-openmpi-1.10.7 with ...)
>
> [mon241:04077] mca: base: component_find: unable to open
> .../lib/openmpi/mca_btl_openib: .../lib/openmpi/mca_btl_openib.so:
> undefined symbol: mca_mpool_grdma_evict (ignored)
> [mon241:04077] mca: base: component_find: unable to open
> .../lib/openmpi/mca_fcoll_individual:
> .../lib/openmpi/mca_fcoll_individual.so: undefined symbol:
> mca_io_ompio_file_write (ignored)
> [mon241:04077] mca: base: component_find: unable to open
> .../lib/openmpi/mca_fcoll_ylib: .../lib/openmpi/mca_fcoll_ylib.so:
> undefined symbol: ompi_io_ompio_scatter_data (ignored)
> [mon241:04077] mca: base: component_find: unable to open
> .../lib/openmpi/mca_fcoll_dynamic:
> .../lib/openmpi/mca_fcoll_dynamic.so: undefined symbol:
> ompi_io_ompio_allgatherv_array (ignored)
> [mon241:04077] mca: base: component_find: unable to open
> .../lib/openmpi/mca_fcoll_two_phase:
> .../lib/openmpi/mca_fcoll_two_phase.so: undefined symbol:
> ompi_io_ompio_set_aggregator_props (ignored)
> [mon241:04077] mca: base: component_find: unable to open
> .../lib/openmpi/mca_fcoll_static: .../lib/openmpi/mca_fcoll_static.so:
> undefined symbol: ompi_io_ompio_allgather_array (ignored)
> Package: Open MPI nixbld@ Distribution
> Open MPI: 1.10.7
> Open MPI repo revision: v1.10.6-48-g5e373bf
> Open MPI release date: May 16, 2017
> Open RTE: 1.10.7
> Open RTE repo revision: v1.10.6-48-g5e373bf
> Open RTE release date: May 16, 2017
> OPAL: 1.10.7
> OPAL repo revision: v1.10.6-48-g5e373bf
> OPAL release date: May 16, 2017
> ...
>
> I dug into the first of these (figured out what library provided it,
> looked at the declared dependencies, poked around in the automake
> file) , and, as far as I could determine, it seems that
> mca_btl_openib.so simply isn't linked to list mca_mpool_grdma.so
> (which provides the symbol) as a dependency.
>
> Seeing as 1.10.7 is no longer supported. I figured I would try 2.1.3
> in case this has been fixed. I compiled it up as well, and it seems
> all but the mca_fcoll_individual one have been resolved (I've replaced
> /nix/store/4kh0zbn8pmdqhvwagicswg70rwnpm570-openmpi-2.1.3 with ...)
>
> [mon241:05544] mca_base_component_repository_open: unable to open
> mca_fcoll_individual: .../lib/openmpi/mca_fcoll_individual.so:
> undefined symbol: ompio_io_ompio_file_read (ignored)
> Package: Open MPI nixbld@ Distribution
> Open MPI: 2.1.3
> Open MPI repo revision: v2.1.2-129-gcfd8f3f
> Open MPI release date: Mar 13, 2018
> Open RTE: 2.1.3
> Open RTE repo revision: v2.1.2-129-gcfd8f3f
> Open RTE release date: Mar 13, 2018
> OPAL: 2.1.3
> OPAL repo revision: v2.1.2-129-gcfd8f3f
> OPAL release date: Mar 13, 2018
> ...
>
> Again I was able to find this symbol in the mca_io_ompio.so library.
> I looked through the source again, and it seems pretty clear that the
> function is indeed called, but the library isn't linked to list the
> mca_io_ompio.so library as a dependency
>
> Looking through the various shared libraries in the .../lib/openmpi
> directory though, and it seems none of them have dependencies on each
> other. How is this suppose to work? Is the component library just
> suppose to load everything so all symbols get resolved? Is the above
> error I'm seeing an error then?
>
> Any insight would be appreciated.
>
> Thanks! -Tyson
>
> PS: Please note that the openmpi code was compiled without any
> patches and without any special configure flags other than
> --prefix=.... (NixOS also adds --diasble-static and
> --disable-dependency-tracking by default, but I removed those, it
> didn't make a difference)..
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