[OMPI users] mca_based_component warnings when running simple example code

[Solal Amouyal]

FYI: It's my first time posting here and I'm quit a beginner in MPI.

I recently updated my gfortran (from 4.7 to 6.1.0) and OpenMPI (from 1.10
to 2.0.1) compilers. Since then, I've been getting warnings at the
beginning of the simulation (one set of warnings per processor).

I reduced my code to the most MPI program and the warnings persist.

program main
use mpi_f08
implicit none
integer :: ierror

call mpi_init(ierror)
call mpi_finalize(ierror)
end program main

I compile my code with mpif90 main.f90, and run it either directly -
./a.out - or with mpirun: mpirun -np 1 ./a.out. The output is the same:

[username:79762] mca_base_component_repository_open: unable to open
mca_grpcomm_bad: dlopen(/usr/local/lib/openmpi/mca_grpcomm_bad.so, 9):
Symbol not found: _orte_grpcomm_base_modex
Referenced from: /usr/local/lib/openmpi/mca_grpcomm_bad.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_grpcomm_bad.so (ignored)
[username:79761] mca_base_component_repository_open: unable to open
mca_grpcomm_bad: dlopen(/usr/local/lib/openmpi/mca_grpcomm_bad.so, 9):
Symbol not found: _orte_grpcomm_base_modex
Referenced from: /usr/local/lib/openmpi/mca_grpcomm_bad.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_grpcomm_bad.so (ignored)
[username:79761] mca_base_component_repository_open: unable to open
mca_pml_bfo: dlopen(/usr/local/lib/openmpi/mca_pml_bfo.so, 9): Symbol
not found: _ompi_free_list_item_t_class
Referenced from: /usr/local/lib/openmpi/mca_pml_bfo.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_pml_bfo.so (ignored)
[username:79761] mca_base_component_repository_open: coll
"/usr/local/lib/openmpi/mca_coll_hierarch" uses an MCA interface that
is not recognized (component MCA v2.0.0 != supported MCA v2.1.0) --
ignored
[username:79761] mca_base_component_repository_open: unable to open
mca_coll_ml: dlopen(/usr/local/lib/openmpi/mca_coll_ml.so, 9): Symbol
not found: _mca_bcol_base_components_in_use
Referenced from: /usr/local/lib/openmpi/mca_coll_ml.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_coll_ml.so (ignored)

I ran and attached the output of ompi_info --all.

I can see in one of the warnings that there's a MCA version mismatch
between v2.0.0 and 2.0.1. I don't know if it might be related but I made
sure to upgrade my OpenMPI *after* gfortran. I am using OSX10.11.4

Thank you,

_________________________

Solal

[Gilles Gouaillardet]

Hi,

it looks like you installed Open MPI 2.0.1 at the same location than
previous Open MPI 1.10, but you did not uninstall v1.10.
the faulty modules have very been likely removed from 2.0.1, hence the error.
you can simply remove the openmpi plugins directory and reinstall openmpi

rm -rf /usr/local/lib/openmpi
make install

Cheers,

Gilles

Post by Solal Amouyal
FYI: It's my first time posting here and I'm quit a beginner in MPI.
I recently updated my gfortran (from 4.7 to 6.1.0) and OpenMPI (from 1.10 to
2.0.1) compilers. Since then, I've been getting warnings at the beginning of
the simulation (one set of warnings per processor).
I reduced my code to the most MPI program and the warnings persist.
program main
use mpi_f08
implicit none
integer :: ierror
call mpi_init(ierror)
call mpi_finalize(ierror)
end program main
I compile my code with mpif90 main.f90, and run it either directly - ./a.out
[username:79762] mca_base_component_repository_open: unable to open
Symbol not found: _orte_grpcomm_base_modex
Referenced from: /usr/local/lib/openmpi/mca_grpcomm_bad.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_grpcomm_bad.so (ignored)
[username:79761] mca_base_component_repository_open: unable to open
Symbol not found: _orte_grpcomm_base_modex
Referenced from: /usr/local/lib/openmpi/mca_grpcomm_bad.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_grpcomm_bad.so (ignored)
[username:79761] mca_base_component_repository_open: unable to open
mca_pml_bfo: dlopen(/usr/local/lib/openmpi/mca_pml_bfo.so, 9): Symbol not
found: _ompi_free_list_item_t_class
Referenced from: /usr/local/lib/openmpi/mca_pml_bfo.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_pml_bfo.so (ignored)
[username:79761] mca_base_component_repository_open: coll
"/usr/local/lib/openmpi/mca_coll_hierarch" uses an MCA interface that is not
recognized (component MCA v2.0.0 != supported MCA v2.1.0) -- ignored
[username:79761] mca_base_component_repository_open: unable to open
mca_coll_ml: dlopen(/usr/local/lib/openmpi/mca_coll_ml.so, 9): Symbol not
found: _mca_bcol_base_components_in_use
Referenced from: /usr/local/lib/openmpi/mca_coll_ml.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_coll_ml.so (ignored)
I ran and attached the output of ompi_info --all.
I can see in one of the warnings that there's a MCA version mismatch between
v2.0.0 and 2.0.1. I don't know if it might be related but I made sure to
upgrade my OpenMPI after gfortran. I am using OSX10.11.4
Thank you,
_________________________
Solal
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

[Solal Amouyal]

Hi Gilles,

Thanks for your help. That indeed fixed it!

Sincerely,

_________________________

Solal Amouyal

Message: 2
Date: Fri, 6 Jan 2017 22:05:54 +0900
Subject: Re: [OMPI users] mca_based_component warnings when running
simple example code
gmail.com>
Content-Type: text/plain; charset=UTF-8
Hi,
it looks like you installed Open MPI 2.0.1 at the same location than
previous Open MPI 1.10, but you did not uninstall v1.10.
the faulty modules have very been likely removed from 2.0.1, hence the
error.
you can simply remove the openmpi plugins directory and reinstall openmpi
rm -rf /usr/local/lib/openmpi
make install
Cheers,
Gilles

Post by Solal Amouyal
FYI: It's my first time posting here and I'm quit a beginner in MPI.
I recently updated my gfortran (from 4.7 to 6.1.0) and OpenMPI (from

1.10 to

Post by Solal Amouyal
2.0.1) compilers. Since then, I've been getting warnings at the

beginning of

Post by Solal Amouyal
the simulation (one set of warnings per processor).
I reduced my code to the most MPI program and the warnings persist.
program main
use mpi_f08
implicit none
integer :: ierror
call mpi_init(ierror)
call mpi_finalize(ierror)
end program main
I compile my code with mpif90 main.f90, and run it either directly -

./a.out

Post by Solal Amouyal
[username:79762] mca_base_component_repository_open: unable to open
Symbol not found: _orte_grpcomm_base_modex
Referenced from: /usr/local/lib/openmpi/mca_grpcomm_bad.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_grpcomm_bad.so (ignored)
[username:79761] mca_base_component_repository_open: unable to open
Symbol not found: _orte_grpcomm_base_modex
Referenced from: /usr/local/lib/openmpi/mca_grpcomm_bad.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_grpcomm_bad.so (ignored)
[username:79761] mca_base_component_repository_open: unable to open
mca_pml_bfo: dlopen(/usr/local/lib/openmpi/mca_pml_bfo.so, 9): Symbol

not

Post by Solal Amouyal
found: _ompi_free_list_item_t_class
Referenced from: /usr/local/lib/openmpi/mca_pml_bfo.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_pml_bfo.so (ignored)
[username:79761] mca_base_component_repository_open: coll
"/usr/local/lib/openmpi/mca_coll_hierarch" uses an MCA interface that

is not

Post by Solal Amouyal
recognized (component MCA v2.0.0 != supported MCA v2.1.0) -- ignored
[username:79761] mca_base_component_repository_open: unable to open
mca_coll_ml: dlopen(/usr/local/lib/openmpi/mca_coll_ml.so, 9): Symbol

not

Post by Solal Amouyal
found: _mca_bcol_base_components_in_use
Referenced from: /usr/local/lib/openmpi/mca_coll_ml.so
Expected in: flat namespace
in /usr/local/lib/openmpi/mca_coll_ml.so (ignored)
I ran and attached the output of ompi_info --all.
I can see in one of the warnings that there's a MCA version mismatch

between

Post by Solal Amouyal
v2.0.0 and 2.0.1. I don't know if it might be related but I made sure to
upgrade my OpenMPI after gfortran. I am using OSX10.11.4
Thank you,
_________________________
Solal
_______________________________________________
users mailing list
https://rfd.newmexicoconsortium.org/mailman/listinfo/users

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