test failing with message /usr/lib/openmpi/lib/libmpi_cxx.so: error: undefined reference to 'opal_list_item_t_class'

[Giovanna Bucci]

Hello,

I have compiled deal II without problems (see attached detailed.log file for settings) on a new machine with Ubuntu 16.04. However all the tests fail. It looks like there is some problem with linking libraries and it is related to openmpi (see quicktest.log file attached), but I can't figure out what it is.

I have installed libopenmpi-dev.  In the attached file installed_pkg I copied the list I get if I run the command    dpkg -l | grep mpi

I have successfully installed and run deal ii in the past on 3 other machines and I never encountered this error. Please let me know if you have any suggestion or if you need any other info.

Thank you,
Giovanna

[Bruno Turcksin]

Giovanna,

can you run a simple "hello world" program with MPI?

Best,

Bruno

[giovanna bucci]

Hello Bruno,

Yes, a simple program like that runs ok.

Thanks,

Giovanna

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[Bruno Turcksin]

Giovanna,

2016-06-09 8:50 GMT-04:00 giovanna bucci <giov....@gmail.com>:
> Yes, a simple program like that runs ok.

I have never seen something like that :-( I haven't had any problem
to install deal.II on Ubuntu 16.04. Can you go where you have
installed deal (probably something like /usr/local/lib) and do:
ldd liddeal_II.so

Best,

Bruno

[Giovanna Bucci]

Hello Bruno,

I know it's weird... I have attached a file with the output of that command.

Thank you!

Gio

[Bruno Turcksin]

Giovanna

2016-06-09 9:25 GMT-04:00 Giovanna Bucci <giov....@gmail.com>:
> I know it's weird... I have attached a file with the output of that command.

Everything is normal. I really don't know what's going on so I am just
going to throw some ideas:
1) you have multiple versions of MPI. It doesn't look like you do but
have you install yourself or let PETSc install its own MPI. This
usually produces strange bugs.
2) there is a problem with your LD_LIBRARY_PATH. Did you change it
yourself? Do you still get the same error if you try to run the tests
in a new terminal?
3) There was a problem when the mpi package was installed. Reinstall
the package and then deal.II
Something else that you probably want to try is to install deal.II
with MPI but no other dependencies. This would let us know if the
problem is really from deal or if another library is the reason for
the error.

Best,

Bruno

[giovanna bucci]

Hello Bruno,

I tried the following
- remove the package libopenmpi-dev and reinstall it
- re-install deal.II (deleting the build folder entirely) with just MPI, but without PETSc

I get the same result (hello world test: ok; deal.II test: fails all).
I know that having both mpich and openmpi may cause problems but this is not the case.

Best regards,
Giovanna

[Bruno Turcksin]

Giovanna,

I see only one solution: you need to find in which library
opal_list_item_t_class and opal_class_initialize are and add it in
your LD_LIBRARY_PATH.

Sorry, it's the only thing I can think of :-(

Bruno

[giovanna bucci]

Hello Bruno,

I forgot to follow up… just in case someone else run in this issue. I fixed it by using mpich, instead of openmpi. Whatever I tried with openmpi was giving me linking problems.

Thank you,
Giovanna

[Bruno Turcksin]

Giovanna,

in case you still encounter this problem. Martin found what the
problem is https://github.com/dealii/dealii/issues/2820#issuecomment-232329108

Best,

Bruno