Error PETSC when running script after upgrade to ubuntu20.04 and pulling newest versions

Question

Hi

I have been able to run several scripts before. I upgraded my system to ubuntu 20.04 LTS and I checked the entire installation of openCARP (pulling recent versions, building and compiling dependencies, installing all the libraries). The installation process seemed to be finished without errors, except that I can't run my scripts anymore.

When I run the python script, I get this error:

application called MPI_Abort(MPI_COMM_WORLD, 50176059) - process 0
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=50176059
:
system msg for write_line failure : Bad file descriptor

After this, I checked the petsc_error_log and I ran it again with option --platform marconi_debug. This gave me the following information:

Traceback (most recent call last):
  File "./run_block.py", line 703, in <module>
    run()
  File "/home/u0132269/Prog/openCARP/carputils/carputils/tools.py", line 509, in wrapped
    job.submit(argv=argv)
  File "/home/u0132269/Prog/openCARP/carputils/carputils/job/job.py", line 162, in submit
    raise Exception('Must specify runtime when running on batch system')
Exception: Must specify runtime when running on batch system

It seems like in the source code, runtime = tpl.format(settings.cli.runtime), is being called and that this returns a NoneType object that is being used later and throws the error.

However, I cannot find in the documentation where and why I should specifiy the runtime. What can I do to fix this error?

Thank you in advance!

Lore

Answer 1

Hi!

The MPI error is probably due to a MPI / PETSc missconfiguration. It is hard to say any more than that without having a closer look at the system.

I do not understand why you run your script with the "--platform marconi_debug" option. This wants to run the simulation in the context of the Marconi supercomputer. On those system you are also required to specify a runtime (e.g. --runtime 1:00:00), this is the second error you encountered.

Cheers, Aurel

Comments

Hi Aurel

Thank you for the quick reply! After completely removing PETSC from my computer and installing/building it again and rebuilding openCARP with make clean setup (the clean needed to be there), it works again!

Cheers

Lore