MPI error while running inside a Docker container

[David Montiel Taboada]

Hello, 

I am running a container of PRISMS-PF (which is built upon the dealii:v9.2.0-focal image). 

Inside the container, the code compiles successfully, but when I run it, I get the following error message:

----------------------------------------------------
PRISMS-PF: Exception on processing:

--------------------------------------------------------
An error occurred in line <6909> of file
</build/deal.ii-vFp8uU/deal.ii-9.2.0/source/base/data_out_base.cc> in
function
     void dealii::DataOutInterface<dim,
spacedim>::write_vtu_in_parallel(const string&, MPI_Comm) const [with
int dim = 2; int spacedim = 2; std::string =
std::__cxx11::basic_string<char>; MPI_Comm = ompi_communicator_t*]
The violated condition was:
     ierr == MPI_SUCCESS
Additional information:
deal.II encountered an error while calling an MPI function.
The description of the error provided by MPI is "MPI_ERR_ACCESS: invalid
access mode".
The numerical value of the original error code is 20.
--------------------------------------------------------

Aborting!
----------------------------------------------------

This appears to happen if I try to run the code in serial. 

However I only have the issue on a Linux machine (I have no problem if I run on a Mac or Windows machine, for instance) which leads me to believe it may be a conflict between the Docker container and the underlying OS. 

Has anyone encountered something similar? Any idea of what may be going on?

Thank you!

David

[David Montiel Taboada]

This is how I am launching the container, by the way:

$ docker run -ti -v ~/DockerWorkspace/phaseField/applications:/home/dealii/phaseField/applications prismspf/prismspf:2.2

[David Montiel Taboada]

Sorry in my original email I wrote "This appears to happen if I try to run the code in serial."

I meant it happens whether I try to run the code in serial or parallel (e.g., using "./main" or "mprun -n 4 main"). It makes no difference.

Thank you,

David

[Bruno Turcksin]

David,

Have you try to create a new file and save it inside docker? What is your user name in docker? Are you root? It could be a problem with your permission.

Best,

Bruno

[David Montiel Taboada]

Hello, Bruno. 

Thank you, I will check. I assumed that was not the issue because when I compile inside docker files are created.

David

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[Bruno Turcksin]

David,

It depends where the build files are written. Do you see the build
files on your computer or do they exist only in the Docker container,
i.e, after you've killed Docker do the files still exist somewhere on
your computer ?

Best,

Bruno

Le mar. 17 août 2021 à 09:00, David Montiel Taboada
<dmon...@umich.edu> a écrit :

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[Timo Heister]

The error appears inside write_vtu_in_parallel, which uses MPI I/O. It
might be that the type of filesystem (docker shared volume) does not
allow parallel IO or that the docker installation does not have MPI IO
enabled.

On Tue, Aug 17, 2021 at 10:15 AM Bruno Turcksin

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Timo Heister
http://www.math.clemson.edu/~heister/