Psydac on fedora:latest, import problem

[spossann]

I am trying to run Psydac on the latest Fedora docker image, which uses Python 3.11 by default. Here is the image I use:

FROM fedora:latest

# install linux packages 
RUN dnf install -y python3-pip \
    && dnf install -y gcc \
    && dnf install -y gfortran \ 
    && dnf install -y blas-devel lapack-devel \ 
    && dnf install -y openmpi openmpi-devel \
    && dnf install -y libgomp \
    && dnf install -y git \
    && dnf install -y environment-modules \
    && dnf install -y python3-mpi4py-openmpi \
    && dnf install -y python3-devel \
    && dnf install -y python3.10 \
    && dnf install -y python3.10-devel 

After launching a container like

docker run -it  fedora_img

I first run

[...]# . /etc/profile.d/modules.sh && module load mpi/openmpi-$(arch) && module list

to import the mpi module. After cloning the repo, the installation from devel works fine. However, when launching Python and trying to import, I get (note that the numpy import works, I tested also several other imports, such as struphy):

[...]# python3
Python 3.11.4 (main, Jun  7 2023, 00:00:00) [GCC 13.1.1 20230511 (Red Hat 13.1.1-2)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
>>> import psydac
dd1baa5f5873:pid267.python3: Failed to get eth0 (unit 0) cpu set
dd1baa5f5873:pid267: PSM3 can't open nic unit: 0 (err=23)
PMIx Log Report:[267]: (nic/PSM)[267]: PSM3 can't open nic unit: 0 (err=23)
dd1baa5f5873:pid267.python3: Failed to get eth0 (unit 0) cpu set
dd1baa5f5873:pid267: PSM3 can't open nic unit: 0 (err=23)
PMIx Log Report:[267]: (nic/PSM)[267]: PSM3 can't open nic unit: 0 (err=23)

I have tried also a virtual environment (even launched with python3.10 -m venv env), but get the same errors.

[yguclu]

I have never seen an error like this before! 😅 For what it's worth, my intuition suggests that this is an MPI problem. Have you tried to import mpi4py?

[spossann]

import mpi4py works.

[yguclu]

Nice that the import of mpi4py works. Have you tried to use it together with mpirun? At a minimum you should write from mpi4py import MPI, and try some basic instructions (e.g. having each process write their MPI rank to the terminal, in order).

[yguclu]

@spossann Do you have any updates on this issue?

[spossann]

I have created an issue on this in the fedora-image Github page. Let's see.

[spossann]

import mpi4py works.

However, from mpi4py import MPI leads to the mentioned crash.

[richardvanderburgh]

Adding these environment variables seemed to resolve this issue for me.
OMPI_MCA_pml=ob1
OMPI_MCA_btl=tcp,self

[yguclu]

@spossann Have you tried the suggestion posted above?

[spossann]

@spossann Have you tried the suggestion posted above?

@richardvanderburgh used this in his testing branch and the job for the Fedora_38 test passed. Here are the job commands.