PETSC error using Docker

[huisophiewang]

Hi,

I installed firedrake through virtualenv before, and now I need to switch to docker in order to run my algorithm in the cluster.
After running "docker run -it firedrakeproject/firedrake bash", and "source activate", I tried to import firedrake, and here's the error I got. I’m not entirely sure what this means. Could someone kindly provide some guidance on how to solve this problem?

(firedrake) firedrake@e67f9aae2552:~/firedrake/bin$ python3
Python 3.12.3 (main, Nov 6 2024, 18:32:19) [GCC 13.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

import firedrake
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 4 Illegal instruction: Likely due to memory corruption
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
[unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
:
system msg for write_line failure : Bad file descriptor
(firedrake) firedrake@e67f9aae2552:~/firedrake/bin$

[Ig-dolci]

Can you please check if the docker image from docker pull firedrakeproject/firedrake-vanilla gives you the same error?

[Ig-dolci]

There are no errors when I use the firedrake-vanilla docker image. Should I use this one instead?

It seems that one of the packages installed in the Firedrake image might have an architecture issue. Could you try the following to troubleshoot the error?

Inside the firedrake image, run:

pip uninstall netgen

Then, try importing Firedrake again to verify if the error persists. I already saw a similar fail associated with Netgen.

[Ig-dolci]

My Python program actually uses PETSc and SLEPc. I'm using firedrake-vanilla as the base image. When I add this to the dockerfile "RUN bash -c "source firedrake/bin/activate; firedrake-update --slepc", it has the same error again. Any suggestions?

124.1 Installing slepc4py/

124.1 Copying slepc4py to virtualenv to install
174.3 /home/firedrake/firedrake/lib/python3.12/site-packages/pytools/persistent_dict.py:52: RecommendedHashNotFoundWarning: Unable to import recommended hash 'siphash24.siphash13', falling back to 'hashlib.sha256'. Run 'python3 -m pip install siphash24' to install the recommended hash.
174.3 warn("Unable to import recommended hash 'siphash24.siphash13', "
174.3 [0]PETSC ERROR: ------------------------------------------------------------------------
174.3 [0]PETSC ERROR: Caught signal
174.3 [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
174.3 [0]PETSC ERROR: or see https://petsc.org/release/faq/#valgrind and https://petsc.org/release/faq/
174.3 [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
174.3 [0]PETSC ERROR: to get more information on the crash.
174.3 application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
174.3 [unset]: PMIU_write error; fd=-1 buf=:cmd=abort exitcode=59 message=application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
174.3 :
174.3 system msg for write_line failure : Bad file descriptor

If you want to have SLEPc working on top of the firedrake_vanilla image, you can follow these steps that are working here on my Mac.

1. Start a Container Using firedrake_vanilla:
   Run the following command:

   docker run -it <image_id_from_firedrake_vanilla> /bin/bash

2. Activate Firedrake and Install SLEPc:
   Inside the container, execute:

   source firedrake/bin/activate
   firedrake-update --slepc

3. Save the Updated Container as a New Image:
   Exit the container, and from your terminal, commit the changes to create a new Docker image:

   docker commit <container_id> firedrake_slepc:v1

Now, you can use the new image firedrake_slepc:v1, which has SLEPc installed.

[connorjward]

I think that our Docker containers do not really work on Macs because we only have x86 images, not ARM ones. We should try and fix that.

[huisophiewang]

I see. I'll switch to Linux for now. Would the latest Ubuntu work well with firedrake or do you have other recommendations?

[connorjward]

Ubuntu will definitely work, but you could also try and regular installation of Firedrake on macOS without Docker.