Assistance Needed with example_prediction.py

[FrancoisPorcher]

Hi

I’m encountering an issue while trying to run the example_prediction.py file. Could you please clarify the exact command you use to execute it?

Here are the commands I’ve tried so far, but none of them worked:

mpiexec example_prediction.py torch run example_prediction.py torch.distributed run example_prediction.py

The error originates from the following line in utilities/distributed.py (line 7):

from mpi4py import MPI

Could you provide guidance on resolving this error?

Thank you for your assistance!

[FrancoisPorcher]

The error I get is:

(biomedparse) [fp427@gpu-q-43 BiomedParse]$ python example_prediction.py 
Abort(1090319) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init_thread: Unknown error class, error stack:
MPIR_Init_thread(192): 
MPID_Init(1538)......: 
MPIR_pmi_init(164)...: PMI_Init returned 14

[Adibvafa]

@FrancoisPorcher Are you setting up a new conda enviornment for it?

[FrancoisPorcher]

@FrancoisPorcher Are you setting up a new conda enviornment for it?

Yes I am I just reproduced the environment from the authors (with mamba and not conda though)

[Adibvafa]

@FrancoisPorcher Are you setting up a new conda enviornment for it?

Yes I am I just reproduced the environment from the authors (with mamba and not conda though)

You should follow the exact steps and setup a new conda environment otherwise you will run into issue.