Error when running schur decomposition

[SohaibRais]

I'm getting an error when I try running schur decomposition with my cellrank estimator. The error is below and I believe it's tied to threading:

g.compute_schur(n_components=20)

[cli_0]: PMIU_write error; fd=10 buf=:cmd=init pmi_version=1 pmi_subversion=1
:
system msg for write_line failure: Bad file descriptior
[cli_0]: PMIU_write error; fd=10 buf=:cmd=abort exitcode=-1 message=PMI_Init failed
:
system msg for write_line failure: Bad file descriptior
[cli_0]: PMIU_write error; fd=10 buf=:cmd=get_appnum
:
system msg for write_line failure: Bad file descriptior
Abort(471460111): Fatal error in internal_Init_thread: Other MPI error, error stack:
internal_Init_thread(71): MPI_Init_thread(argc=0x2abf3fc71a18, argv=0x2abf3fc71a10, required=1, provided=0x7ffc4b779dac) failed
MPII_Init_thread(205)...:
MPIR_pmi_init(150)........:
(unknown)(): Other MPI error

Has anyone ever ran into this bug before or know how to fix it? I'm using a HPC cluster and my cellrank version is 2.0.7

[WeilerP]

Hi @SohaibRais, could you please try

1. Wrap your code in a main function; that helped with multiprocessing-related issues before (EOF Error when running Cellrank with experimental time #1257)
2. Running your code in a different shell (Errors for compute_transition_matrix  #1205)

[SohaibRais]

Hi @WeilerP , I tried option 2 using command line python and it seemed to resolve my issue. I noticed the command line python version wasn't the same as what I was using in iPython. Python 3.1.3 is the command line version that worked for me. I think the environment in my command line was also different as I deprecated packages like MPI in hopes that would resolve the error.

[WeilerP]

@SohaibRais, glad to hear things are working, but just to double-check: Are you really using Python 3.1.3? That would be a very old Python version, and I would be very surprised to learn that CellRank runs on it. Either way, I suggest you use at least Python 3.10 and set up a clean environment; you can follow these instructions to install everything you should need to run CellRank in a Jupyter Notebook; just replace the reproducibility part with pip install jupyterlab ipywidgets.

[SohaibRais]

@WeilerP Sorry, I miswrote. It worked with python version 3.13.3.