I saw that this error occured to some people before but none of the suggested solutions worked for me. I’m trying to run fmriprep (version 20.2.0) on my bids-compatible data (4.3GB in total) but receive the following error after some time:
concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.
Since this message seems to appear when memory is limited, I made sure to add the
--low-mem flag and tried different values for
--nthreads from 8 to 2 and for
--omp-nthreads from 2 to 1 without success. Later, I also specified
--mem-mb with values between 28000 and 31000 for my machine with 31GB of available RAM but the problem remains. One difference is that reducing the number of threads does not lead to the following warning anymore at the beginning of the execution:
nipype.workflow WARNING: Some nodes exceed the total amount of memory available (28.15GB).
To rule out that Ubuntu limits the amount of RAM allocated to the docker container, I also checked
docker stats and see that the expected 31GB are available.
Does anyone have any idea of how to make it run successfully?