Closed ssnn-airr closed 2 years ago
Original comment by Julian Zhou (Bitbucket: jqz, GitHub: julianqz).
I’ve actually not encountered this particular problem, or anything to do with multiprocessing or FilterSeq
really. @{557058:4550da01-a8bf-43cd-9876-9fde3f096568} I think you might be thinking of my getting stuck with AssemblePairs
, but rather because of blastn
and something to do with the file system, and not because of MPI.
Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
This one is hard to debug. We do see this on some computing clusters, more often with AssemblePairs or AlignSets. I think it’s caused by running out of allocated memory.
@{557058:17032cad-7aa5-47e3-a2ff-083ece1e1478} , did you have any luck working around this on farnam?
Original report by Ido Tamir (Bitbucket: ido, GitHub: ido).
Hello,
I run presto in a singularity 3.4.1 container on a slurm cluster with nextflow and when having multiple instances running I randomly get the error:
This happens more or less randomly and I suspect it happens when the processes are on the same node. It did not happen when I processed only one dataset. Is this possible?
Its a bit difficult to debug. Do you know what I could do?
Thank you very much,
ido