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GARD fails due to MPI setup (?) #30
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Hi @Shellfishgene , thanks for your interest in the pipeline! All should happen inside the container: but it seems there is some issue with the Singularity container version for GARD+MPI. I will try to look into it asap I guess you have no way on your cluster to run the Docker profile? |
No Docker on the cluster, I can run it on a workstation though. It's not urgent anyway... Thanks for having a look! |
Getting similar problem, different log with singularity: Failed to create a completion queue (CQ): Hostname: endeavour2 Check the CQE attribute.Open MPI has detected that there are UD-capable Verbs devices on your You job will continue, but Open MPI will ignore the "ud" oob component Hostname: endeavour2Failed to create a completion queue (CQ): Hostname: endeavour2 Check the CQE attribute.Open MPI has detected that there are UD-capable Verbs devices on your You job will continue, but Open MPI will ignore the "ud" oob component Hostname: endeavour2No OpenFabrics connection schemes reported that they were able to be Local host: endeavour2
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Hey @Shellfishgene!
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I figured out what the problem was: I forgot to set the |
@Shellfishgene ah great, thanks for letting us know! So it seems that when no "execution" profile is defined, the default core number as defined here: is not distributed to the processes. With @fischer-hub maybe we can just add a check to the |
@hoelzer Yes good idea probably, I also ran into some other issues with the gard process when running with |
Hi!
I just tried to run the pipeline with profile local and singularity, with the test data
bats_mx1_small.fasta
. However GARD fails, apparently due some MPI setup stuff. I'm not sure if that should all happen in the container or if I have to deal with configuring that to run on the server/cluster?This is
gard.log
:The text was updated successfully, but these errors were encountered: