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Test fails when running pipeline on HPC with singularity: "destination is already in the mount point list" #383
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It's possible that you need to unset the SINGULARITY_BIND variable and tell Nextflow to automount. On systems that run singularity, I have a nextflow config file (
Setting |
@robsyme Line 125 in 3b6df9b
@FloWuenne I wouldn't add the bind paths to your .bashrc . You can add them in like so using a custom config file and pass it to the pipeline using -c custom.config :https://github.com/nf-core/configs/blob/b23e9d5a9f8772d83acfdf0dfb8c9d68de5d8087/conf/genouest.config#L11 |
Thanks for your help @robsyme and @drpatelh! So I have configured a custom config like the following:
and run the command like this:
But still, get the exact same error. Did I specify anything wrong? The pipeline, by the way, creates all files correctly until the following command for some reason:
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What is the contents of |
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Could it be due to me having numpy installed on in my home and the singularity container mounting my home and replacing the numpy from the container? I usually would try to circumvent this by running singularity with --no-home but how would I do it in this case? |
That's exactly it. I think that @poquirion has a nice solution, which I'm sure he'll include here. |
the python/conda installed in the container is looking in your You can prevent that by setting the
Also I would recommend to the the dev team in charge of the container to set that in there system. The Dockerfile seems like a good place to set that variable. @drpatelh ? |
Indeed running the pipeline with a custom config file as described above that contains this:
Finally it makes this step of the pipeline work without a problem! Thanks for the help @poquirion and everyone else! |
Great debugging guys 😎 We have indeed added that to the pipeline template already: This will be added to the I think the Did you figure out whether the bind paths are an essential requirement? If not, I would be tempted to try re-running the pipeline with this custom config:
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I just tested without the bind paths and worked as well. So for anyone still running into the same issue in the future, the only essential component is to make a custom.config script and add this block to it:
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I have put the env into xin.config and run Still got the following error: |
Has anyone else had luck resolving this? Singularity version 3.8.7-1.el8 |
Hi, Command error: The .command.sh is the following: cat <<-END_VERSIONS > versions.yml The previous solution "env { PYTHONNOUSERSITE = 1 } did not worked" Thanks! |
Hi there,
thanks for the great implementation and documentation. I was trying to run the rnaseq pipeline on our HPC this week and I was running into the following issue. This might be related to nextflow but I couldn't figure out how to fix this so any help or pointing me to the right nextflow documentation to fix this would be highly appreciated.
I am running the following command for testing :
I am using the singularity image which is stored in /work/singularity. The pipeline starts fine but then immediately throws this error:
Nextflow report error:
When I enter the singularity shell and run the commands for get_software_versions inside the container, it completes without an error. I think this might be related to a bind path issue but adding the following to my .bashrc did not solve the issue:
I would really appreciate any help with this since I was unable to fix it for now...
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