Add docker.runOptions to avoid memory swap error #351

olgabot · 2019-06-25T00:38:21Z

Hello! I had been running into some docker errors and tracked down some magic settings that made them go away. This PR adds those settings to the default nf-core created sample.

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If you've fixed a bug or added code that should be tested, add tests!
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ewels · 2019-06-25T04:37:54Z

I feel like we've talked about adding this to the main template before, but were nervous that it would cause problems for some users (which is why it's not already a default in nextflow). Maybe @pditommaso can remember?

Generally I tend to think that stuff like this should be addressed upstream in nextflow rather than being patched in pipelines downstream though, if possible..

pditommaso · 2019-06-25T08:19:09Z

Basically enforcing the user and group id changes some env variables such as USER and HOME, however, it should be just fine 99% of the cases. More details here.

Yes, the plan is to include as default. If you could stress test it a bit with nf-core pipelines and confirm there's no impact, I would be happy to make it the default option.

ewels · 2019-06-27T12:13:01Z

Ok great, thanks! Then yes maybe we can merge this PR so it (eventually) goes out to all pipelines. Would be good to add a comment that this will hopefully be a default in the future and can be removed at a later date...

maxulysse · 2019-06-27T12:19:02Z

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config

+// Avoid this error:
+// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
+// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker
+docker.runOptions = '-u $(id -u):$(id -g)'


Shouldn't it be -u \$(id -u):\$(id -g)?
cf: https://github.com/nf-core/sarek/blob/10eff4e8ff71e672d73a3bf4aa43a3693342bfb2/nextflow.config#L63

Not sure that is required - the '...' should be enough if it's in nextflow.config right?

sorry, I didn't understood what you meant ;-)

I mean I'm not sure whether we need to escape the $ with a \$ here as they are inside a '...' single quotes block :)

Aaaah, now I understand.
I'm pretty sure I copied that from someone else (probably Paolo) at some point.
I'm guessing the double quotes render the escaping the $ a necessity

Then we need to address this as well - I was looking for another place where this is used but couldn't find it. Wouldn't fixOwnership as listed here do the same? https://www.nextflow.io/docs/latest/config.html#config-docker

apeltzer · 2019-06-27T12:47:58Z

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config

@@ -58,6 +58,11 @@ profiles {
  test { includeConfig 'conf/test.config' }
 }

+// Avoid this error:
+// WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
+// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker


Suggested change

// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker

// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker

// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351, once this is established and works well, nextflow might implement this behavior as new default.

Could you add this in @olgabot? That should be enough to be able to trace things back once they're in the template.

apeltzer · 2019-06-28T06:43:10Z

Merging this to dockerrunOptions to make the final changes required 👍

maxibor · 2020-02-03T09:32:07Z

@apeltzer @pditommaso @ewels : -u $(id -u):$(id -g) doesn't seem to be a jack of all trades: when using the Ete toolkit python package in the coproID pipeline, with these docker run options, I get an error:

NCBI database not present yet (first time used?)
  Traceback (most recent call last):
    File "/opt/conda/envs/nf-core-coproid-1.1dev/bin/sourcepredict", line 176, in <module>
      sm.compute_distance(distance_method=distance_method, rank=RANK)
    File "/opt/conda/envs/nf-core-coproid-1.1dev/bin/sourcepredictlib/ml.py", line 257, in compute_distance
      ncbi = NCBITaxa()
    File "/opt/conda/envs/nf-core-coproid-1.1dev/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 110, in __init__
      self.update_taxonomy_database(taxdump_file)
    File "/opt/conda/envs/nf-core-coproid-1.1dev/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 129, in update_taxonomy_database
      update_db(self.dbfile)
    File "/opt/conda/envs/nf-core-coproid-1.1dev/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 731, in update_db
      os.mkdir(basepath)
  PermissionError: [Errno 13] Permission denied: '/.etetoolkit'

Using the default Docker run parameters works like a charm in this context.

When running dsl2 branch --profile test,docker the following error occurs: "WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap." This is fixed by adding "docker." prior to "runOptions", as per the discussion here: nf-core/tools#351

Add docker.runOptions to avoid memory swap error

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maxulysse reviewed Jun 27, 2019

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apeltzer requested changes Jun 27, 2019

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apeltzer changed the base branch from master to dockerrunOptions June 28, 2019 06:42

apeltzer merged commit 5f1f453 into dockerrunOptions Jun 28, 2019

apeltzer mentioned this pull request Jun 28, 2019

Options for DockerRun #352

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apeltzer deleted the olgabot-patch-1 branch September 20, 2019 12:15

This was referenced Sep 3, 2020

Process writes to host home directory which is mounted in the container #734

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Fix mhcflurry docker permission problem nf-core/epitopeprediction#52

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Add docker.runOptions to avoid memory swap error #351

Add docker.runOptions to avoid memory swap error #351

olgabot commented Jun 25, 2019

ewels commented Jun 25, 2019

pditommaso commented Jun 25, 2019

ewels commented Jun 27, 2019

maxulysse Jun 27, 2019

apeltzer Jun 27, 2019

maxulysse Jun 27, 2019

apeltzer Jun 27, 2019

maxulysse Jun 27, 2019

apeltzer Jun 27, 2019

apeltzer Jun 27, 2019

apeltzer Jun 27, 2019

apeltzer commented Jun 28, 2019

maxibor commented Feb 3, 2020 •

edited

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	// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker
	// Thanks to: https://github.com/alesssia/YAMP/wiki/How-to-use-Docker
	// Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351, once this is established and works well, nextflow might implement this behavior as new default.

Add docker.runOptions to avoid memory swap error #351

Add docker.runOptions to avoid memory swap error #351

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olgabot commented Jun 25, 2019

PR checklist

ewels commented Jun 25, 2019

pditommaso commented Jun 25, 2019

ewels commented Jun 27, 2019

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apeltzer commented Jun 28, 2019

maxibor commented Feb 3, 2020 • edited Loading

maxibor commented Feb 3, 2020 •

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