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vatlab / sos

SoS workflow system for daily data analysis
http://vatlab.github.io/sos-docs
BSD 3-Clause "New" or "Revised" License
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Additional flags for containers #1500

Closed tfabiha closed 2 years ago

tfabiha commented 2 years ago

Hi Bo,

I'd like to run scripts in singularity with the --nv flag, similar to the command singularity run --nv {filename}.sif, but haven't been able to find any information about including flags for containers in the SoS docs.

I was wondering if there already is a way to include flags?

Thank you in advance!

BoPeng commented 2 years ago

You are right, currently the singularity mode only supports the bind option, not nv. There are also a number of other options that could be supported.

It also does not support singularity run, only singularity exec.

Let me see if I can come out with a quick fix.

BoPeng commented 2 years ago

This has been fixed in the 1500 branch, but I am not sure what to do with singularity run since it runs the script built in the container, not the scripts we provide. If you actually meant docker exec --nv, I can merge the branch and close the ticket.

tfabiha commented 2 years ago

I'll be able to run with singularity exec. Thank you so much for such a quick response!

BoPeng commented 2 years ago

I have updated test and doc, and released sos 0.23.2.