How to redirect output in SIngularity container

[Sam]

Hell all,

I'm very new to Singularity and i built and ran my first HPC application in a container. Now i need to save the output somewhere. I just did :

%runscript

./binary  | tee $SINGULARITY_ROOTFS/tempdir/resultsfile

or

./binary > $SINGULARITY_ROOTFS/tempdir/resultsfile

But im getting a permission error 

How and where can i save the output of a container run?

Thank you,

[v]

Hey Sam!

The runscript is what gets executed after the container is built, so the environment variable `$SINGULARITY_ROOTFS` is long gone (it's only relevant in a build specification file in the %setup section at build time). So if you want to write an output file, if you direct it somewhere in the container you will get an error (the container is read only!) Instead, try binding a directory that you have write access for to the container, eg:

singularity run --bind /path/with/write:/opt container.simg

and then in the runscript, make sure to write your result to whatever that directory is (in the above example, /opt)

%runscript

./binary  | tee /opt/resultsfile

Most default installations will bind /tmp automatically where you would have write, so you could also skip the bind and write there. If you want more specific details or help, please share your recipe and the output that you are getting, and we can go from there!

Best,

Vanessa

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Vanessa Villamia Sochat
Stanford University '16

(603) 321-0676

[Rémy Dernat]

Hi,

FYI, you can pipe the output of a command to a singularity container : http://singularity.lbl.gov/user-guide#compatibility-with-standard-work-flows-pipes-and-io

I would not store the results in a container, but rather in a bind directory.

Best regards,

Rémy

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Vanessa Villamia Sochat
Stanford University '16

(603) 321-0676

[Tyler Trafford]

I would recommend leaving the redirect out of the runscript.  Just let it go to stdout and redirect that output when you run the container image.

-Tyler

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Tyler Trafford

[Sam]

Every suggestion here worked. THank you all.