A bit more text about Singularity?

[bids-apps]

A bit more text about Singularity?

[chrisgorgo]

It depends on the particular singularity configuration. /home and /tmp are
good bets. In addition the docker2singularity converter creates mount
points used in Sherlock and XSEEDE clusters

https://github.com/chrisfilo/docker2singularity/blob/master/docker2singularity.sh#L147

We can add the mount points used in your system to the converter.

It would be good to asjust the tutorial http:/ /bit.do/r_testing

On Mon, Sep 5, 2016 at 9:14 AM, justbennet [email protected] wrote:

I had a some bit of trouble with figuring out the appropriate paths that
would be available to the Singularity container. Do you think that adding a
bit more text after the example to explain that, when running the
Singularity container version, the paths to the data and the output need to
be determined specifically for the cluster being used, but that using paths
from /home/ are a good bet?

As you note, different folders will be accessible in different places, and
I got confused about which to use.

I can write some text and submit via PR if this seems a good idea.

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[justbennet]

The only one we might want is /nfs, which would be where persistent storage
from labs might be kept. Otherwise, our standard mounts are /home and
/scratch, and I was just able to get /scratch to work.

If it makes a difference, folders under /nfs are handled via autofs on the
host system, I think. I think you should probably hold off on that until
we have someone who needs it. There are not a lot of people using the
cluster yet, and there is a layer of support people -- mainly me and Daniel
-- between them and the cluster, so we'll get warning.

-- bennet

On Mon, Sep 5, 2016 at 12:18 PM, Chris Filo Gorgolewski <
[email protected]> wrote:

It depends on the particular singularity configuration. /home and /tmp are
good bets. In addition the docker2singularity converter creates mount
points used in Sherlock and XSEEDE clusters

https://github.com/chrisfilo/docker2singularity/blob/
master/docker2singularity.sh#L147

We can add the mount points used in your system to the converter.

It would be good to asjust the tutorial http:/ /bit.do/r_testing

On Mon, Sep 5, 2016 at 9:14 AM, justbennet [email protected]
wrote:

I had a some bit of trouble with figuring out the appropriate paths that
would be available to the Singularity container. Do you think that
adding a
bit more text after the example to explain that, when running the
Singularity container version, the paths to the data and the output need
to
be determined specifically for the cluster being used, but that using
paths
from /home/ are a good bet?

As you note, different folders will be accessible in different places,
and
I got confused about which to use.

I can write some text and submit via PR if this seems a good idea.

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