Enable spras in CHTC with new executor and profile #172
Conversation
There was a problem hiding this comment.
I was able to follow the instructions and run the example SPRAS workflow in CHTC. It's incredible to see this working in parallel on multiple EPs. I did not carefully scrutinize all of the output and logs. The SPRAS output files I checked did look as expected, however.
Edit: some of my initial comments were hidden when I finished reviewing, so I rewrote them. Then I noticed and deleted the duplicates.
|
One more suggestion: can you please add a small section to the main SPRAS readme about how it can be run with HTCondor and refer to the instructions here? |
jhiemstrawisc
force-pushed
the
run-spras-executor
branch
from
853e610 to
3027693
Compare
|
@agitter, Neha and I worked through this together, and I think I came away with a few small improvements. The main issue was that the spras container I point to (v0.1.0) is old enough that using the Snakefile from the current master branch in the workflow causes errors in the container's config module. I'll update the workflow to use the new version you released. |
That makes me curious how I ran it successfully? I must have been using some old version of SPRAS somewhere in my tests. |
Two issues solved with this commit -- first, Apptainer seems to be the way to go when working with HTCondor, both in and out of the OSPool. Instead of having instructions that say "if you encounter problem XXX, use Apptainer", this just tells the user to build the Apptainer image in the first place. Secondly, Neha encountered an issue while testing HTCondor compatibility where the container's Snakefile version was incompatible with the version of the Snakefile being transferred from the AP to the EP. This resulted in a confusing error message and wouldn't be straight forward to recognize for most people, so I decided I'd urge the users to build their own containers in the first place. If they do this, then they can be sure there are no compatibility issues.
jhiemstrawisc
force-pushed
the
run-spras-executor
branch
from
3027693 to
2655d1b
Compare
|
@agitter I just included a few small updates that are worth looking over. Notably, I changed the default behavior I steer the user toward when selecting an image to use with HTCondor. Previously I pointed them to Docker and told them "use Apptainer if you have issues." The issues seem prevalent, however, so now I just tell them to use Apptainer in the first place. The second change encourages them to build their own containers to make sure the version of SPRAS installed in the container is compatible with the version they've cloned onto the AP. This was the issue Neha ran into mentioned above. |
@agitter I think this gets us to the point where we can run a full SPRAS workflow in both the CHTC pool and the OSPool. At least, I've done testing in both and it works for me 😉
When you've got a chance, can you test out my new instructions and let me know how it goes?