Further info on simpleaf index on HPCs

[wmacnair]

Hi @rob-p, hope you're doing well!

I have been trying to build an index for the first time in a while, and so I'm returning to an issue that has been raised a couple of times, for example here: https://github.com/COMBINE-lab/simpleaf/issues/161.

I've put in a bit more debugging effort than previously, and have managed to get it to work for me. In my case, I had to use /tmp rather than /scratch, as it turns out /scratch for me is (I think) a super-fast NFS server and therefore has the same issues.

Here are a few bits of information that will hopefully be interesting to you:

• In my case, the main problem is not how long the process takes, but the fact that many tiny / empty files named cuttlefish-path-output-... are created, but not all deleted, by simpleaf index. This becomes a real problem, as at some point you hit 1M files and you get kicked off the cluster 😅
• I tried using /scratch as working and index directory and had the same problem, as it turns out our scratch is fast but non-local.
• Using /tmp worked! I checked the directory and there were the same cuttlefish-path-output-... files as before, but deletion was keeping up with creation.
• Another strange observation is that this problem didn't happen in an interactive job on the cluster, independent of working directory.

I'm wondering about easy ways to fix this. A thought is something like:

1. Add a local_dir parameter to simpleaf index, and then once it is finished, copy the outputs over to the output_dir.
2. Include some testing that the local_dir really is local.

I imagine the second part is a bit more tricky. Maybe a possible approach is not to check whether the dir is local, but to check that it is sufficiently fast? And/or include checks of whether the number of cuttlefish-path-output files is getting out of hand? It feels like something should be possible...

Hope this is helpful! Will