Irfan Alibay

Following up from discussions with @jchodera on slack - how would folks feel about a first pass of just moving the base HTF class without the TopologyProposal requirements into openmmtools?...

@ijpulidos I think this switch would still be really useful for us. Is there anything we can help out with to get this to a merged state?

@ijpulidos - I'm currently debugging this but things seem to have changed a bit since yesterday. What we've found is: 1. There is a large performance drop after a certain...

As per a slack conversation with @ijpulidos, I tested also this on OpenMM 7.7 and it also fails there (i.e. it fails on both 8 and 7.7)

@tylerjereddy do you know if this is still an issue? I'm fixing our tests against nightly wheels here https://github.com/MDAnalysis/mdanalysis/actions/runs/8870195702/job/24351713441?pr=4502#step:9:127 and can't seem to be able to reproduce the test failure.

Thanks for the update @tylerjereddy - I'd say let's leave it open. At least on my end I'm not 100% sure the nightly CI is working exactly as expected, I'll...

Updating the userguide and testing on dask `2024.4.2` this no longer seems to be an issue. Could someone please double check? cc @yuxuanzhuang and @pgbarletta

@samuelmurail any chance the exact number it fails at is 4096 files? That would be the default file open limit in modern Linux if I remember correctly.

Off the top of my head options here could be to increase your hard limit using ulimit or to concatenate chunks of your PDBs into a multi frame trajectory file.

Sorry my capacity is a bit limited this week - maybe someone from @MDAnalysis/coredevs has some insights here?