Hi Szilárd,
I did some digging and came across this post which suggested to me that the inability to do updates on the GPU may be due to the fact I have constraints = h-bonds and then the ordering of my small molecule PDB file doesn’t place hydrogens directly following the heavy atoms they are attached to. Is this thinking correct? If so I can look into potentially making adjustments to the ordering.
I also have managed to re-produce the initial issue I was encountering (seemingly random performance loss). I realised this issue only arises when slurm runs simulation jobs on compute nodes that haven’t completely shut down after running a previous job. I.e., if a simulation has just finished but the compute node is still running and a new job is submitted to that node, the simulation will experience insane performance degradation. However, if the node is allowed to shut down, and a job is then submitted to a new node instance, this performance degradation isn’t exhibted. I’m a bit lost as to why this might be happening and any advice would be greatly appreciated!
Thanks,
Noah