Closed BJWiley233 closed 1 year ago
We are looking into this. This usually happens when a frame of the trajectory is broken. We believed for the problems we recently saw, the simulation was fine, but for some reason, the frame saved in trajectory was broken on rare occasions. Before we catch this bug, I don't have a better suggestion than ignoring/removing this frame from the arc file.
Ok. BAR reports 100 frames at a time so if I have 5000 frames and I get this after Completed 5000 Coordinate Frames
does that mean it's one of the frames in the last 100?
I think when bar is running, it will handle two trajectory files. This looks like the first trajectory is fine, but something is broken in the next trajectory.
This is my first attempt to fix the problem: docker pull tinkertools/tinker9:cuda10.1-20220822-e2585f00
and docker pull tinkertools/tinker9:cuda11.2.2-20220822-e2585f00
As you may have noticed, the corrupted frames don't happen very often, I can't say this issue is definitely fixed with limited tests so far, but I definitely caught something in the code that was suspicious to me. We will also do more tests in our lab. Thanks again.
Yes I think I may have been getting read/write issues on my HPC w.r.t the GPUs and so corrupted frames could be my issue. Will test with new image but I think I have to rerun the end of some simulations.
Hi Zhi,
I am running
bar9
on 2 trajectories each with 5000 frames. BAR finishes withCompleted 5000 Coordinate Frames
but then I get this error that I think we talked about before:I am using tinker9 from this image
tinkertools/tinker9:cuda10.1-20220606-09e1bfcc