OpenMM 6.3 slowing down parmed netcdf reporter

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George Pantelopulos
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OpenMM 6.3 slowing down parmed netcdf reporter

Post by George Pantelopulos » Mon Feb 22, 2016 9:53 am

Hi all,

I've been running simulations on a new setup with a Titan X with OpenMM 6.3 and it seems that all simulations I am running are experiencing a gradual dropoff in performance in a variety of different simulation setups.
nsday_step.pdf
ns/day over steps
(13.41 KiB) Downloaded 55 times
Has anyone encountered something such as this before? I've attached the script used to produce the particular run here in case it might have some helpful info.
Attachments
production.txt
Simulation script
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Last edited by George Pantelopulos on Mon Feb 22, 2016 3:41 pm, edited 2 times in total.

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George Pantelopulos
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Re: OpenMM 6.3 slowing down over the course of a run

Post by George Pantelopulos » Mon Feb 22, 2016 1:55 pm

It appears that this is somehow related to parmed's netcdf reporter. Running with openmm's dcdreporter avoids this issue.

I'm using the netcdf reporter because I want to save the velocities. I've tried to obtain velocities by appending them as numpy arrays (after removing the units from velocities) to pytables, which appears to cause the same performance loss. Writing the velocities to numpy arrays with this same writing frequency appears to avoid this performance loss, though this is obviously a very ugly solution.

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Jason Swails
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Re: OpenMM 6.3 slowing down over the course of a run

Post by Jason Swails » Mon Feb 22, 2016 2:11 pm

This is a consequence of scipy's NetCDF class slowing down as the NetCDF file grows in size. The reader is the fastest Python option, but the writer is slower than the one from NetCDF 4 and slows down over time.

I could probably work around this issue by supporting NetCDF writing through the netCDF4 package. How severe is the slowdown? how long does it take to be significant? (Say about a 5% performance hit or more?)

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George Pantelopulos
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Re: OpenMM 6.3 slowing down with netcdf reporter

Post by George Pantelopulos » Mon Feb 22, 2016 3:39 pm

Hi Jason,

Thanks for the reply! There is a pdf I had attached in the original post that shows the slowdown, particularly a huge shift in performance around 0.9e7 steps, before which there is a small performance loss. The system has 15720 particles.

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