VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jul 31 2014 - 09:43:50 CDT

I've noticed this too, and it isn't just a bigdcd phenomenon. I had
noticed it mostly when going through a whole trajectory: initial dcds
loaded would have huge I/O rates (especially if I had run the script
before. The dcd was probably still in RAM), and then each successive
load would get progressively slower (It should be replicable with an
appropriate mol addfile with a suitable stride on big systems). I had
always chalked it up to having to copy data across from the dcd plugin
to VMD internal data structures, or perhaps I/O nonsense when it came to
running out of cache somewhere along the pipeline between disk and
display and falling back to unbuffered I/O. How big is the system? It
looks like any of these should fit individually into RAM, and loading a
whole trajectory file at once without interspersed computation then
operating on the whole loaded file feels faster to me (although I've
done it both ways).

-Josh Vermaas

On 7/30/14, 10:20 PM, Mayne, Christopher G wrote:
> I'm using the bigdcd script for analysis and I'm seeing huge drop-offs in IO speed followed by fluctuations. The per-frame proc is building a histogram -- measure bond distances (indices stored in global variables) and increment an element (i.e. my "bin") held in a global array. The only thing I can think of is that the initial array is small, and hence, fast. Because of structural constraints on my system, the final array size converges at around 100 elements, which I wouldn't guess is this much slower and it doesn't explain the fluctuations with the later dcd loads.
>
> Any ideas?
>
> Thanks,
> Chris
>
> VMD 1.9.2a39 running in text mode
> Linux, CentOS
>
> DCD IO output
> Info) Coordinate I/O rate 1429.2 frames/sec, 1652 MB/sec, 4.5 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.0.dcd.
> Info) Coordinate I/O rate 446.1 frames/sec, 515 MB/sec, 6.1 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.1.dcd.
> Info) Coordinate I/O rate 73.8 frames/sec, 85 MB/sec, 86.8 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.2.dcd.
> Info) Coordinate I/O rate 22.3 frames/sec, 25 MB/sec, 120.9 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.3.dcd.
> Info) Coordinate I/O rate 37.7 frames/sec, 43 MB/sec, 238.9 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.4.dcd.
> Info) Coordinate I/O rate 25.4 frames/sec, 29 MB/sec, 353.9 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.5.dcd.
> Info) Coordinate I/O rate 11.3 frames/sec, 13 MB/sec, 416.6 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.6.dcd.
> Info) Coordinate I/O rate 11.7 frames/sec, 13 MB/sec, 482.8 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.7.dcd.
> Info) Coordinate I/O rate 34.0 frames/sec, 39 MB/sec, 806.0 sec
> Info) Finished with coordinate file <redacted>.0.eq.0.8.dcd.
>
>
> VMD Startup Details:
> Info) VMD for LINUXAMD64, version 1.9.2a39 (March 21, 2014)
> Info) Exiting normally.
>
> Info) VMD for LINUXAMD64, version 1.9.2a39 (March 21, 2014)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 8 CPUs detected.
> Info) Free system memory: 23683MB (98%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 1 available CUDA accelerator:
> Info) [0] GeForce GTX 570 15 SM_2.0 @ 1.46 GHz, 1.2GB RAM, KTO, OIO, ZCP
> Info) Dynamically loaded 2 plugins in directory:
> Info) /Projects/vmd/pub/linux64/lib/vmd192a39/plugins/LINUXAMD64/molfile
>