VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Jul 30 2014 - 21:20:53 CDT

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