Difference between revisions of "Namd on BGQ"
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(Created page with "Taking into consideration the official (test)[NAMD performance tuning recommendations], a parameter study was undertaken to test simulation performance and efficiency on the B...") |
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|16 | |16 | ||
|4096 | |4096 | ||
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|12.9322 | |12.9322 | ||
|0.58 | |0.58 | ||
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|17.2722 | |17.2722 | ||
|0.77 | |0.77 | ||
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|0.63 | |0.63 |
Revision as of 17:26, 29 October 2012
Taking into consideration the official (test)[NAMD performance tuning recommendations], a parameter study was undertaken to test simulation performance and efficiency on the BG/Q cluster.
The following study was undertaken for a 246,000 atom membrane protein (Cytochrome c Oxdaise embedded in a TIP3P solvated DPPC bilayer) using the CHARMM36 forcefield (protein and lipids). Efficiency was measured with respect to the 16 ranks-per-node 512 core simulation.
Ranks | Cores | NAMD Config Options | ns/day | Efficiency |
16 | 512 | 2.7874 | 1.00 | |
16 | 1024 | 5.0483 | 0.91 | |
16 | 1024 | twoAwayX (default) | 5.6204 | 1.01 |
16 | 2048 | twoAwayX (default) | 10.0699 | 0.90 |
16 | 2048 | twoAwayXY | 10.5875 | 0.95 |
16 | 4096 | twoAwayX | 14.3285 | 0.64 |
16 | 4096 | twoAwayXY (default) | 17.6313 | 0.79 |
16 | 4096 | twoAwayXYZ | 16.7962 | 0.75 |
16 | 8192 | twoAwayX | 23.5198 | 0.53 |
16 | 8192 | twoAwayXY (default) | 24.9981 | 0.56 |
16 | 16384 | twoAwayX | 23.6706 | 0.27 |
16 | 16384 | twoAwayXY | 28.3096 | 0.32 |
16 | 16384 | twoAwayXYZ (default) | 27.9791 | 0.31 |
16 | 4096 | twoAwayXY, PMEPencils=8, lblUnload=yes | 12.9322 | 0.58 |
16 | 4096 | twoAwayXY, PMEPencils=12, lblUnload=yes | 17.2722 | 0.77 |
16 | 4096 | twoAwayXY, PMEPencils=16, lblUnload=yes | 16.0208 | 0.72 |
16 | 4096 | twoAwayXY, PMEPencils=20, lblUnload=yes | 15.4154 | 0.69 |
16 | 4096 | twoAwayXY, PMEPencils=12 | 16.2079 | 0.73 |
16 | 4096 | twoAwayXY, PMEPencils=16 | 17.9231 | 0.80 |
16 | 4096 | twoAwayXY, PMEPencils=20 | 17.9949 | 0.81 |
16 | 4096 | twoAwayXY, PMEPencils=24 | 17.8308 | 0.80 |
16 | 4096 | twoAwayXY, PMEPencils=36 | 16.9666 | 0.76 |
8 | 4096 | twoAwayXY, PMEPencils=20 | 18.2473 | 0.82 |
16 | 4096 | twoAwayXY, PMEPencils=20 | 17.9949 | 0.81 |
32 | 4096 | twoAwayXY, PMEPencils=20 | 13.9414 | 0.63 |
4 | 512 | 2.8589 | 1.03 | |
8 | 512 | 2.8367 | 1.02 | |
16 | 512 | 2.7874 | 1.00 | |
32 | 512 | 2.2951 | 0.82 | |
16 | 512 | unloadZero | 2.7932 | 1.00 |