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cluster:111 [2013/02/02 15:07] hmeij [Results] |
cluster:111 [2013/02/02 16:08] hmeij [Script] |
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^ PMEMD implementation of SANDER, Release 12 ^ | ^ PMEMD implementation of SANDER, Release 12 ^ | ||
- | |Minimzing the system with 25 kcal/mol restraints on protein, 500 steps of steepest descent and 500 of conjugated gradient| | + | |Minimzing the system with 25 kcal/mol restraints on protein, 500 steps of steepest descent and 500 of conjugated gradient |
+ | |||
+ | ^CPU Jobs (1,000 steps)^ Serial ^ -np 2 ^ -np 4 ^ -np 8 ^ -np 16 ^ -np 24 ^ -np 32 ^ | ||
+ | |Wall Time (secs)| | ||
+ | |||
+ | * MPI speedup near -np 24 is 8x serial | ||
+ | |||
+ | ^GPU Jobs^ Serial ^ -np 2 ^ -np 4 ^ -np 8 ^ -np 16 ^ -np 24 ^ -np 32 ^ | ||
+ | |Wall Time (secs)| | ||
+ | |||
+ | * GPU serial speedup is 17.5x CPU serial performance and outperforms MPI by at least 2x | ||
+ | * GPU parallel unable to measure | ||
+ | |||
+ | ^AMBER BENCHMARK EXAMPLES^^^^^^ | ||
+ | |JAC_PRODUCTION_NVE - 23,558 atoms PME|||||| | ||
+ | | 16 cpu cores | 1xK20 | 2xK20 | ||
+ | | 12.87 | 80.50 | 88.76 | 103.09 | ||
+ | | 6713.99 | ||
+ | |||
+ | |FACTOR_IX_PRODUCTION_NVE - 90,906 atoms PME|||||| | ||
+ | | 16 cpu cores | 1xK20 | 2xK20 | ||
+ | | 3.95 | 22.25 | 27.47 | 32.56 | ||
+ | | 21865.59 | ||
+ | |||
- | ^Job Type^ Serial ^ -np 2 ^ | ||
- | |Wall Time (secs| 211 | 120 | | ||
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< | < | ||
- | echo $i | + | [TestDriveUser0@K20-WS]$ cat run |
- | mpirun --machinefile=nodefile$i -np $i pmemd.cuda.MPI -O -i inp/mini.in -p 1g6r.cd.parm \ | + | |
- | -c 1g6r.cd.randions.crd.1 -ref 1g6r.cd.randions.crd.1 2>& | + | |
- | cp mdout ${i}gpu.parallel.log | + | |
- | done | + | |
- | + | ||
- | [TestDriveUser0@K20-WS ec]$ | + | |
- | [TestDriveUser0@K20-WS ec]$ w | + | |
- | | + | |
- | USER | + | |
- | TestDriv pts/0 engineering-pc.e Thu09 | + | |
- | TestDriv pts/1 greentail.wesley 05:31 4:50 | + | |
- | TestDriv pts/2 hmeij.its.wesley 05:31 0.00s 0.19s 0.01s w | + | |
- | [TestDriveUser0@K20-WS ec]$ uptime | + | |
- | | + | |
- | [TestDriveUser0@K20-WS ec]$ | + | |
- | [TestDriveUser0@K20-WS ec]$ | + | |
- | [TestDriveUser0@K20-WS ec]$ | + | |
- | [TestDriveUser0@K20-WS ec]$ | + | |
- | [TestDriveUser0@K20-WS | + | |
#!/bin/bash | #!/bin/bash | ||
rm -rf err out logfile mdout restrt mdinfo | rm -rf err out logfile mdout restrt mdinfo |