HP ProLiant DL980 G7を使ったドメインドッキングの高速化
Contents
1. 6 1 500 IOOO 00 2 4 8 16 3e 64 80 7 4 2 8 8 4 9 32 14 9 64 27 4 80 33 3 0 10 0 0 0 30 0 40 0 N 03 5749 8328 95 00 19 00 10 0017 00 5 1 HP ProLiant httD www hp com jp proliant Intel Intel Intel Inside Intel Inside Xeon Xeon Inside Intel Corporation2. 3 2 2 4 1 3 2 1 2 2 3 W Technical white paper HP ProLiant DL980 G7 4 HP ProLiant DL980 G7 Open MPI ZD0CK Python 2 1 2 2 Xeon E7 8 80 HP ProLiant DL98
3. 2 2 2 2 1 2 2 000 MI 1 2 3 3 2 3 4 4 3 2
4. Technical white paper HP ProLiant DL980 G7 2 2 2 2 2 000 3 10 2
5. EK 2013 3 Copyright 2013 Hewlett Packard Development Company L P 136 871 1 2 2 1
6. 80 HP ProLiant DL980 G7 Open MPI ZDOCK Python multiprocessing 71 1 1 0 PDZ4 638 724 1 human LNX 1 PDZ1 PDZ2 PDZ3 PDZ4 human LNX 1 PDZ1 274 359 lt PDZ3 504 594 PDZz 381 464 lt
7. 0 G7 05S Cent05 Open MPI ZDOCK Python multiprocessing 4 python 1 Cee 4 inteD s e pa Xeor Xeon E7 HP VMA3205 5TB HP ProLiant DL980 G7 Xeon E7 4870 2 4GHz 8 80 1TB 900GB SAS HDDX8 7 2TB 0S C
8. Technical white Daper HP ProLiant DL980 G7 WI inteD inside me Xeor Xeon E7 Xeon E7 8
9. ent0S 0pen MPI ZD0CK Oo Python multiprocessing 5 34 def RunZDOCK e1f s 35 mark sur self zdock dir mark sur 36 zdock self zdock dir zdock 37 if os path exists self work dir UNniCHARMM False 38 shutil copy self zdock dir UniCHARMM self work dir 39 pdbFiles 40 dockFiles 41 for tag in 1 2 s 42 domainFrile self work dir domain str tag pdb 43 pdbFrile self work dir pdb str tag pdb 44 dockFile self work dir dock str tag out 45 pdbFiles append pdbFile 46 dockFiles append dockFile 47 subprocess CheCK call mark sur domainFrile pdbFile 48 49 cmd 50 cmd append zdock 0 dockFiles 0 N str self pose num 8 1 F R pdbFiles 0 L pdbFiles 1 51 cmd append zdock o dockFiles 1 N str self pose num S 2 F R pdbFiles 1 L pdbFiles 0 52 processList 53 for tag in 1 2 s 54 if self coreNum 1l 55 self ExecZDOCK tag cmd tag 1 56 else 57 process multiprocessing Process target self ExecZDOCK args tag cmd tag 1 58 processList append process 59 process start 60 for process in processList 61 process join 62 63 self Mod1fyPDB 64 65 def ExecZDOCK self tag cmd 66 1f self processNum 1l 67 subprocess call Cmd 68 else 69
10. moi usr local bin mpiexec n str self processNum 70 subprocess check call mpi cmd 71 self Mod1ifyZDOCK aq Technical white paper HP ProLiant DL980 G7 5 80 133 4 HP ProLiant DL980 G7 2 6 7 7 2 1 7 1 6 1 187 20 80 36
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