大規模共有メモリーシステムでの GAMESSの利点
Contents
1. 512 500 Technical white paper GAMESS 40 35 30 gt GAMESS with DS on 5 25 SL230 g 20 GAMESS with DS on a 15 DL980 10 GAMESS without DS on DL980 5 0 0 20 40 60 80 COreS 3 DL980 DS 2 MP2 CCSD Hatree Fock HF MP2 CCSD SCF 2 MPz2 z CCSD 5 6 4 CCSD MP2. GPGPU libcchem 1 http www msg ameslab goVgamess 2 http classic Chem msu su gran gamess index html 3 http www spec org cDu2000 4 http www chem waseda ac jp nakai research_dc html HP ProLiant DL980 G7 9 Xeon9 05 Red Hat 6 4 32GB DIMM X128 E7 4870 2 4GHz 8 80 A E 03 5749 8328 00 19 00 10 00 17 00 5 1 HP ProLiant
3. CCSD CCSD T Gradient 4 CCSD CCSD T GAMESS replicated distributed storage node replicated process replicated distributed storage MEMDDI shmmax DDI TCP E node P 9 EXETYP CHECK CCSD
4. CC MAXCC 1 30 MAXCC 30 HF 2000 CCSD A0 MO A0 MO MO CPU CP 0 CP 1 CP 2 CP 79 MWORDS MWORDS MWORDS a MWORDS t ai t ai t ai t ai node replicated t ij ab fully distributed storage of the VVI001 VVI00 VOIVO1 V0I00 00I00 integrals The area of this entire big box is MEMDDI DS 80 DS 81 DS 82 ee DS 159 4 CCSD CCSD T Gamess DrOCeSS SysV shared memory sedment More SysV shared memory segment Gamess DrOCeSS Technical white paper inteD inside NE Xeon Xeon E7 E
5. 1 RHF ROHF UHF GVB MCSCF SCF Energy CDFpEP CDFpEP CDFpEP CD pEP CDFpEP SCF Gradient CDFpEP CDFpEP CDFpEP CD pEP CDFpEP SCF Hessian CD D CD D CD p D p MP2 energy CDFpEP CDFpEP CD pEP CD pEP MP2 gradient CDFpEP D pEP CD pEP Clenergy CDFp CD D CD p CD p Cl gradient CD _ CC energy CDFpE CDE E _ EOMCC excitations CD E CD E Semi empirical DFT energy CDFpEP CD pEP CD pEP DFT gradient CDFpEP CD pEP CD pEP TD DFT energy CDFDED CD p TD DFT gradient CDFDED Mopac enerdy y y y Mopac gradient y y n 1 p parallel in teD ns de er P Xeor Xeon E7 Technical white paper E GAMESS chem code DDI code Replicated data Distributed
6. GAMESS GAMESS Gordon Group 1 Gaussian Gaussian 1 Xeon9 E7 58 80 GAMESS
7. I0 2 C540 fullerene C540 PC Gamess test2 2 MOPAC PM3 SCFTYPE RHF PM3 1 PM3 GAMESS http spec org cpu2000 3 3 xHOST CPU SSE AVX
8. DDI DDI GAMESS VERSION 1 MAY 2012 R2 Inte MPI 4 1 0 Mathlib Intel MKL 13 0 Fortran Intel fortran 13 0 composer_xe_2013 2 146 Technical white paper GAMESS PC GAMESS test6 7 DDI 1 16 CP DS 8 4 2 1024 256 Cores Elapsed Time sec FINAL RHF ENERGY SCFiter 85381 983 5780915418 24 6 10730 983 5780915569 16 32 5618 983 5780915613 23 64 2927 983 5780915656 25 28 1555 983 5780915563 g1 256 919 983 5780915667 28 512 662 983 5780915603 g1 024 444 983 5780915592 20 4
9. ipo Nehelam TURBO0 CONTRL SCFTYP RHF RUNTYP gradient nprint 5 ISPHER 1 END SYSTEM TIMLIM 3000 MWORDS 100 END BASIS GBASIS PM3 END GUESS GUESS HUCKEL END scf soscf t end DATA Case Elapsed Time sec R PM3 ENERGY SCF iter 1 default 175 2349 3718701794 15 2 optimize 178 2349 3718701796 16 3 optimize turbo 141 2349 3718701796 16 3 PM3 Default i8 02 Optimize i8 xHOST ipo 03 no prec div unroll2 static scalar reD 3 C20H16N4 porphyrin 4 7 CONTRL RUNTYP GRADIENT INTTYP HONDO ICUT 10 CITYP CIS NPRINT 5 END SYSTEM TIMLIM 6000 MWORDS 100 END GUESS GUESS HUCKEL END SCF DIRSCF TT END CIS NSTATE 1 CHFSLV DIIS END DATA GAMESS MPI
10. 1 RHF SCF DENSITY MATRIX lt 2 00E 05 100000 250 10000 200 RE 8 g 1000 150 Elapsed time scale m 100 100 LH 1 10 FE 50 1 0 0 200 400 600 800 1000 cores 2 2 7 MPI GAMESS SCF MAXIT 30 30 UNCONVERGED MPI ERROR Infinibad FDR Gigabit
11. http www hp com jp proliant tel Inte Intel Corporation 2013 3 Intel Inside Intel Inside Xeon Xeon Inside Copyright 2013 Hewlett Packard Development Company L P 136 8711 2 2 1 PRINTED WITH SOYINK
12. mpiexec Inte MPI _MPI_DEVICE shm or rdssm or ssm Infiniband rdssm Gagabit ssm 5 SCF 256 512 Cores SCF iterations SCF iterations Elapsed Time infiniband Gigabit Infiniband rdssm Gigabit ssm 64 25 21 0 99 128 21 25 0 95 256 28 16 0 97 512 21 19 0 88 1024 20 23 0 67 5 Technical white paper E GAMESS GAMESS GAMESS SL230Gen8 DL980G7 Processor ntel E5 2670 2 7Ghz Intel E7 4870 2 4Ghz Sockets Core 2socket 16core 8socket 80core Memory 8GB
13. DS 7 8 6 DL980G7 Cores CP Elapsed Time RHF ENERGY ITERATIONS 8 4 23373 983 5780915653 15 16 8 11792 983 5780915632 15 32 16 6202 983 5780915587 22 64 32 3672 983 5780915634 15 80 40 3032 983 5780915579 18 7 DS Cores CP Elapsed Time RHF ENERGY ITERATIONS 8 8 12064 983 5780915633 15 16 16 6384 983 5780915652 15 32 32 3590 983 5780915622 15 64 64 2427 983 5780915633 15 80 80 2348 983 5780915652 15 8 DS DS 8 2 80 1 3 8 80 386 16 DS off 80
14. 1 1 1 2 compute process CP 16 p 0 p 1 p 2 p 0 DS DS MB 3 1 GAMESS CP DS runtype optimize runtype hessian FCM VEC HES runtype VSCF cc pV
15. GAMESS Replicated memory MB Distributed memory MB HF 36 0 3 MP2 89 4171 CCSD 240 332 152 CCSD T gz 75 752 9 EXETYP CHECK 1000 100 1 MIE gt io MP2 g DFT b3lyp 1 CCSD CCSD T 0 1 0 01 50 100 150 200 cores 5 CCSD MAXCC 30 1 Data Server 2 CPU Compute Process 80 128 3 MP2 4 2 CCSD 4 CCSD CCSD
16. data E SYSTEM MWORD MEMDDI GAMESS GAMESS 1 4 2 Node O p 0 Node 1 p 1 GAMESS quantum GAMESS quantum chem code chem code DDI code DDI code a Se I EN RE ER Et ES NE I A EN a a I I A a RR 1 GAMESS 1 core Memory MWORD MEMDDI MWORD MEMDDI word 8x10 6 1 2 data server DS 8 p 2 Node 0 p 0 Node 1 p 2 GAMESS quantum GAMESS quantum chem code chem code AN X MM DDI code DDI code Replicated data Replicated data Node O p 1 Node 1 p 3 GAMESS quantum GAMESS quantum chem code chem code DDlcode X DDlcode X Distributed data Distributed data
17. DIMM x16 32GB DIMM x128 0S RedHat 6 3 RedHat 6 4 Interconnect nfiniBand FDR 6 SMP CP MEMDD MEMDDI distributed data MEMDDI DS CPU CP 2 CPU InteLMPI LMPI_WAIT_MODE csh setenv _MPI_WAIT_MODE enable SystemV ipcs sysctl w kernel shmmax xxx kernel shmmax 68 719 476 736 64GB kernel shmall 4 294 967 296 4GB kernel shmmni 4 096 4GB kernel shm_rmid_forced 0 vm hugetlb_shm_group 0
18. DZ MP2 CCSD CCSD T 3 CONTRL SCFTYP RHF RUNTYP VSCF CCTYP CCSD T ISPHER 1 END SYSTEM TIMLIM 100000 MWORDS 100 END BASIS GBASIS CCD END VSCF NGRID 16 PETYP DIRECT END GUESS GUESS HUCKEL END DATA H20 CCSD T cc pVDZ Anharmonic Frequency CNV 2 0 8 0 0 0000000000 0 0000000000 0 1403674299 H 1 0 0 7493341373 0 0000000000 0 4675002149 END Exp MP2 CCSD CCSD T v1 1595 1610 1629 1622 v2 3657 3670 3658 3628 V3 3756 3757 3728 3699 SATA DISK 143 163 131 RAM DISK deWshm 77 83 66 2 Technical white paper GAMESS MP2 I0 HDD RAM DISK RAM DISK 2
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