PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

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PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid

Transcript of PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

Page 1: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007

Amber 8

on

PRAGMA Gfarm-V2 Datagrid

Page 2: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007

Motivation

• The running of AMBER in GFarm Data Grid is intended– to provide information useful in assessing the

performance of running molecular dynamics simulations on a range of computer architectures found PRAGMA testbeds with and without GFarm.

Page 3: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007

PRAGMA Clusters

• gfml17• gfml18

– All running in Gfarm and without Gfarm.

Page 4: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007

AMBER 8 (Sander) Benchmark system

18056 atoms

Generalized Born model on Sander 8--thermalization&cntrl nstlim=10,nrespa=4, ntx=5, irest=1, ntpr=8, ntf=2, ntc=2, ntb=0, temp0 = 298.0, ntt=1, tautp=1.0, cut=12.0, rgbmax=12.0, igb=1, saltcon=0.2, gbsa=0, nmropt=1 /

&wt type='END' /DISANG=heme_tether.rstEND

Page 5: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007

Protocols

• Identify clusters with GFARM installed• Make sure all the identified clusters have

gridmpi installed• Login to each cluster and mount gfarm

directory.• Recompile amber with gridmpi• Copy the compiled program to gfarm• Create rsl file for each job• Make sure globus is working from the

current working cluster to the execution clusters.

Page 6: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007

execution time in second

System Completion time (s)

Gfml17 (local NFS) 63.78

gfml17-GfarmV2 68.02

Gfml18 (local NFS) 63.78

gfml18-GfarmV2 66.82

rock32 (local NFS) 60.60

rock32 GfarmV2 (Metaserver in Japan)

75.15

Note:

No recompilation on the cluster – the binaries are the same

Executable binary and all input/output files are stored in Global Gfarm file system

Page 7: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007

Previous Benchmark GfarmV1

Page 8: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007

Xcluster-GFARMXcluster

Page 9: PRAGMA 13, NCSA, 24 th September 2007 Amber 8 on PRAGMA Gfarm-V2 Datagrid.

PRAGMA 13, NCSA, 24th September 2007 1 h 3mins

NOT ON GFARM

1 hour

GFARM

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PRAGMA 13, NCSA, 24th September 2007

Advantage

• All files are shared across clusters. This will save time for copying all the input files to each desired cluster.

• User can save time by log in only once and not every time they change to other cluster.


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