[gmx-users] mdrun mpi problem
Mark.Abraham at anu.edu.au
Mon Dec 15 07:53:34 CET 2008
> I have 3 computer and I want to do mdrun_mpi.
> I define this system in hostfile, lambhost-def, lam-hostmap.txt
> after lamboot and lamnodes It defines me that I have 3 nodes:
> homa at dma210:~/etc> lamnodes
> n0 dma210.dma:2:origin,this_node
> n1 dma211.dma:2:
> n2 dma212.dma:2:
> then I do:
> homa at dma210:~/gromacs5> mpirun -np 6 mdrun_mpi4 -v -s md300.tpr -o md300.trr
> -c md300.pdb -e md300.edr -g md300.log
> Getting Loaded...
> Reading file md300.tpr, VERSION 3.3.3 (single precision)
This should still work, but generating a .tpr with a corresponding
grompp has to be more appropriate.
> Note: tpx file_version 40, software version 58
> Loaded with Money
> Making 1D domain decomposition 6 x 1 x 1
> WARNING: This run will generate roughly 14158 Mb of data
> starting mdrun 'SWISS-MODEL SERVER (http:'
> 10000000 steps, 10000.0 ps.
> step 0
> imb F 23% step 100, will finish Thu Jan 8 20:24:20 2009
> imb F 21% step 200, will finish Sat Jan 10 16:52:31 2009
> imb F 32% step 300, will finish Mon Jan 12 02:15:15 2009
> it works and when I do top it seems that on every computer 2 mdrun_mpi
> execute. for example in one computer:
> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
> 2507 homa 16 0 48232 19m 4096 R 42 0.5 1:29.30 mdrun_mpi4
> 2508 homa 16 0 45868 16m 3768 S 33 0.4 0:57.30 mdrun_mpi4
> 2511 homa 16 0 67668 18m 15m R 1 0.5 0:00.48 konsole
> one of my question is why doesn't the cpu percent of these 2 mpi is not
If you don't have a dual-core machine, then one would not expect such
> when I excecute this command one node this process is faster (will be
> finished on 19 Dec. and the cpu percent is about 100% for all 6 job.
> Is my setting will be problemic?
Probably your network connections are not fast enough to get benefit
from your parallelism. There have been many discussions of this nature
on this list. Have a search.
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