[gmx-users] mdrun mpi problem
hazizian at razi.tums.ac.ir
Mon Dec 15 07:38:01 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
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
Reading file md300.tpr, VERSION 3.3.3 (single precision)
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.
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
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?
Tehran University of Medical Sciences
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