[gmx-users] mdrun mpi problem

[hazizian]

Hi

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)
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 
100%?

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?

thanks 

Tehran University of Medical Sciences
www.tums.ac.ir


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