[gmx-users] About system requirement to gromacs

[rama david]

Thank you Mark for reply......

I run mdrun and mpirun with following command. I pasted output also..
Please help me to parse it..


1.   mdrun -v -deffnm topol1
2.   mpirun -np 4 mdrun -v -deffnm topol1


1.    mdrun -v -deffnm topol1


step 30, will finish Wed Aug  1 16:49:28 2012
 Average load imbalance: 12.3 %
 Part of the total run time spent waiting due to load imbalance: 5.1 %

NOTE: 5.1 % performance was lost due to load imbalance
      in the domain decomposition.
      You might want to use dynamic load balancing (option -dlb.)


	Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:      2.035      2.035    100.0
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:    109.127      5.744      2.632      9.117

gcq#98: "You're About to Hurt Somebody" (Jazzy Jeff)



2. mpirun -np 4 mdrun -v -deffnm topol1

Getting Loaded...
Reading file topol1.tpr, VERSION 4.5.5 (single precision)
Starting 4 threads
Starting 4 threads
Starting 4 threads
Starting 4 threads
Loaded with Money

Loaded with Money

Loaded with Money

Loaded with Money

Making 1D domain decomposition 4 x 1 x 1
Making 1D domain decomposition 4 x 1 x 1


Making 1D domain decomposition 4 x 1 x 1
Making 1D domain decomposition 4 x 1 x 1

starting mdrun 'Protein in water'
50000 steps,    100.0 ps.
starting mdrun 'Protein in water'
50000 steps,    100.0 ps.

starting mdrun 'Protein in water'
50000 steps,    100.0 ps.
starting mdrun 'Protein in water'
50000 steps,    100.0 ps.

NOTE: Turning on dynamic load balancing


NOTE: Turning on dynamic load balancing

step 0
NOTE: Turning on dynamic load balancing

step 100, will finish Wed Aug  1 19:36:10 2012vol 0.83  imb F  2% vol
0.84  imb step 200, will finish Wed Aug  1 19:32:37 2012vol 0.87  imb
F 16% vol 0.86  imb step 300, will finish Wed Aug  1 19:34:59 2012vol
0.88  imb F  4% vol 0.85  imb step 400, will finish Wed Aug  1
19:36:27 2012^Cmpirun: killing job...

--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 4257 on node  VPCEB34EN
exited on signal 0 (Unknown signal 0).
--------------------------------------------------------------------------
4 total processes killed (some possibly by mpirun during cleanup)
mpirun: clean termination accomplished




As you can also see the mdun command estimate to complete Aug  1 16:49:28 2012
while mpirun taking the time Wed Aug  1 19:36:10 2012vol....

Mpirun command taking more time...

so from above output I can  guess In mpirun 4 processor are used


Sorry if I take any wrong meaning from output..

Thank you for giving your valuable time..


With best wishes and regards

Rama David