On 1/08/2012 8:36 PM, rama david wrote:
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)
Here you let your threaded mdrun use the default for the -nt flag of -1,
which lets it use all the available cores...
2. mpirun -np 4 mdrun -v -deffnm topol1
... and here you used mpirun to start four copies of *threaded*
*non-MPI* mdrun, which each tried to do something sensible...
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
... and here you can see the four independent runs all writing their own
output...
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...
... and here they are writing output that wasn't meant to look pretty in
a silly usage case.
--------------------------------------------------------------------------
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...
Your job took two seconds to run, so expecting it to form a reliable
estimate of how long it will take to finish based on its current
progress is a bit tough. For all we know, you were over-allocating
processes with mpirun and threads, too.
so from above output I can guess In mpirun 4 processor are used
Read the .log files if you want to know what they were doing.
Mark
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