​Here is what I did...
I changed the cutoff-method to Verlet as suggested by
http://www.gromacs.org/Documentation/Cut-off_schemes#
How_to_use_the_Verlet_scheme


Then I followed two scenarios:

1) On the frontend, where gromacs and openmpi have been installed, I ran

​mahmood@cluster:LPN$ date
Mon Oct 17 11:06:40 2016
mahmood@cluster:LPN$ /share/apps/computer/openmpi-2.0.1/bin/mpirun -np 2
/share/apps/chemistry/gromacs-5.1/bin/mdrun_mpi -v
...
...
starting mdrun 'Protein in water'
50000000 steps,  50000.0 ps.
step 0
[cluster.scu.ac.ir:28044] 1 more process has sent help message
help-mpi-btl-base.txt / btl:no-nics
[cluster.scu.ac.ir:28044] Set MCA parameter "orte_base_help_aggregate" to 0
to see all help / error messages
imb F  0% step 100, will finish Tue Dec  6 11:41:44 2016
imb F  0% step 200, will finish Sun Dec  4 23:06:02 2016
^Cmahmood@cluster:LPN$ date
Mon Oct 17 11:07:01 2016


​So, roughly 21 seconds for about 200 steps. As I checked 'top' command,
two cpus were 100%. Full log is available at http://pastebin.com/CzViEmRb



2) I specified two nodes instead of the frontend. Two nodes have at least
one free core. So, one process on each of them is similar to the previous
scenario.

mahmood@cluster:LPN$ cat hosts.txt
compute-0-2
compute-0-1
mahmood@cluster:LPN$ date
Mon Oct 17 11:12:34 2016
mahmood@cluster:LPN$ /share/apps/computer/openmpi-2.0.1/bin/mpirun -np 2
--hostfile hosts.txt /share/apps/chemistry/gromacs-5.1/bin/mdrun_mpi -v
...
...
starting mdrun 'Protein in water'
50000000 steps,  50000.0 ps.
step 0
^CKilled by signal 2.
Killed by signal 2.
mahmood@cluster:LPN$ date
Mon Oct 17 11:15:47 2016

So, roughly 3 minutes without any progress!! As I ssh'ed to compute-0-2,
the 'top' command shows

23153 mahmood   39  19  190m  15m 6080 R  1.3  0.0   0:00.39 mdrun_mpi
23154 mahmood   39  19  190m  16m 5700 R  1.3  0.0   0:00.39 mdrun_mpi

And that is very very low cpu utilization. Please see the log at
http://pastebin.com/MZbjK4vD



Any idea is welcomed.
​




Regards,
Mahmood
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