[Dock-fans] dock6 jobs using 7 cpu mins, but run for 15 hours.

[Scott Brozell]

Hi,

On Wed, 4 Feb 2009, Mary Ellen Fitzpatrick wrote:

> I have a dual-dual core Opteron cluster running Cento5, torque-2.3.6, 
> maui-3.2.6p21, mpich2-1.0.8(64bit) and  parallel dock6.
> I installed dock6 serial as 32-bit, then installed dock6 parallel as 
> 32-bit. 
> 
> I have configured my queues and scripts to run the dock mpi jobs and 
> they do run to completion without errors.
> 
> The problem I am seeing is that my mpi job is running for a total of 
> 15hours, but is using only ~ 7minutes of cputime.
> outfile
> Limits:         ncpus=4,neednodes=1,nodes=1,walltime=48:00:00
> Resources:      cput=00:06:55,mem=9964kb,vmem=279836kb,walltime=15:12:46
> 
> When the job is running, I log into the node, and can see the cpu's at 
> 100%, so it is not sitting idle and there is not an nfs traffic to speak 
> of.
> 
> Anyone run into this issue before?  Is this an mpi issue?

Not me.  Doubtful.
My guess is that the reported cput is for only processor - 
probably the master which in parallel dock does very little computing.
What are the Total elapsed times from the output file tails; e.g., using
dock6/install/test/mpi
you should have 4 output files:
mpi.dockmpiout.1
mpi.dockmpiout.2
mpi.dockmpiout.3
mpi.dockmpiout
ending with
12 Molecules Processed
Total elapsed time:  2 seconds

An alternative reality check would be to compare the processed molecules
to the number in your input database,
and consider the performance of your hardware.

Also with parallel dock one of the 4 cpu's should not usually be at 100%.

Scott