[gmx-users] problem with checking performance

[Justin A. Lemkul]

Albert wrote:
>   Hello:
>   I submit MD jobs to cluster with the following scrips:
> 
> 
> # @ job_name = gromacs_job
> # @ class = kdm-large
> # @ account_no = G07-13
> # @ error = gromacs.out
> # @ output = gromacs.out
> # @ environment = COPY_ALL
> # @ wall_clock_limit = 2:00:00
> # @ notification = error
> # @ notify_user = albert at icm.edu.pl
> # @ job_type = bluegene
> # @ bg_size = 128
> # @ queue
> mpirun -exe /opt/gromacs/4.5.4/bin/mdrun_mpi -args "-nosum -dlb yes -s 
> nvt" -mode VN -np 128
> 
> 
> and it generate the following files;
> 
> gromacs.out
> md.log
> traj.trr
> ener.edr
> 
> I check the tail of each file and cannot find the performance of my job, 
> such as: how long it will take to be finished. Does anybody have any 
> idea to fix this?
> 

"mdrun -v" prints a running estimate of job completion time, otherwise there is 
no indication of performance until the job is over and final statistics are 
printed to the end of the .log file.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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