[gmx-users] Re: jobs failed

[Dr. Vitaly V. Chaban]

> Hello:
>   I am using the following script to run Gromacs in cluster, but it failed:
>
> # @ job_name = bm
> # @ class = kdm-large
> # @ error = gromacs.info
> # @ output = gromacs.out
> # @ environment = COPY_ALL
> # @ wall_clock_limit = 10:00:00
> # @ notification = error
> # @ job_type = bluegene
> # @ bg_size = 64
> # @ queue
> mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-v -s md.tpr -o
> md.trr -cpo md.cpt -c md.gro -g md-out.log -launch" -mode VN -np 256
>
>
> and here is the log file
>
>
> Back Off! I just backed up md-out.log to ./#md-out.log.1#
> Getting Loaded...
> Reading file md.tpr, VERSION 4.5.5 (single precision)
> Loaded with Money
>
>
> Will use 192 particle-particle and 64 PME only nodes
> This is a guess, check the performance at the end of the log file
> Making 3D domain decomposition 8 x 4 x 6
>
> Back Off! I just backed up md.trr to ./#md.trr.2#
>
> Back Off! I just backed up traj.xtc to ./#traj.xtc.3#
>
> Back Off! I just backed up ener.edr to ./#ener.edr.3#
>
> WARNING: This run will generate roughly 3302 Mb of data
>
> starting mdrun 'BmEH-complex-POA in water'
> 50000000 steps, 100000.0 ps.
> step 0
>
> NOTE: Turning on dynamic load balancing
>
> vol 0.41  imb F 18% pme/F 0.61 step 100, will finish Tue Apr 17 13:49:51
> 2012
> vol 0.42  imb F 12% pme/F 0.60 step 200, will finish Sun Apr 15 23:46:30
> 2012
> vol 0.44  imb F 12% pme/F 0.57 step 300, will finish Sun Apr 15 12:20:49
> 2012
> vol 0.45  imb F 12% pme/F 0.58 step 400, will finish Sun Apr 15 07:01:25
> 2012
> vol 0.48  imb F 12% pme/F 0.57 step 500, will finish Sun Apr 15 03:46:13
> 2012
> vol 0.49! imb F 11% pme/F 0.57 step 600, will finish Sun Apr 15 01:43:05
> 2012
> vol 0.46! imb F 10% pme/F 0.59 step 700, will finish Sun Apr 15 00:01:14
> 2012
> vol 0.42! imb F 10% pme/F 0.58 step 800, will finish Sat Apr 14 22:56:06
> 2012
> vol 0.45! imb F 12% pme/F 0.56 step 900, will finish Sat Apr 14 22:16:49
> 2012
> vol 0.46! imb F 10% pme/F 0.57 step 1000, will finish Sat Apr 14
> 21:49:10 2012
> vol 0.46! imb F  9% pme/F 0.58 step 1100, will finish Sat Apr 14
> 21:26:04 2012
> vol 0.47! imb F 10% pme/F 0.57 step 1200, will finish Sat Apr 14
> 21:02:35 2012
> vol 0.45  imb F  9% pme/F 0.58 step 1300, will finish Sat Apr 14
> 20:34:22 2012
> vol 0.45! imb F  9% pme/F 0.58 step 1400, will finish Sat Apr 14
> 20:15:54 2012
> vol 0.48! imb F 11% pme/F 0.57 step 1500, will finish Sat Apr 14
> 20:07:48 2012
> vol 0.47! imb F 10% pme/F 0.58 step 1600, will finish Sat Apr 14
> 19:57:46 2012
> vol 0.47! imb F 13% pme/F 0.58 step 1700, will finish Sat Apr 14
> 19:51:47 2012
> vol 0.45! imb F 11% pme/F 0.58 step 1800, will finish Sat Apr 14
> 19:44:37 2012
> vol 0.46! imb F 13% pme/F 0.57 step 1900, will finish Sat Apr 14
> 19:37:10 2012
> vol 0.50! imb F 12% pme/F 0.58 step 2000, will finish Sat Apr 14
> 19:29:20 2012
> vol 0.50! imb F 12% pme/F 0.58 step 2100, will finish Sat Apr 14
> 19:23:00 2012
> vol 0.48  imb F 10% pme/F 0.57 step 2200, will finish Sat Apr 14
> 19:15:43 2012
> vol 0.50! imb F 11% pme/F 0.57 step 2300, will finish Sat Apr 14
> 19:13:30 2012
> vol 0.49! imb F 11% pme/F 0.57 step 2400, will finish Sat Apr 14
> 19:10:14 2012
> vol 0.48  imb F 10% pme/F 0.58 step 2500, will finish Sat Apr 14
> 19:01:51 2012
> vol 0.47! imb F 12% pme/F 0.58 step 2600, will finish Sat Apr 14
> 18:55:11 2012
> vol 0.48! imb F 11% pme/F 0.58 step 2700, will finish Sat Apr 14
> 18:49:47 2012
> vol 0.46! imb F 12% pme/F 0.58 step 2800, will finish Sat Apr 14
> 18:45:32 2012


Check what happens to your volume.



Dr. Vitaly V. Chaban, 430 Hutchison Hall, Chem. Dept.
Univ. Rochester, Rochester, New York 14627-0216
THE UNITED STATES OF AMERICA