> 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
