This is the output
Begin Batch Job Epilogue Sat Aug 2 09:07:19 EDT 2019 Job ID: 341185 Username: tuf73544 Group: chem Job Name: NVT Session: 45173 Limits: walltime=01:00:00,neednodes=1:ppn=28,nodes=1:ppn=28 Resources: cput=19:59:39,vmem=1986008kb,walltime=00:42:53,mem=198008kb,energy_used=0 Queue: normal Account: Deleting /dev/shm/*... ---------------------------------------- End Batch Job Epilogue Sat Aug 2 09:08:39 EDT 2019 ---------------------------------------- Command line: gmx mdrun -deffnm nvt Running on 1 node with total 28 cores, 28 logical cores Hardware detected: CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz SIMD instructions most likely to fit this hardware: AVX2_256 SIMD instructions selected at GROMACS compile time: SSE4.1 Hardware topology: Full, with devices Compiled SIMD instructions: SSE4.1, GROMACS could use AVX2_256 on this machine, which is better. *Reading file nvt.tpr, VERSION 2016.3 (single precision)* Changing nstlist from 10 to 20, rlist from 1 to 1.029 The number of OpenMP threads was set by environment variable OMP_NUM_THREADS to 1 Will use 24 particle-particle and 4 PME only ranks This is a guess, check the performance at the end of the log file Using 28 MPI threads Using 1 OpenMP thread per tMPI thread starting mdrun 'DNA in water' 500000 steps, 1000.0 ps. step 40 Turning on dynamic load balancing, because the performance loss due to load imbalance is 4.1 %. Writing final coordinates. Average load imbalance: 1.5 % Part of the total run time spent waiting due to load imbalance: 1.2 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Z 0 % Average PME mesh/force load: 0.752 Part of the total run time spent waiting due to PP/PME imbalance: 3.1 % Core t (s) Wall t (s) (%) Time: 71996.002 2571.286 2800.0 42:51 (ns/day) (hour/ns) Performance: 33.602 0.714 On Fri, Aug 2, 2019 at 11:00 AM John Whittaker < johnwhitt...@zedat.fu-berlin.de> wrote: > > Hi Justin, > > > > Yes, I'm using a queuing system with a submission script. > > > > #-l nodes=1:ppn=16 > > > > #PBS -l walltime=10:00:00 > > > > #PBS -qmedium > > > > #PBS -N NVT > > > > #PBS -e out.err > > > > #PBS -o out > > > > > > > > module load gromacs > > > > > > cd ${PBS_O_WORKDIR}/; > > > > > > gmx mdrun -deffnm nvt > > > > > > Well, based on your hint, I executed a trial mdrun job without using the > > queue. It seems to be working well and reading the .tpr file, I had to > > kill > > the job once I made sure that it is reading the tpr file due to the > > regulations of using the cluster out of the queue. > > So, I should suspect that there is something wrong with executing the > > script. It is worthy to note that I used the same script without any kind > > of change multiple times and it's working well. This's more confusing for > > me now, any hints? > > What is the output from the cluster? I'm guessing the output is in the > file called "out" that's created each time the simulation fails. > > > > > > Thanks for the ionization/neutralization advice; surely I did that. > > > > Thanks, > > Mohammed > > > > On Thu, Aug 1, 2019 at 9:22 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> > >> On 8/1/19 7:04 PM, Mohammed I Sorour wrote: > >> >> Hi, > >> > > >> > that's what the ls -l prints, > >> > > >> > > >> > > >> > > >> >> ls -l > >> >> total 193120 > >> >> drwxr-xr-x 2 tuf73544 chem 4096 Jul 26 17:20 amber99sb_dyes.ff > >> >> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro > >> >> -rw-r--r-- 1 tuf73544 chem 191 Aug 1 15:04 > >> equilibration_NVT_script > >> >> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:11 full_solv_ions.gro > >> >> -rw-r--r-- 1 tuf73544 chem 2164 Jul 8 2016 ions.itp > >> >> -rw-r--r-- 1 tuf73544 chem 33866956 Jul 31 19:08 ions.tpr > >> >> -rw-r--r-- 1 tuf73544 chem 11962 Aug 1 14:57 mdout.mdp > >> >> -rw-r--r-- 1 tuf73544 chem 11962 Aug 1 14:56 #mdout.mdp.1# > >> >> -rw-r--r-- 1 tuf73544 chem 1875 Jul 27 08:22 nvt.mdp > >> >> -rw-r--r-- 1 tuf73544 chem 39455312 Aug 1 14:57 nvt.tpr > >> >> -rw------- 1 tuf73544 chem 1032 Aug 1 15:04 out > >> >> -rw------- 1 tuf73544 chem 2395 Aug 1 15:04 out.err > >> >> -rw-r--r-- 1 tuf73544 chem 38899 Jul 31 18:58 > >> posre_DNA_chain_A.itp > >> >> -rw-r--r-- 1 tuf73544 chem 39953 Jul 31 18:58 > >> posre_DNA_chain_B.itp > >> >> -rw-r--r-- 1 tuf73544 chem 3215 Aug 1 14:57 residuetypes.dat > >> >> -rw-r--r-- 1 tuf73544 chem 4873 Jul 18 13:03 specbond.dat > >> >> -rw-r--r-- 1 tuf73544 chem 69176 Jul 16 11:40 tip3p.gro > >> >> -rw-r--r-- 1 tuf73544 chem 588482 Jul 31 18:58 > >> topol_DNA_chain_A.itp > >> >> -rw-r--r-- 1 tuf73544 chem 589283 Jul 31 18:58 > >> topol_DNA_chain_B.itp > >> >> -rw------- 1 tuf73544 chem 1264 Jul 31 19:10 topol.top > >> >> drwxr-xr-x 3 tuf73544 chem 4096 Aug 1 14:18 trial > >> > >> Are you executing mdrun interactively, or via some kind of queuing > >> system with a submission script? > >> > >> Also you should *not* be running dynamics on a system with such a net > >> charge. Add salt and neutralize! It's not the source of your problem, > >> though. > >> > >> -Justin > >> > >> -- > >> ================================================== > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.com > >> > >> ================================================== > >> > >> -- > >> Gromacs Users mailing list > >> > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > >> posting! > >> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> * For (un)subscribe requests visit > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >> send a mail to gmx-users-requ...@gromacs.org. > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send > > a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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