[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Mohammed I Sorour]

Yeah, I deeply appreciate your help. But any idea/recommendation why the
same command doesn't work through the script? I can't run any jobs,
especially such a big calculation, out of the queue system.

On Fri, Aug 2, 2019 at 11:13 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/2/19 11:09 AM, Mohammed I Sorour wrote:
> > 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
>
> This output indicates that the job finished successfully and did not
> produce the original error you posted.
>
> -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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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