[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

[Justin Lemkul]

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
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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