[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]

Thank you so much, Carlos, using the full path helped me figure out the
problem.


So it turned out to be a problem with the path.

When using cd ${PBS_O_WORKDIR}/
it executes the job in my local directory --------------->
work/md/sequence_8_md/equilibration /nvt (When I made the directory
equilibration, I added a space at the end by mistake),

Renaming the equilibration directory and removing that space ---->
 work/md/sequence_8_md/equilibration/nvt     (That solved the problem and
the calculation is running)


Thank you so much, everyone!!

On Fri, Aug 2, 2019 at 11:34 AM Carlos Navarro <carlos.navarro87 at gmail.com>
wrote:

> Did you try replacing the line
> cd ${PBS_O_WORKDIR}/
> with
> cd ‘YOUR_CURRENT_PATH’/
> ?
> Maybe as people already pointed out, the variable is not working properly.
> Maybe this could work.
> Best,
>
> ——————
> Carlos Navarro Retamal
> Bioinformatic Engineering. PhD.
> Postdoctoral Researcher in Center of Bioinformatics and Molecular
> Simulations
> Universidad de Talca
> Av. Lircay S/N, Talca, Chile
> E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl
>
> On August 2, 2019 at 5:20:33 PM, Mohammed I Sorour (
> mohammed.sorour at temple.edu) wrote:
>
> 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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