[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]

Sounds great, thank you so much!!

On Fri, Aug 2, 2019 at 11:21 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/2/19 11:18 AM, Mohammed I Sorour 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.
>
> See my previous message about checking the working directory. Beyond
> that, this is not a GROMACS problem - your system runs fine. Your
> sysadmins are the people to ask about how to run jobs on your cluster.
>
> -Justin
>
> > 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
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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