[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 11:18 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
>>
>> ==================================================
>>
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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

==================================================