[gmx-users] different mdrun errors in different machines

[Justin Lemkul]

On 3/5/15 8:59 AM, Rebeca García Fandiño wrote:
> I forgot to say...the version of GROMACS is exactly the same for both machines...
>
> rober at caffesito:~$ mdrun --version
>
> GROMACS:    gmx mdrun, VERSION 5.0.4
>
>
>
> ubuntu at ip-172-31-26-213:~$ mdrun --version
>
> GROMACS:    gmx mdrun, VERSION 5.0.4
>
> The only difference is architecture.
>
> The 32-architecture is the one that fails. :-(
>

Let's get more specific.  What you posted below is neither an error nor a 
failure.  Does the run actually stop, or crash, or does it simply produce notes? 
  Notes are FYI, they are not indicators of failure.

If the first machine did not complain about the Verlet scheme, for instance, I 
suspect your .tpr files are different, so compare them with gmx check.  The same 
version of GROMACS will always produce the same messages if provided the same 
input.  If it didn't, things would be pretty insane.

-Justin

> Cheers,
>
> Rebeca.
>
> Dr. Rebeca Garcia
> Santiago de Compostela University
>
>
>> Date: Thu, 5 Mar 2015 07:53:56 -0500
>> From: jalemkul at vt.edu
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] different mdrun errors in different machines
>>
>>
>>
>> On 3/5/15 7:45 AM, Rebeca García Fandiño wrote:
>>> Dear GROMACS users,
>>> I am carrying out a MD simulation in GROMACS, and I am having problems in the mdrun step. We have tried it in two different machines:
>>>
>>> -The first of them is a 64 bytes system. There is no problem at all in this machine.
>>>
>>> -However, in another machine of 32 bytes system,  mdrun step leads to an error:
>>>
>>> NOTE: the minimum cell size is smaller than 1.05 times the cell size limit, will not turn on dynamic load balancing
>>>
>>> NOTE: This file uses the deprecated 'group' cutoff_scheme. This will
>>>
>>> be removed in a future release when 'verlet' supports all interaction forms.
>>>
>>> This error could be associated to the size of the box, as it has been previously suggested
>>>
>>> http://comments.gmane.org/gmane.science.biology.gromacs.user/24594
>>>
>>> However, if it was the problem, why is it not taking place in both machines? Could it be maybe a problem related with the architecture?
>>>
>>
>> More likely the machines have different versions of GROMACS.  If the first is
>> not complaining about the group cutoff scheme, then it is using an older version
>> of GROMACS.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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>   		 	   		
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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