[gmx-users] symtab get_symtab_handle error

[Zhaleh Ghaemi]

Dear Justin,

Thanks for your reply. For several reasons I'd like to do the rest of the
simulations with Gromacs 5.0.
I read on the previous posts that one solution to avoid this problem would
be to extend the simulation using grompp. Following that gives really
strange results: I generated the tpr file with grompp and ran a short test
simulation (on stampede machine) and the run generates normal output and
went fine. But if I send the longer version (for a day) it generates
the get_symtab_handle
799 error and the run crashes at the start of simulation. Namely, this line
works:

ibrun -np 16 mdrun_mpi -s md2.tpr -cpi md.cpt -deffnm md2-test  (10 mins on
stampede on normal queue)

But using *the same input files *does* not *work,

ibrun -np 80 mdrun_mpi -s md2.tpr -cpi md.cpt -deffnm md2 (24 hrs on the
same queue)

Any suggestion what could be the reason?

Thanks,
Zhaleh

On Thu, Nov 19, 2015 at 3:57 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/19/15 12:05 PM, Zhaleh Ghaemi wrote:
>
>> Dear all,
>>
>> I'm running Gromacs 5.0 on a protein-RNA system. The simulations need to
>> be
>> extended. I used the replacement of the tpbconv in version 5.0, namely
>> "gmx
>> convert-tpr" to extend the simulations with the command:
>>
>> mx convert-tpr -s md.tpr -f md.cpt -extend 20000 -o md2.tpr
>>
>> the md2.tpr file was generated with no errors, however the  mdrun crashed
>> generating this error:
>>
>>
>> *Fatal error:symtab get_symtab_handle 799 not found*
>>
>> So my questions are, why this error is happening? and what is the correct
>> way with which the simulations can be extended (or restarted in the case
>> of
>> crashed simulations) with Gromacs 5.0?
>>
>>
> Do not supply a .cpt file to convert-tpr.  If a correctly generated .tpr
> file still generates an error, trying upgrading to the latest version
> (5.1.1) and try again.
>
> -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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