[gmx-users] Problem with OpenMP+MPI

[Justin Lemkul]

On 2/27/13 8:53 AM, jesmin jahan wrote:
> Thanks Crasten for your reply.
>
> Even after removing comment, I am getting the same error message.

You need to re-create the .tpr file after modifying the .mdp file.  If you're 
getting the same error, you're using the wrong .tpr file.

> Do you have any sample .mdp file that can be used while using MPI+OPENMP?
>
> I am trying to compute the GB energy (implicit solvent based).
>

Note that implicit solvent calculations can be run on no more than 2 processors. 
  You'll get a fatal error if you try to use more.

-Justin

> On Wed, Feb 27, 2013 at 2:59 AM, Carsten Kutzner <ckutzne at gwdg.de> wrote:
>> Hi,
>>
>> On Feb 27, 2013, at 6:55 AM, jesmin jahan <shraban03 at gmail.com> wrote:
>>
>>> Dear Gromacs Users,
>>>
>>> I am trying to run the following command on gromacs 4.6
>>>
>>> mdrun -ntmpi 2 -ntomp 6 -s imd.tpr
>>>
>>> But I am getting the following error
>>>
>>> OpenMP threads have been requested with cut-off scheme Group, but
>>> these are only supported with cut-off scheme Verlet
>>>
>>> Does any one know a solution to the problem?
>>>
>>> I am using the following .mdp file
>>>
>>> constraints         =  none
>>> integrator          =  md
>>> ;cutoff-scheme       = Verlet
>> yes, as the note says, use the verlet cutoff scheme (by deleting the ";")
>>
>> Carsten
>>
>>> pbc                 =  no
>>> dt                  =  0.001
>>> nsteps              =  0
>>> rcoulomb            = 300
>>> rvdw                = 300
>>> rlist               = 300
>>> nstgbradii          = 300
>>> rgbradii            = 300
>>> implicit_solvent    =  GBSA
>>> gb_algorithm        =  HCT ;
>>> sa_algorithm        =  None
>>> gb_dielectric_offset    = 0.02
>>> ;optimize_fft             = yes
>>> energygrps               = protein
>>>
>>> Please let me know what to change so that it runs perfectly!
>>>
>>> Thanks,
>>> Jesmin
>>> --
>>> Jesmin Jahan Tithi
>>> PhD Student, CS
>>> Stony Brook University, NY-11790.
>>> --
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>>
>>
>> --
>> Dr. Carsten Kutzner
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical and Computational Biophysics
>> Am Fassberg 11, 37077 Goettingen, Germany
>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> http://www.mpibpc.mpg.de/grubmueller/kutzner
>> http://www.mpibpc.mpg.de/grubmueller/sppexa
>>
>> --
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>
>
>

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

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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