[gmx-users] REMD error

[bharat gupta]

It says that "The number of cores must be a multiple of the number of
replicas (given with -multi, which must equal the number of
.tpr<http://www.gromacs.org/Documentation/File_Formats/Topology_%28.tpr%29_File>files
i.e., 10 for the above general example using
prefix_0.tpr through prefix_9.tpr)"

I gave the options -multi 5 . But still I am getting the same error. Can
you please explain, why is it so. Do I need to have the same no. of cores
as the no. of .tpr files ??

On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 12/01/2012 5:29 PM, bharat gupta wrote:
>
> Thanks for the advice I re-complied everything again with static libraries
> and the installation went fine. But while executing the following command I
> am again getting error :-
>
>
> mdrun_mpi mdrun  -s prefix_.tpr -multi 20 -replex 500 -v
>
>
> Fatal error:
> The number of nodes (1) is not a multiple of the number of simulations (3)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>
> Halting program mdrun_mpi
>
> gcq#155: "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff)
>
> application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
>
>
> I am trying to simulate 5 replicas and I have 4 cpu .
>
>
> See http://www.gromacs.org/Documentation/How-tos/REMD Execution Steps
> point 2. You cannot simulate an arbitrary number of replicas on an
> arbitrary number of processors.
>
> Mark
>
>
>
>
>
> On Thu, Jan 12, 2012 at 1:37 PM, lina <lina.lastname at gmail.com> wrote:
>
>> On Thursday 12,January,2012 08:54 AM, bharat gupta wrote:
>>
>>> Hi,
>>>
>>> I am trying to run a REMD of a peptide. But while executing the
>>> following command after nvt and npt equilibration , I am getting the
>>> following error:-
>>>
>>> mdrun_mpi mdrun -s prefix_.tpr -multi 20 -replex 1000
>>> mdrun_mpi: error while loading shared libraries: libgmx_mpi.so.6: cannot
>>> enable executable stack as shared object requires: Permission denied
>>>
>>
>>  Can you run a normal md smoothly?
>> try:
>> mdrun_mpi mdrun -deffnm prefix_0
>>
>> if it works, then some of your trajectories not sound. means system does
>> not equilibrium well.
>>
>>
>>>
>>> Can anybody suggest me how could I rectify this error.
>>>
>>> --
>>> Bharat
>>>
>>>
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>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>
>
>
>
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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