[gmx-users] REMD error

Thu Jan 12 07:53:08 CET 2012

On 12/01/2012 5:45 PM, bharat gupta wrote:
> 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 ??

You can't be getting an identical error, the numbers are different now.

If mdrun is reporting the number of nodes is 1, then you have not 
configured your MPI environment correctly so that it knows how many 
processors you have available. You will need to solve this by reading 
your MPI documentation.

If you have only four processors, you will not be able to run efficient 
REMD on five replicas, even if you can work out how to get MPI to 
over-allocate MPI processes to your physical processors.

Please copy and paste command line and error together, so that people 
who might help don't feel like they might be wasting their time 
guessing. They have other things to do. Your example input below did not 
produce your error below, because 20 != 3.

Mark

>
> On Thu, Jan 12, 2012 at 3:38 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto: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
>>     <mailto: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 <mailto: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 <mailto:monu46010 at yahoo.com>
>
>
>

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