[gmx-users] REMD error

Thu Jan 12 08:11:27 CET 2012

The command I used this time :-

mdrun_mpi mdrun -s prefix_.tpr -multi 5 -replex 100

Here's the error that I got :-

Fatal error:
The number of nodes (1) is not a multiple of the number of simulations (5)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"Look at these, my work-strong arms" (P.J. Harvey)

Halting program mdrun_mpi

gcq#345: "Look at these, my work-strong arms" (P.J. Harvey)

application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0

On Thu, Jan 12, 2012 at 3:53 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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
>>>>
>>>>
>>>   --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>
>>
>>
>> --
>> 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
>>
>>
>>
>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> 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
>
>
>
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>

-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120112/c0bc47bd/attachment.html>