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.abra...@anu.edu.au
<mailto:mark.abra...@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.lastn...@gmail.com
<mailto:lina.lastn...@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 : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
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