Error: no domain decomposition, Source code file: domdec.c, line: 6436

[Ashalatha Sreshty]

Dear Gromacs users,

I am performing MD simulation of an 14 units oligosaccharide on Gromacs 4.5.4. I am able to successfully do a 10 ns simulation on a DELL-precision workstation and also a 5ns simulation on tyrone cluster using a PBS script (shown below). However, when I am trying to proceed for further consecutive 5ns simulation, I get an error saying no domain decompositions error. I have tried changing the number of nodes by making it to 16 but it showed the same error. whereas, when I tried it on the same workstation as before, the mdrun has successfully executed. Please help me in letting me know what is the problem with the system and what parameters or argument I am missing while running it in tyrone cluster. I am providing the md.mdp parameter and the PBS script are also provided as attachments to this mail

the error is:

Program mdrun_mpi_d, VERSION 4.5.4
Source code file: domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 32 nodes that is compatible with the given box and a minimum cell size of 1.33444 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

and the PBS script is as below:

#!/bin/sh
#PBS -N test
#PBS -l nodes=1:ppn=32:debug
#PBS -l walltime=2:00:00
#PBS -S /bin/sh
#PBS -j oe

curr_dir=${PBS_O_WORKDIR}
cd ${PBS_O_WORKDIR}
NPROCS='wc -l < $PBC_NODEFILE'
HOSTS='cat $PBS_NODEFILE | uniq |tr '\n' ""'
echo Running Directory is 'pwd'
/opt/mvapich2-1.7rc1/gcc/bin/mpirun -np 32 /home/proj/11/mbumasha/programs/gromacs-4.5.4/bin/mdrun_mpi_d -deffnm triglc-MD4 -c triglc-MD6.pdb

Please suggest me how to resolve this error.

Thank you in advance.

Dr. M. Asha Latha Sreshty,
PDF,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore,
INDIA

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[Mark Abraham]

On 23/03/2012 2:14 AM, Ashalatha Sreshty wrote:

Dear Gromacs users,

I am performing MD simulation of an 14 units oligosaccharide on Gromacs 4.5.4. I am able to successfully do a 10 ns simulation on a DELL-precision workstation and also a 5ns simulation on tyrone cluster using a PBS script (shown below). However, when I am trying to proceed for further consecutive 5ns simulation, I get an error saying no domain decompositions error. I have tried changing the number of nodes by making it to 16 but it showed the same error. whereas, when I tried it on the same workstation as before, the mdrun has successfully executed. Please help me in letting me know what is the problem with the system and what parameters or argument I am missing while running it in tyrone cluster. I am providing the md.mdp parameter and the PBS script are also provided as attachments to this mail

the error is:

Program mdrun_mpi_d, VERSION 4.5.4
Source code file: domdec.c, line: 6436

Fatal error:
There is no domain decomposition for 32 nodes that is compatible with the given box and a minimum cell size of 1.33444 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Following this link will lead you to a further link with some helpful discussion.

Mark

and the PBS script is as below:

#!/bin/sh
#PBS -N test
#PBS -l nodes=1:ppn=32:debug
#PBS -l walltime=2:00:00
#PBS -S /bin/sh
#PBS -j oe

curr_dir=${PBS_O_WORKDIR}
cd ${PBS_O_WORKDIR}
NPROCS='wc -l < $PBC_NODEFILE'
HOSTS='cat $PBS_NODEFILE | uniq |tr '\n' ""'
echo Running Directory is 'pwd'
/opt/mvapich2-1.7rc1/gcc/bin/mpirun -np 32 /home/proj/11/mbumasha/programs/gromacs-4.5.4/bin/mdrun_mpi_d -deffnm triglc-MD4 -c triglc-MD6.pdb

Please suggest me how to resolve this error.

Thank you in advance.

Dr. M. Asha Latha Sreshty,
PDF,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore,
INDIA

--
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