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On 23/03/2012 2:14 AM, Ashalatha Sreshty wrote:
<blockquote
cite="mid:CANV=m+9A6qLsDboJYW2d45CpsvekWMF1tNUKTmQ6DVejEGkjqw@mail.gmail.com"
type="cite">Dear Gromacs users,<br>
<div class="gmail_quote"><br>
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<br>
<b><br>
</b><b>the error is:</b><br>
<br>
Program mdrun_mpi_d, VERSION 4.5.4<br>
Source code file: domdec.c, line: 6436<br>
<br>
Fatal error:<br>
There is no domain decomposition for 32 nodes that is compatible
with the given box and a minimum cell size of 1.33444 nm<br>
Change the number of nodes or mdrun option -rdd or -dds<br>
Look in the log file for details on the domain decomposition<br>
For more information and tips for troubleshooting, please check
the GROMACS<br>
website at <a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors"
target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>
</div>
</blockquote>
<br>
Following this link will lead you to a further link with some
helpful discussion.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CANV=m+9A6qLsDboJYW2d45CpsvekWMF1tNUKTmQ6DVejEGkjqw@mail.gmail.com"
type="cite">
<div class="gmail_quote"><b>and the PBS script is as below:</b><br>
<br>
#!/bin/sh<br>
#PBS -N test<br>
#PBS -l nodes=1:ppn=32:debug<br>
#PBS -l walltime=2:00:00<br>
#PBS -S /bin/sh<br>
#PBS -j oe<br>
<br>
curr_dir=${PBS_O_WORKDIR}<br>
cd ${PBS_O_WORKDIR}<br>
NPROCS='wc -l < $PBC_NODEFILE'<br>
HOSTS='cat $PBS_NODEFILE | uniq |tr '\n' ""'<br>
echo Running Directory is 'pwd'<br>
/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<br>
<br>
<b>Please suggest me how to resolve this error.<br>
</b><br>
Thank you in advance.<br>
<br>
Dr. M. Asha Latha Sreshty,<br>
PDF,<br>
Molecular Biophysics Unit,<br>
Indian Institute of Science,<br>
Bangalore,<br>
INDIA<br>
<br>
</div>
<br>
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