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<font size="+1"><font face="WenQuanYi WenQuanYi Bitmap Song">Hello:<br>
I found that each time I would like to increase my nodes for
MD run, my job always failed. it said:<br>
<br>
Will use 192 particle-particle and 64 PME only nodes<br>
This is a guess, check the performance at the end of the log
file<br>
<br>
-------------------------------------------------------<br>
Program mdrun_mpi_bg, VERSION 4.5.5<br>
Source code file: ../../../src/mdlib/domdec.c, line: 6436<br>
<br>
Fatal error:<br>
There is no domain decomposition for 192 nodes that is
compatible with the given box and a minimum cell size of<br>
1.02425 nm<br>
Change the number of nodes or mdrun option -rcon or -dds or your
LINCS settings<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 class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
"Ohne Arbeit wird das Leben Oede" (Wir Sind Helden)<br>
<br>
<br>
Does anybody have any idea for this? here is my scrips for
submitting jobs;<br>
# @ job_name = I213A<br>
# @ class = kdm-large<br>
# @ account_no = G07-13 <br>
# @ error = gromacs.err<br>
# @ output = gromacs.out<br>
# @ environment = COPY_ALL<br>
# @ wall_clock_limit = 12:00:00<br>
# @ notification = error<br>
# @ notify_user = <a class="moz-txt-link-abbreviated" href="mailto:albert@icm.edu.pl">albert@icm.edu.pl</a><br>
# @ job_type = bluegene<br>
# @ bg_size = 64<br>
# @ queue<br>
mpirun -exe /opt/gromacs/4.5.5/bin/mdrun_mpi_bg -args "-nosum
-dlb yes -v -s npt.tpr" -mode VN -np 256<br>
<br>
<br>
if I change the bg_size=32 and -np=128, everything goes well....<br>
<br>
<br>
THX<br>
<br>
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