Hi All,<div><br></div><div>I get the following error when running replica exchange. I have 32 replica's with each replica running on 4 processors (128 total). How do I decrease the domain decomposition cell size, -dss? What should I set it to?</div>
<div><br></div><div>Thanks,</div><div><br></div><div>Ilya</div><div><br></div><div><div>DD cell 2 0 0: Neighboring cells do not have atoms: 22217 20764 20762 21782 21780 22244 22249 21863 21734 21739 22223 22240</div><div>
<br></div><div>DD cell 3 0 0: Neighboring cells do not have atoms: 21856 21868</div><div><br></div><div>DD cell 4 0 0: Neighboring cells do not have atoms: 21807 21809</div><div><br></div><div>DD cell 5 0 0: Neighboring cells do not have atoms: 22240 21765 20764 20762 21253 21250 21863 21860 22246 22251 21771 21789</div>
<div>DD cell 7 0 0: Neighboring cells do not have atoms: 21858 22221 21736</div><div><br></div><div>DD cell 0 0 0: Neighboring cells do not have atoms: 21789 21811 21253 21769 21742 21724</div><div><br></div><div>DD cell 7 0 0: Neighboring cells do not have atoms: 22221 21742</div>
<div>DD cell 1 0 0: Neighboring cells do not have atoms: 22223 22240</div><div>DD cell 2 0 0: Neighboring cells do not have atoms:</div><div>DD cell 4 0 0: Neighboring cells do not have atoms: 21807 21809 20764 20762 21782 21780 21739 21745 21722 21727</div>
<div><br></div><div>DD cell 5 0 0: Neighboring cells do not have atoms: 21765 20764 20762 21253 21250 21863 21860 21771 21789</div><div><br></div><div>-------------------------------------------------------</div><div>Program mdrun_mpi, VERSION 4.0.4</div>
<div>Source code file: domdec_con.c, line: 679</div><div><br></div><div>Fatal error:</div><div>DD cell 5 0 0 could only obtain 96 of the 108 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or use the -rcon option of mdrun.</div>
<div>-------------------------------------------------------</div><div><br></div><div>"Live for Liposuction" (Robbie Williams)</div><div><br></div><div>Error on node 45, will try to stop all the nodes</div><div>
Halting parallel program mdrun_mpi on CPU 45 out of 128</div><div><br></div><div>-------------------------------------------------------</div><div>Program mdrun_mpi, VERSION 4.0.4</div><div>Source code file: domdec_con.c, line: 679</div>
<div><br></div><div>Fatal error:</div><div>DD cell 0 0 0 could only obtain 40 of the 45 atoms that are connected via vsites from the neighboring cells. This probably means your vsite lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells or use the -rcon option of mdrun.</div>
<div>-------------------------------------------------------</div><div><br></div><div>"Live for Liposuction" (Robbie Williams)</div><div><br></div><div>Error on node 40, will try to stop all the nodes</div><div>
Halting parallel program mdrun_mpi on CPU 40 out of 128</div><div><br></div></div>