<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>What is happening is that you've got bonds too long and the <div>dd can not manage to cut things in 4 subsystems ... </div><div><br></div><div>try particle decomposition but you might end up with the same</div><div>problem :((<br><div><br><div><div>On Sep 29, 2010, at 5:35 PM, jayant james wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br clear="all">Hi!<br>I am trying to perform distance restrained MD simulations of a protein with Gromacs4.0.5.<br>I have a bunch of FRET distances ranging from 10Angs to 40 angs that I am incorporating simular to NOE distance restraints in NMR.<br> When I use one processor for the simulations its all fine, but, when I use multiple processors I get a bunch of errors<br>lets me start with the "NOTE" found below. Well do not want to increase the cut-off distance but want the program to use multiple processors. How can I overcome this problem?<br>I would appreciate your input<br>Thanks<br>JJ<br><br><span style="color: rgb(255, 0, 0);">NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd)</span><br style="color: rgb(255, 0, 0);"> <br style="color: rgb(255, 0, 0);"><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">WARNING: Can not write distance restraint data to energy file with domain decomposition</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">Loaded with Money</span><br style="color: rgb(255, 0, 0);"><br style="color: rgb(255, 0, 0);"><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">-------------------------------------------------------</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">Program mdrun_mpi, VERSION 4.0.5</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Source code file: ../../../src/mdlib/domdec.c, line: 5873</span><br style="color: rgb(255, 0, 0);"> <br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Fatal error:</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">There is no domain decomposition for 4 nodes that is compatible with the given box and a minimum cell size of 8.89355 nm</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">Change the number of nodes or mdrun option -rdd or -dds</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Look in the log file for details on the domain decomposition</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">-------------------------------------------------------</span><br style="color: rgb(255, 0, 0);"><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">"What Kind Of Guru are You, Anyway ?" (F. Zappa)</span><br style="color: rgb(255, 0, 0);"> <br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Error on node 0, will try to stop all the nodes</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">Halting parallel program mdrun_mpi on CPU 0 out of 4</span><br style="color: rgb(255, 0, 0);"> <br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">gcq#21: "What Kind Of Guru are You, Anyway ?" (F. Zappa)</span><br style="color: rgb(255, 0, 0);"><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">--------------------------------------------------------------------------</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">mpirun has exited due to process rank 2 with PID 28700 on</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">node compute-3-73.local exiting without calling "finalize". This may</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">have caused other processes in the application to be</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">terminated by signals sent by mpirun (as reported here).</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">-------------------------------------------------------------------------</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">with errorcode -1.</span><br style="color: rgb(255, 0, 0);"><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">You may or may not see output from other processes, depending on</span><br style="color: rgb(255, 0, 0);"><span style="color: rgb(255, 0, 0);">exactly when Open MPI kills them.</span><br style="color: rgb(255, 0, 0);"> <span style="color: rgb(255, 0, 0);">--------------------------------------------------------------------------</span><br style="color: rgb(255, 0, 0);"><br><br><br><br><br><br><br><br>-- <br>Jayasundar Jayant James<br><br> <a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br><br> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/Support/Mailing_Lists</blockquote></div><br></div></div></body></html>