<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><P>Hello,</P><P></P><P>in reply to my previous question even with options in compilation with mpi_d I wasn't able to solve my problem. Every time I choose to run gromacs in more than one node, after some number of steps I get that error. It is very annoying, because I cannot increase the speed of my runs, yet only up to two processors (that means that I can at least run in parallel somehow). In order to see if the compilation was successful I even restarted the whole cluster,yet to no avail. The runs are ok if I run them in only one node though. Any help would be greatly appreciated!<BR></P><P></P><P>Regards,</P><P>Nikos</P><BR>--- Claus Valka <I><lastexile7gr@yahoo.de></I> schrieb am <B>Fr, 19.9.2008:<BR><BLOCKQUOTE style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;">Von: Claus Valka
<lastexile7gr@yahoo.de><BR>Betreff: [gmx-users] ci range checking error even applying the patch / parallel runs<BR>An: gmx-users@gromacs.org<BR>Datum: Freitag, 19. September 2008, 16:24<BR><BR><DIV id="yiv2089180667"><TABLE cellspacing="0" cellpadding="0" border="0"><TBODY><TR><TD valign="top" style="font:inherit;"><P>Hello,</P><P>after searching extensively the mailing lists I wasn' able to solve my problem. This has to do with running gromacs in parallel (more than one nodes) in a rocks cluster. I 'm able to run a simulation both in one or two processors in a dual core node, yet every time I try to use more than one nodes, this error appears :</P><P>Program mdrun_mpi, VERSION 3.3.2<BR>Source code file: nsgrid.c, line: 226<BR> <BR> Range checking error:<BR> Explanation: During neighborsearching, we assign each particle to a grid based on its coordinates. If your system contains collisions or parameter errors that give
particles very high velocities you might end up with some coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot put these on a grid, so this is usually where we detect those errors. Make sure
your system is properly energy-minimized and that the potential energy seems reasonable before trying again.<BR> <BR> Variable ci has value 741. It should have been within [ 0 .. 740 ]<BR><BR>There isn't only me who is facing that problem so searching the forums I came accross a patch, that is : [gmx-users] fix for range checking errors in parallel double precision mdrun <BR></P><P>Compiling gromacs with this version of xtcio.c doesn't seem to solve the problem. Is there anything else I'm missing?</P><P>I give you my configure options in case this is helpful:</P><P>./configure --prefix=/export/local/gromacs-3.3.2 --program-suffix= --enable-double --disable-float --disable-fortran --with-x --with-fft=fftw3<BR><BR></P><P>My commands to run a simulation are for example in six nodes :</P><P>grompp -f *.mdp -c *.gro -p *.top -np 6</P><P>and in my script the arguments for running are:</P><P>-pe mpi 6</P><P>mpirun -np 6 --hostfile
$TMPDIR/machines mdrun_mpi</P><P>Thank you in advance,</P><P>Nikos</P></TD></TR></TBODY></TABLE><BR>__________________________________________________<BR>Do You Yahoo!?<BR>Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. <BR>http://mail.yahoo.com </DIV><PRE>_______________________________________________
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