[gmx-users] ci range checking error even applying the patch / parallel runs
lastexile7gr at yahoo.de
Fri Sep 19 16:24:49 CEST 2008
Hello,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 :Program mdrun_mpi, VERSION 3.3.2
Source code file: nsgrid.c, line: 226
Range checking error:
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.
Variable ci has value 741. It should have been within [ 0 .. 740 ]
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
Compiling gromacs with this version of xtcio.c doesn't seem to solve the problem. Is there anything else I'm missing?I give you my configure options in case this is helpful:./configure --prefix=/export/local/gromacs-3.3.2 --program-suffix= --enable-double --disable-float --disable-fortran --with-x --with-fft=fftw3
My commands to run a simulation are for example in six nodes :grompp -f *.mdp -c *.gro -p *.top -np 6and in my script the arguments for running are:-pe mpi 6mpirun -np 6 --hostfile $TMPDIR/machines mdrun_mpiThank you in advance,Nikos
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