David van der Spoel wrote: > [EMAIL PROTECTED] wrote: >> This email refers to my original posts on this topic: >> http://www.gromacs.org/pipermail/gmx-users/2006-October/024154.html >> http://www.gromacs.org/pipermail/gmx-users/2006-October/024333.html >> >> I have previously posted some of this information to somebody else's >> bugzilla post #109 including a possible workaround >> http://bugzilla.gromacs.org/show_bug.cgi?id=109 >> >> I have compiled my gromacs always using one of the gcc3.3* distros. I >> didn't do anything fancy, just the usual configure,make,make install. >> I did have trouble with a gromacs version compiled using a gcc4* >> distro and somebody on this user list assisted me in determining that >> I should just roll back my gcc verison. I run on all sorts of >> computers, opterons and intel chips, 32 and 64 bit, and this >> particular ci problem is the same for me on all of them. >> >> Matteo, I want to be sure that we are on the same page here: your ci >> is just *barely* out of bounds right? This is a different problem >> than when your ci is a huge negative number. In that case you have >> some other problem and your system is exploding. >> >> There is one test and one workaround included in my bugzilla post. >> The test is to recompile gromacs with the -DEBUG_PBC flag and see if >> the problem still occurs. For me this solved the problem (although >> gromacs runs much slower so it is not a great workaround). The >> solution was to remake my system with a few more or a few less waters >> so that the number of grids wasn't changing as the volume of the box >> fluctuates (slightly) during constant pressure simulations. >> >> I here include the text that I added to that bugzilla post: >> Did you try with a version of mdrun that was compiled with -DEBUG_PBC ? >> I have some runs that reliably (but stochastically) give errors about >> an atom >> being found in a grid just one block outside of the expected boundary >> only in >> parallel runs, and often other nodes have log files that indicate >> that they have >> just updated the grid size (constant pressure simulation). This error >> disappears >> when I run with a -DEBUG_PBC version. My assumption here is that >> there is some >> non-blocking MPI communication that is not getting through in time. The >> -DEBUG_PBC version spends a lot of time checking some things and >> although it >> never reports having found some problem, I assume that a side-effect >> of these >> extra calculations is to slow things down enough at the proper stage >> so that the >> MPI message gets through. I have solved my problem by adjusting my >> simulation >> cell so that it doesn't fall close to the grid boundaries. Perhaps >> you are >> experiencing some analogous problem? >> >> Quoting Matteo Guglielmi <[EMAIL PROTECTED]>: >> >>> Hello Chris, >>> I have the same problem with gromacs and did not understand >>> what's going wrong yet. >>> >>> I did not try to run a serial job (as you did) but all my 7 simulations >>> (6 solvated pores in membranes + 1 protein in water... all of them >>> with positional restrains - double precision) keep crashing in the >>> same way. >>> >>> Did you finally understand why they do crash (in parallel)? >>> >>> How did you compile gromacs? >>> >>> I used the intel copilers (ifort icc icpc 9.1 series) whith the >>> following optimization flags: -O3 -unroll -axT. >>> >>> I've also tried the 8.0 series but no chance to get rid of the problem. >>> >>> I'm running on woodcrest (xeon cpu 5140 2.33GHz) and xeon cpu >>> 3.06GHz. >>> >>> Thanks for your attention, >>> MG > > Do you use pressure coupling? In principle that can cause problems > when combined with position restraints. Further once again, please try > to reproduce the problem with gcc as well. If this is related to > bugzilla 109 as Chris suggests then please let's continue the > discussion there. > Yes I do (anysotropic pressure).
I got the same problem with the same system using a compiled version of gromacs with gcc 3.4.6. So, in my case, doesn't matter which compiler I do use to compile gromacs (either Intel series 9.1 or gcc 3.4.6), I always get the same error right after the "update" of the Grid size. .... step 282180, will finish at Tue May 29 15:57:31 2007 step 282190, will finish at Tue May 29 15:57:32 2007 ------------------------------------------------------- Program mdrun_mpi, VERSION 3.3.1 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 1472. It should have been within [ 0 .. 1440 ] Please report this to the mailing list ([email protected]) ------------------------------------------------------- "BioBeat is Not Available In Regular Shops" (P.J. Meulenhoff) Looking forward to have a solution, thanks to all of you, MG. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
