________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, August 13, 2010 7:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] the mdrun choked or maybe braked.
#ZHAO LINA# wrote: > Hi, > > The problem just like this, in md.log > \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ > There are: 130889 Atoms > splitting topology... > Walking down the molecule graph to make constraint-blocks > There are 43925 charge group borders and 43271 shake borders > There are 43271 total borders > Division over nodes in atoms: > 9348 9348 9348 9351 9348 9351 9348 9351 > 9348 9351 > 9348 9351 9348 9350 > Walking down the molecule graph to make constraint-blocks > CPU= 0, lastcg= 3245, targetcg=25208, myshift= 8 > CPU= 1, lastcg= 6361, targetcg=28324, myshift= 8 > CPU= 2, lastcg= 9477, targetcg=31440, myshift= 8 > CPU= 3, lastcg=12594, targetcg=34557, myshift= 8 > CPU= 4, lastcg=15710, targetcg=37673, myshift= 8 > CPU= 5, lastcg=18827, targetcg=40790, myshift= 8 > CPU= 6, lastcg=21943, targetcg=43906, myshift= 7 > CPU= 7, lastcg=25060, targetcg= 3098, myshift= 7 > CPU= 8, lastcg=28176, targetcg= 6214, myshift= 7 > CPU= 9, lastcg=31293, targetcg= 9331, myshift= 7 > CPU= 10, lastcg=34409, targetcg=12447, myshift= 7 > CPU= 11, lastcg=37526, targetcg=15564, myshift= 7 > CPU= 12, lastcg=40642, targetcg=18680, myshift= 7 > CPU= 13, lastcg=43924, targetcg=21962, myshift= 8 > pd->shift = 8, pd->bshift= 0 > Division of bonded forces over processors > CPU 0 1 2 3 4 5 6 7 8 > 9 10 > 11 12 13 > G96ANGLES 2376 0 0 0 0 0 0 0 0 > 0 0 > 0 0 0 > PDIHS 774 0 0 0 0 0 0 0 0 > 0 0 > 0 0 0 > IDIHS 852 0 0 0 0 0 0 0 0 > 0 0 > 0 0 0 > LJ14 2436 0 0 0 0 0 0 0 0 > 0 0 > 0 0 0 > CONSTR 1614 0 0 0 0 0 0 0 0 > 0 0 > 0 0 0 > SETTLE 2586 3116 3116 3117 3116 3117 3116 3117 3116 > 3117 3116 > 3117 3116 3034 > Workload division > nnodes: 14 > pd->shift: 8 > pd->bshift: 0 > Nodeid atom0 #atom cg0 #cg > 0 0 9348 0 3246 > 1 9348 9348 3246 3116 > 2 18696 9348 6362 3116 > 3 28044 9351 9478 3117 > 4 37395 9348 12595 3116 > 5 46743 9351 15711 3117 > 6 56094 9348 18828 3116 > 7 65442 9351 21944 3117 > 8 74793 9348 25061 3116 > 9 84141 9351 28177 3117 > 10 93492 9348 31294 3116 > 11 102840 9351 34410 3117 > 12 112191 9348 37527 3116 > 13 121539 9350 40643 3282 > > Max number of connections per atom is 27 > Total number of connections is 32076 > Max number of graph edges per atom is 4 > Total number of graph edges is 13572 > Initial temperature: 303.113 K > > Started mdrun on node 0 Fri Aug 13 14:38:46 2010 > > Step Time Lambda > 0 0.00000 0.00000 > > Grid: 10 x 45 x 10 cells > Energies (kJ/mol) > G96Angle Proper Dih. Improper Dih. LJ-14 Coulomb-14 > 2.96784e+03 1.16372e+03 9.89996e+02 -1.07478e+01 2.63019e+04 > LJ (SR) LJ (LR) Coulomb (SR) Coulomb (LR) RF excl. > 3.11913e+05 -8.40005e+03 -2.19295e+06 -1.39523e+04 -3.36479e+04 > Potential Kinetic En. Total Energy Temperature Pressure (bar) > -1.90563e+06 3.31599e+05 -1.57403e+06 3.04444e+02 1.07070e+01 > Cons. rmsd () > 2.63140e-05 > \\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\ > > Nothing more at the end, > I changed the 16 cores to 14 cores, still has the same problem. And when > I checked the status, it showed me it's finished. > Please provide more information. It mdrun stopped, it must have had a reason. Please provide your .mdp file, description of the system, and what you did as far as energy minimization and/or equilibration prior to whatever this run was doing. If mdrun fails, there's always a reason, and it would be very odd if Gromacs simply stopped without providing some kind of indicative output. -Justin Can you tell me the possible reasons? Mainly which part I need to check? Thanks, lina -- -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
