Re: [gmx-users] the mdrun choked or maybe braked.
#ZHAO LINA# wrote: 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: 93489348934893519348935193489351 93489351 9348935193489350 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 8 910 111213 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 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 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 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 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 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+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 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+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? Based on what you posted before, there is no possible way to tell you what's wrong, and hence why I asked for more information. Check all output - stdout, stderr, log files, whatever other files your queuing system (if applicable) might give you. There are numerous reasons for
RE: [gmx-users] the mdrun choked or maybe braked.
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: > 93489348934893519348935193489351 > 93489351 > 9348935193489350 > 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 > 910 > 111213 > 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 > CONSTR1614 0 0 0 0 0 0 0 0 > 0 0 >0 0 0 > SETTLE2586 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 09348 0 3246 > 1934893483246 3116 > 2 1869693486362 3116 > 3 2804493519478 3117 > 4 373959348 12595 3116 > 5 467439351 15711 3117 > 6 560949348 18828 3116 > 7 654429351 21944 3117 > 8 747939348 25061 3116 > 9 841419351 28177 3117 > 10 934929348 31294 3116 > 11 1028409351 34410 3117 > 12 1121919348 37527 3116 > 13 1215399350 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 > 00.00.0 > > Grid: 10 x 45 x 10 cells >Energies (kJ/mol) >G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 > 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+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 > PotentialKinetic En. Total EnergyTemperature Pressure (bar) >-1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+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 ver
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: 93489348934893519348935193489351 93489351 9348935193489350 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 8 910 111213 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 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 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 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 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 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+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 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+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 Thanks for any advice, lina -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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 po
[gmx-users] the mdrun choked or maybe braked.
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: 9348934893489351934893519348935193489351 9348935193489350 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 8 910 111213 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 CONSTR1614 0 0 0 0 0 0 0 0 0 0 0 0 0 SETTLE2586 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 09348 0 3246 1934893483246 3116 2 1869693486362 3116 3 2804493519478 3117 4 373959348 12595 3116 5 467439351 15711 3117 6 560949348 18828 3116 7 654429351 21944 3117 8 747939348 25061 3116 9 841419351 28177 3117 10 934929348 31294 3116 11 1028409351 34410 3117 12 1121919348 37527 3116 13 1215399350 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 00.00.0 Grid: 10 x 45 x 10 cells Energies (kJ/mol) G96AngleProper Dih. Improper Dih. LJ-14 Coulomb-14 2.96784e+031.16372e+039.89996e+02 -1.07478e+012.63019e+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 PotentialKinetic En. Total EnergyTemperature Pressure (bar) -1.90563e+063.31599e+05 -1.57403e+063.0e+021.07070e+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. Thanks for any advice, lina -- gmx-users mailing listgmx-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
