Re: [gmx-users] maxh not causing termination
On Mon, Jan 9, 2012 at 3:46 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 10/01/2012 7:19 AM, Ben Reynwar wrote: On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/19/2011 1:51 PM, Ben Reynwar wrote: I'm having a problem with gromacs not terminating as expected when using the maxh option. It is an REMD simulation with 32 replicas. I'm specifying -maxh 24 and as expected see the following in the stderr output. Step 773882: Run time exceeded 23.760 hours, will terminate the run Step 773876: Run time exceeded 23.760 hours, will terminate the run Step 773880: Run time exceeded 23.760 hours, will terminate the run etc However I can see that the output files continued to be written for another hour until at 25 hours the simulation was terminated by the queueing system. No checkpoint files were produced. The output files show that the simulation continued until about step 797000. I've done similar things previously without running into this problem. Anyone have any ideas for what stupid mistake I could be making? Perhaps none. What GROMACS version is this? Does the latest version have the same behaviour? Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists Sorry for the slow response. I've been away on holiday. The version used is 4.5.5 with a bug fix applied from http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html It was a replica exchange simulation. I've narrowed down the problem to be specific to using infinite cutoff. With a finite cutoff there are no problems. The initial run works fine and creates checkpoints. However a run started from one of these checkpoints fails to create checkpoints itself. All that sounds very much like a bug. Please open an issue here http://redmine.gromacs.org and attach the lowest four .tpr and .cpt input files for the failing case. This will allow someone to find out why and perhaps fix it. Mark Done (http://redmine.gromacs.org/issues/860) The diff between the an mdp that works fine and one that doesn't is: 53,57c53,58 ; [nm] cut-off distance for the short-range neighbor list. ; Set to zero for infinite cut-off. rlist = 0 ; Recalculating pair-list is not necessary with an infinite cut-off nstlist = 0 --- ; [nm] cut-off distance for the short-range neighbor list ; For Generalized Born this must be equal to the cut-off length for ; the born radius calculation. rlist = 1.6 ; [steps] freq to update neighbor list nstlist = 1 67,68c68,69 ; infinite coloumb cut-off radius rcoulomb = 0 --- ; coloumb cutoff radius rcoulomb = 1.6 76,77c77,78 ; Infinite VsW cutoff radius. rvdw = 0 --- ; Increasing VdW cutoff to same as everything else. rvdw = 1.6 144c145 rgbradii = 0 --- rgbradii = 1.6 The complete offending mdp file will follow. Also if there's anything stupid in here unrelated to my current problem, please let me know too :). ; 7.3.2 Preprocssing ; -- ; Apply constaint to alpha carbon atoms in alpha-crystalline domain. define = -DALPHACRYST_POSRES -DCHIRRES ; 7.3.3 Run Control ; - ; group(s) for center of mass motion removal comm_grps = System ; Do Langevin dynamics. integrator = sd ; maximum number of steps to integrate nsteps = 1 ; remove center of mass translation and rotation around centre of mass comm_mode = Angular ; [ps] time step for integration dt = 0.002 ; [steps] frequency of mass motion removal nstcomm = 10 ; [ps] starting time for run tinit = 0 ; 7.3.4 Langevin Dynamics ; --- ; Use PID to seed random number. ld_seed = -1 ; 7.3.8 Output Control ; ; [steps] freq to write velocities to trajectory nstvout = 0 ; [steps] freq to write energies to log file nstlog = 1000 ; [steps] freq to write energies to energy file nstenergy = 1000 ; group(s) to write to xtc trajectory xtc_grps = System ; [real] precision to write xtc trajectory xtc_precision = 1000 ; [steps] freq to write coordinates to xtc trajectory nstxtcout = 1000 ; [steps] freq to write coordinates to trajectory nstxout = 0 ; group(s) to write to energy file energygrps = System ; [steps] freq to write forces to trajectory nstfout = 0 ; 7.3.9 Neighbour Searching ; - ; [nm] cut-off distance for the short-range neighbor list. ; Set to zero for infinite cut-off. rlist = 0 ; Recalculating pair-list is not necessary with an infinite cut-off
Re: [gmx-users] maxh not causing termination
On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham mark.abra...@anu.edu.au wrote: On 12/19/2011 1:51 PM, Ben Reynwar wrote: I'm having a problem with gromacs not terminating as expected when using the maxh option. It is an REMD simulation with 32 replicas. I'm specifying -maxh 24 and as expected see the following in the stderr output. Step 773882: Run time exceeded 23.760 hours, will terminate the run Step 773876: Run time exceeded 23.760 hours, will terminate the run Step 773880: Run time exceeded 23.760 hours, will terminate the run etc However I can see that the output files continued to be written for another hour until at 25 hours the simulation was terminated by the queueing system. No checkpoint files were produced. The output files show that the simulation continued until about step 797000. I've done similar things previously without running into this problem. Anyone have any ideas for what stupid mistake I could be making? Perhaps none. What GROMACS version is this? Does the latest version have the same behaviour? Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists Sorry for the slow response. I've been away on holiday. The version used is 4.5.5 with a bug fix applied from http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html It was a replica exchange simulation. I've narrowed down the problem to be specific to using infinite cutoff. With a finite cutoff there are no problems. The initial run works fine and creates checkpoints. However a run started from one of these checkpoints fails to create checkpoints itself. The diff between the an mdp that works fine and one that doesn't is: 53,57c53,58 ; [nm] cut-off distance for the short-range neighbor list. ; Set to zero for infinite cut-off. rlist = 0 ; Recalculating pair-list is not necessary with an infinite cut-off nstlist = 0 --- ; [nm] cut-off distance for the short-range neighbor list ; For Generalized Born this must be equal to the cut-off length for ; the born radius calculation. rlist = 1.6 ; [steps] freq to update neighbor list nstlist = 1 67,68c68,69 ; infinite coloumb cut-off radius rcoulomb = 0 --- ; coloumb cutoff radius rcoulomb = 1.6 76,77c77,78 ; Infinite VsW cutoff radius. rvdw = 0 --- ; Increasing VdW cutoff to same as everything else. rvdw = 1.6 144c145 rgbradii = 0 --- rgbradii = 1.6 The complete offending mdp file will follow. Also if there's anything stupid in here unrelated to my current problem, please let me know too :). ; 7.3.2 Preprocssing ; -- ; Apply constaint to alpha carbon atoms in alpha-crystalline domain. define = -DALPHACRYST_POSRES -DCHIRRES ; 7.3.3 Run Control ; - ; group(s) for center of mass motion removal comm_grps = System ; Do Langevin dynamics. integrator = sd ; maximum number of steps to integrate nsteps = 1 ; remove center of mass translation and rotation around centre of mass comm_mode = Angular ; [ps] time step for integration dt = 0.002 ; [steps] frequency of mass motion removal nstcomm = 10 ; [ps] starting time for run tinit = 0 ; 7.3.4 Langevin Dynamics ; --- ; Use PID to seed random number. ld_seed = -1 ; 7.3.8 Output Control ; ; [steps] freq to write velocities to trajectory nstvout = 0 ; [steps] freq to write energies to log file nstlog = 1000 ; [steps] freq to write energies to energy file nstenergy = 1000 ; group(s) to write to xtc trajectory xtc_grps = System ; [real] precision to write xtc trajectory xtc_precision = 1000 ; [steps] freq to write coordinates to xtc trajectory nstxtcout = 1000 ; [steps] freq to write coordinates to trajectory nstxout = 0 ; group(s) to write to energy file energygrps = System ; [steps] freq to write forces to trajectory nstfout = 0 ; 7.3.9 Neighbour Searching ; - ; [nm] cut-off distance for the short-range neighbor list. ; Set to zero for infinite cut-off. rlist = 0 ; Recalculating pair-list is not necessary with an infinite cut-off nstlist = 0 ; method of updating neighbor list ns_type = grid ; no periodic boundary conditions pbc = no ; 7.3.10 Electrostatics ; - ; apply a cut-off to electostatic coulombtype = cut-off ; infinite coloumb cut-off radius rcoulomb = 0 ; 7.3.11 VdW ; -- ; Dispersion correction makes no sense without box size. DispCorr = no ; twin-range cut-off with rlist where rvdw rlist vdwtype = cut-off ; Infinite VsW cutoff radius. rvdw = 0 ; 7.3.13 Ewald ; ; [nm] grid
Re: [gmx-users] maxh not causing termination
On 10/01/2012 7:19 AM, Ben Reynwar wrote: On Tue, Dec 20, 2011 at 7:16 PM, Mark Abrahammark.abra...@anu.edu.au wrote: On 12/19/2011 1:51 PM, Ben Reynwar wrote: I'm having a problem with gromacs not terminating as expected when using the maxh option. It is an REMD simulation with 32 replicas. I'm specifying -maxh 24 and as expected see the following in the stderr output. Step 773882: Run time exceeded 23.760 hours, will terminate the run Step 773876: Run time exceeded 23.760 hours, will terminate the run Step 773880: Run time exceeded 23.760 hours, will terminate the run etc However I can see that the output files continued to be written for another hour until at 25 hours the simulation was terminated by the queueing system. No checkpoint files were produced. The output files show that the simulation continued until about step 797000. I've done similar things previously without running into this problem. Anyone have any ideas for what stupid mistake I could be making? Perhaps none. What GROMACS version is this? Does the latest version have the same behaviour? Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists Sorry for the slow response. I've been away on holiday. The version used is 4.5.5 with a bug fix applied from http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html It was a replica exchange simulation. I've narrowed down the problem to be specific to using infinite cutoff. With a finite cutoff there are no problems. The initial run works fine and creates checkpoints. However a run started from one of these checkpoints fails to create checkpoints itself. All that sounds very much like a bug. Please open an issue here http://redmine.gromacs.org http://redmine.gromacs.org/ and attach the lowest four .tpr and .cpt input files for the failing case. This will allow someone to find out why and perhaps fix it. Mark The diff between the an mdp that works fine and one that doesn't is: 53,57c53,58 ; [nm] cut-off distance for the short-range neighbor list. ; Set to zero for infinite cut-off. rlist = 0 ; Recalculating pair-list is not necessary with an infinite cut-off nstlist = 0 --- ; [nm] cut-off distance for the short-range neighbor list ; For Generalized Born this must be equal to the cut-off length for ; the born radius calculation. rlist = 1.6 ; [steps] freq to update neighbor list nstlist = 1 67,68c68,69 ; infinite coloumb cut-off radius rcoulomb = 0 --- ; coloumb cutoff radius rcoulomb = 1.6 76,77c77,78 ; Infinite VsW cutoff radius. rvdw = 0 --- ; Increasing VdW cutoff to same as everything else. rvdw = 1.6 144c145 rgbradii = 0 --- rgbradii = 1.6 The complete offending mdp file will follow. Also if there's anything stupid in here unrelated to my current problem, please let me know too :). ; 7.3.2 Preprocssing ; -- ; Apply constaint to alpha carbon atoms in alpha-crystalline domain. define = -DALPHACRYST_POSRES -DCHIRRES ; 7.3.3 Run Control ; - ; group(s) for center of mass motion removal comm_grps = System ; Do Langevin dynamics. integrator = sd ; maximum number of steps to integrate nsteps = 1 ; remove center of mass translation and rotation around centre of mass comm_mode = Angular ; [ps] time step for integration dt = 0.002 ; [steps] frequency of mass motion removal nstcomm = 10 ; [ps] starting time for run tinit = 0 ; 7.3.4 Langevin Dynamics ; --- ; Use PID to seed random number. ld_seed = -1 ; 7.3.8 Output Control ; ; [steps] freq to write velocities to trajectory nstvout = 0 ; [steps] freq to write energies to log file nstlog = 1000 ; [steps] freq to write energies to energy file nstenergy = 1000 ; group(s) to write to xtc trajectory xtc_grps = System ; [real] precision to write xtc trajectory xtc_precision = 1000 ; [steps] freq to write coordinates to xtc trajectory nstxtcout = 1000 ; [steps] freq to write coordinates to trajectory nstxout = 0 ; group(s) to write to energy file energygrps = System ; [steps] freq to write forces to trajectory nstfout = 0 ; 7.3.9 Neighbour Searching ; - ; [nm] cut-off distance for the short-range neighbor list. ; Set to zero for infinite cut-off. rlist = 0 ; Recalculating pair-list is not necessary with an infinite cut-off nstlist = 0 ; method of updating neighbor list ns_type = grid ; no periodic boundary conditions pbc = no ; 7.3.10 Electrostatics ; - ; apply a cut-off to electostatic coulombtype = cut-off ;
Re: [gmx-users] maxh not causing termination
On 12/19/2011 1:51 PM, Ben Reynwar wrote: I'm having a problem with gromacs not terminating as expected when using the maxh option. It is an REMD simulation with 32 replicas. I'm specifying -maxh 24 and as expected see the following in the stderr output. Step 773882: Run time exceeded 23.760 hours, will terminate the run Step 773876: Run time exceeded 23.760 hours, will terminate the run Step 773880: Run time exceeded 23.760 hours, will terminate the run etc However I can see that the output files continued to be written for another hour until at 25 hours the simulation was terminated by the queueing system. No checkpoint files were produced. The output files show that the simulation continued until about step 797000. I've done similar things previously without running into this problem. Anyone have any ideas for what stupid mistake I could be making? Perhaps none. What GROMACS version is this? Does the latest version have the same behaviour? Mark -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] maxh not causing termination
I'm having a problem with gromacs not terminating as expected when using the maxh option. It is an REMD simulation with 32 replicas. I'm specifying -maxh 24 and as expected see the following in the stderr output. Step 773882: Run time exceeded 23.760 hours, will terminate the run Step 773876: Run time exceeded 23.760 hours, will terminate the run Step 773880: Run time exceeded 23.760 hours, will terminate the run etc However I can see that the output files continued to be written for another hour until at 25 hours the simulation was terminated by the queueing system. No checkpoint files were produced. The output files show that the simulation continued until about step 797000. I've done similar things previously without running into this problem. Anyone have any ideas for what stupid mistake I could be making? Cheers, Ben -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
