Re: [gmx-users] help about Inconsistent DD boundary staggering limits
On 4/26/12 2:52 PM, Desheng Zheng wrote: Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Based on the comment that precedes the error call in the code: /* Make sure that the grid is not shifted too much */ I would assume that this means your system has simply become unstable and is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 102, will try to stop all the nodes Halting parallel program mdrun on CPU 102 out of 120 Error on node 105, will try to stop all the nodes Halting parallel program mdrun on CPU 105 out of 120 Error on node 51, will try to stop all the nodes Halting parallel program mdrun on CPU 51 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 81, will try to stop all the nodes Halting parallel program mdrun on CPU 81 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 63, will try to stop all the nodes Halting parallel program mdrun on CPU 63 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 33, will try to stop all the nodes Halting parallel program mdrun on CPU 33 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 54, will try to stop all the nodes Halting parallel program mdrun on CPU 54 out of 120 Error on node 24, will try to stop all the nodes Halting parallel program mdrun on CPU 24 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The
Re: [gmx-users] help about Inconsistent DD boundary staggering limits
On 4/26/12 3:30 PM, Desheng Zheng wrote: Thanks Justin! about the Software inconsistency error: Inconsistent DD boundary staggering limits! I still have three concerts. 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 environmentwith the gro file and top file which were builed under Gromacs 4.0.7 ? Coordinate files and topologies are largely independent of version. There was a reorganization of the force fields between 4.0.7 and 4.5, but you can easily work around such things. 2. In my protein-DPPC lipid membrane, I use the electric filed Ez is 0.3V/nm. whether is the value too high to induce the bowling up? I don't know. The easiest way to deduce the source of the problem is to do so scientifically. Turn off the electric field, does the simulation run? Eliminate other factors systematically until you arrive at the root of the problem. 3. why do the generated edr file in gromacs 4.5.5 environment larger than the edr file in gromacs 4.0.7 environment, even with the same gro file and top file and the same commands? There have been changes to the .edr format and its contents to allow for more features. -Justin -- 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/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
RE: [gmx-users] help about Inconsistent DD boundary staggering limits
Thanks Justin! about the Software inconsistency error: Inconsistent DD boundary staggering limits! I still have three concerts. 1. Is it ok, if i use grompp to generate the edr file in gromacs 4.5.5 environmentwith the gro file and top file which were builed under Gromacs 4.0.7 ? 2. In my protein-DPPC lipid membrane, I use the electric filed Ez is 0.3V/nm. whether is the value too high to induce the bowling up? 3. why do the generated edr file in gromacs 4.5.5 environment larger than the edr file in gromacs 4.0.7 environment, even with the same gro file and top file and the same commands? Best wishes, Desheng From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Thursday, April 26, 2012 3:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] help about Inconsistent DD boundary staggering limits On 4/26/12 2:52 PM, Desheng Zheng wrote: Hi Guys, I have done the simulation. The total steps is 500. At around 90 steps, the error information appear like the followings. Please give me some suggestions to fix it. Based on the comment that precedes the error call in the code: /* Make sure that the grid is not shifted too much */ I would assume that this means your system has simply become unstable and is blowing up. http://www.gromacs.org/Documentation/Terminology/Blowing_Up -Justin Best wishes, Desheng -- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 102, will try to stop all the nodes Halting parallel program mdrun on CPU 102 out of 120 Error on node 105, will try to stop all the nodes Halting parallel program mdrun on CPU 105 out of 120 Error on node 51, will try to stop all the nodes Halting parallel program mdrun on CPU 51 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 81, will try to stop all the nodes Halting parallel program mdrun on CPU 81 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 63, will try to stop all the nodes Halting parallel program mdrun on CPU 63 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) Error on node 33, will try to stop all the nodes Halting parallel program mdrun on CPU 33 out of 120 --- Program mdrun, VERSION 4.5.5 Source code file: domdec.c, line: 3266 Software inconsistency error: Inconsistent DD boundary staggering limits! For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If it weren't for bad luck, we'd have no luck at all (The Unthanks) --- Program mdrun, VERSION
