Re: [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm
4.5 can only handle about 500-1000 atoms per processor. Details vary. Mark On Oct 17, 2013 5:39 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Thanks for you reply. I am doing simulation for ionic liquids BMIM + CL. Total number of atoms are 3328. Nilesh Assuming you're using LINCS, from the manual: With domain decomposition, the cell size is limited by the distance spanned by *lincs-order*+1 constraints. Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance for 5 bonds. Which means that you're probably using too many nodes for the size of your system. Hope that helps. If it doesn't you'll need to provide some information about your system. -Trayder On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am getting the following error for simulation. I am using Gromacs VERSION 4.5.5 and running on 24 processors. Should I reduce the number of processor or the problem is in bonded parameters. If I use -nt 1 option. I could run the simulation. Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Nilesh -- 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 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 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 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] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm
Hello, I am getting the following error for simulation. I am using Gromacs VERSION 4.5.5 and running on 24 processors. Should I reduce the number of processor or the problem is in bonded parameters. If I use -nt 1 option. I could run the simulation. Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Nilesh -- 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] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm
Assuming you're using LINCS, from the manual: With domain decomposition, the cell size is limited by the distance spanned by *lincs-order*+1 constraints. Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance for 5 bonds. Which means that you're probably using too many nodes for the size of your system. Hope that helps. If it doesn't you'll need to provide some information about your system. -Trayder On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am getting the following error for simulation. I am using Gromacs VERSION 4.5.5 and running on 24 processors. Should I reduce the number of processor or the problem is in bonded parameters. If I use -nt 1 option. I could run the simulation. Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Nilesh -- 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 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] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm
Thanks for you reply. I am doing simulation for ionic liquids BMIM + CL. Total number of atoms are 3328. Nilesh Assuming you're using LINCS, from the manual: With domain decomposition, the cell size is limited by the distance spanned by *lincs-order*+1 constraints. Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance for 5 bonds. Which means that you're probably using too many nodes for the size of your system. Hope that helps. If it doesn't you'll need to provide some information about your system. -Trayder On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am getting the following error for simulation. I am using Gromacs VERSION 4.5.5 and running on 24 processors. Should I reduce the number of processor or the problem is in bonded parameters. If I use -nt 1 option. I could run the simulation. Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Nilesh -- 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 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 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
