[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76
Hi Abdul, please keep Gromacs-related questions on the list. The error is exactly as printed: You have more than 128 backups of md.log in your directory, at this point mdrun does not make more backups of md.log any more. You have to delete the #md.log.*# files. Carsten On Jun 18, 2010, at 7:24 AM, abdul wadood wrote: > Dear Carsten > > When I reduce the number of steps in mdp file the error change which now > > 0: Fatal error: > 0: Won't make more than 128 backups of md.log for you > 0: --- > 0: > 0: "I Wonder, Should I Get Up..." (J0: p0_27074: p4_error: : -1 > . Lennon) > 0: > 0: Halting program mdrun_mpi > 0: > 0: gcq#46: "I Wonder, Should I Get Up..." (J. Lennon) > 0: > 0: [0] MPI Abort by user Aborting program ! > 0: [0] Aborting program! > 0: p4_error: latest msg from perror: No such file or directory > > > Abdul Wadood, > Research Scholar, > Dr.Panjwani Center for Molecular Medicine and > Drug Research, > International Center for Chemical and > Biological Science, > University of Karachi, Karachi-75720, Pakistan. > Email:wadoodbiochem...@hotmail.com > > > > > From: ckut...@gwdg.de > Subject: Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76 > Date: Thu, 17 Jun 2010 16:36:51 +0200 > To: wadoodbiochem...@hotmail.com > > On Jun 17, 2010, at 3:57 PM, abdul wadood wrote: > > Dear Carsten > > I give the path for the topol.tpr file now the error is change which is > > Fatal error: > 3: Too many LINCS warnings (4254) > 3: If you know what you are doing you can adjust the lincs warning threshold > in your mdp file > 3: or set the environment variable GMX_MAXCONSTRWARN to -1, > 3: but normally it is better to fix the problem > 3: --- > 3: > Maybe your system is not well equilibrated, or your time step is too long. > > Carsten > > Hotmail is redefining busy with tools for the New Busy. Get more from your > inbox. See how. -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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
[gmx-users] RE: Parallel instalation: gmx-users Digest, Vol 74, Issue 76
Dear Carsten I give the path for the topol.tpr file now the error is change which is Fatal error: 3: Too many LINCS warnings (4254) 3: If you know what you are doing you can adjust the lincs warning threshold in your mdp file 3: or set the environment variable GMX_MAXCONSTRWARN to -1, 3: but normally it is better to fix the problem 3: --- 3: 3: "You're About to Hurt Somebody" (Jazzy Jeff) 3: 3: Halting program mdrun_mpi 3: 3: gcq#98: "You're About to Hurt Somebody" (Jazzy Jeff) 3: 3: [0] MPI Abort by user Aborting program ! 3: [0] Aborting program! 3: p4_error: latest msg from perror: No such file or directory Abdul Wadood, Research Scholar, Dr.Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Science, University of Karachi, Karachi-75720, Pakistan. Email:wadoodbiochem...@hotmail.com Subject: Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76 From: ckut...@gwdg.de Date: Thu, 17 Jun 2010 15:46:40 +0200 CC: wadoodbiochem...@hotmail.com To: gmx-users@gromacs.org On Jun 17, 2010, at 3:42 PM, abdul wadood wrote:Dear Carsten the command which i give is mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr with this command the same error come which is Can not open file: 3: topol.tpr 3: --- Maybe "." (the current directory) is not in your path. Either try mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s ./topol.tpr or give the full path name: mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s /absolute/path/to/topol.tpr Carsten _ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_3-- 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
[gmx-users] Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76
On Jun 17, 2010, at 3:42 PM, abdul wadood wrote: > Dear Carsten > > the command which i give is > > mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s topol.tpr > > with this command the same error come which is > > Can not open file: > 3: topol.tpr > 3: --- Maybe "." (the current directory) is not in your path. Either try mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s ./topol.tpr or give the full path name: mpiexec -l -np 4 /usr/local/gromacs/bin/mdrun_mpi -s /absolute/path/to/topol.tpr Carsten -- 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
