[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
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
[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
