Re: [gmx-users] Parellel Gromacs
Hello, I have tried using the mdrun_mpi and it can't run. It gives me this error: Failed to find the following executable: Executable: mdrun_mpi Cannot continue. Belquis I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename did you try the following mpirun -np 2 mdrun_mpi -deffnm filename XAvier Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
Ask the system manager where the executables are and what are their names. I have tried using the mdrun_mpi and it can't run. It gives me this error: Failed to find the following executable: Executable: mdrun_mpi Cannot continue. Belquis I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename did you try the following mpirun -np 2 mdrun_mpi -deffnm filename XAvier Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
Please build gromacs with MPI-support. Check website for configuration. Regards, Yang Ye - Original Message From: [EMAIL PROTECTED] [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Thursday, August 2, 2007 12:26:17 AM Subject: Re: [gmx-users] Parellel Gromacs Hello, I have tried using the mdrun_mpi and it can't run. It gives me this error: Failed to find the following executable: Executable: mdrun_mpi Cannot continue. Belquis I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename did you try the following mpirun -np 2 mdrun_mpi -deffnm filename XAvier Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Parellel Gromacs
Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was made for 2 nodes, while mdrun expected it to be for 1 nodes. --- Fresh Air, Green Hair (Frank Black) Halting program mdrun gcq#303: Fresh Air, Green Hair (Frank Black) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_31660: p4_error: : -1 p4_error: latest msg from perror: No such file or directory p0_31659: p4_error: : -1 I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was made for 2 nodes, while mdrun expected it to be for 1 nodes. --- Fresh Air, Green Hair (Frank Black) Halting program mdrun gcq#303: Fresh Air, Green Hair (Frank Black) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_31660: p4_error: : -1 p4_error: latest msg from perror: No such file or directory p0_31659: p4_error: : -1 I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
Hi, I am not the one who built it, but it is MPI supported. Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was made for 2 nodes, while mdrun expected it to be for 1 nodes. --- Fresh Air, Green Hair (Frank Black) Halting program mdrun gcq#303: Fresh Air, Green Hair (Frank Black) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_31660: p4_error: : -1 p4_error: latest msg from perror: No such file or directory p0_31659: p4_error: : -1 I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
you should use the mdrun_mpi probably XAvier Hi, I am not the one who built it, but it is MPI supported. Have your built the GROMACS with MPI-support? Regards, Yang Ye On 8/1/2007 4:35 AM, [EMAIL PROTECTED] wrote: Dear Gromacs users, I am trying to do Parellel calculations using Gromacs on a Rocks cluster that has MPI enabled. Has anybody encountered the following error: Program mdrun, VERSION 3.3.1 Source code file: init.c, line: 69 Fatal error: run input file RecpAntiP-cl#1-SG-consP-L0-1-G.tpr was made for 2 nodes, while mdrun expected it to be for 1 nodes. --- Fresh Air, Green Hair (Frank Black) Halting program mdrun gcq#303: Fresh Air, Green Hair (Frank Black) [0] MPI Abort by user Aborting program ! [0] Aborting program! p0_31660: p4_error: : -1 p4_error: latest msg from perror: No such file or directory p0_31659: p4_error: : -1 I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Parellel Gromacs
I ran this command for Parellel calculation: mpirun -np 2 mdrun -deffnm filename did you try the following mpirun -np 2 mdrun_mpi -deffnm filename XAvier Thanks in advance, ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php - XAvier Periole - PhD 1- Institute of Molecular Assemblies City University of New York - USA 2- Molecular Dynamics-Group University of Groningen - The Netherlands http://md.chem.rug.nl/~periole - ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
