Re: [gmx-users] Segmentation fault with gromacs executables
On 26/04/2010 3:44 PM, Mark Abraham wrote: On 26/04/2010 2:45 PM, Sikandar Mashayak wrote: Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without specifying full path of gromacs/bin. And when I execute, say grompp, I get segmentation fault. Use "which grompp" and/or "echo $PATH" just before they execute to be sure which version you're getting. Of course, there's no need to execute grompp on the remote - only mdrun is MPI-aware, so you could/should do your preparation on your local machine, and merely run the MPI-enabled mdrun on the remote. Mark But when I use the same command by specifying full path /home/.../gromacs/bin/grompp , it executes without any issues!! It sounds like some kind of dynamic linking issue. Perhaps LD_LIBRARY_PATH or LD_RUN_PATH needs to be configured differently. Talk to your system admins - this issue will very likely not be specific to GROMACS. Mark -- 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
Re: [gmx-users] Segmentation fault with gromacs executables
On 26/04/2010 2:45 PM, Sikandar Mashayak wrote: Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without specifying full path of gromacs/bin. And when I execute, say grompp, I get segmentation fault. Use "which grompp" and/or "echo $PATH" just before they execute to be sure which version you're getting. But when I use the same command by specifying full path /home/.../gromacs/bin/grompp , it executes without any issues!! It sounds like some kind of dynamic linking issue. Perhaps LD_LIBRARY_PATH or LD_RUN_PATH needs to be configured differently. Talk to your system admins - this issue will very likely not be specific to GROMACS. Mark -- 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] Segmentation fault with gromacs executables
Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without specifying full path of gromacs/bin. And when I execute, say grompp, I get segmentation fault. But when I use the same command by specifying full path /home/.../gromacs/bin/grompp , it executes without any issues!! Whats wrong going on here? thanks sikandar -- 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
