Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

Hi, You're not compiling properly for your cluster, which might have different hardware in different places. Read its docs and talk to your admins. Mark On Mon, Sep 18, 2017 at 4:07 AM Vidya R wrote: > Thank you for your reply. > > When I try to run my job in a single

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

Thank you for your reply. When I try to run my job in a single processor through qsub command, (by feeding the gromacs mdrun command in script file), it says SEGMENTATION FAULT, CORE DUMPED... But, when I run my job in login node (which we are not supposed to do), it works very well... Can

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

Hi, You're running a thread-MPI version of GROMACS, which is probably not what you want to do if you're running mpirun. It should work even so, but whatever quirks exist with SGE are unfortunately between you, its docs and your cluster's docs and admins :-( Mark On Sun, Sep 17, 2017 at 7:23 AM

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

https://drive.google.com/file/d/0BxGqxeGwTDLbLWJ5SExDblVhRFU /view?usp=sharing=59be86ad On Sun, Sep 17, 2017 at 6:35 PM, Justin Lemkul wrote: > > > On 9/17/17 1:22 AM, Vidya R wrote: > >> My log file is provided in the link below >> >> Can you please look into it and let me

Re: [gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

On 9/17/17 1:22 AM, Vidya R wrote: My log file is provided in the link below Can you please look into it and let me know why the error arises? I am feeding my commands in SGE cluster. When I run it in my login node, gmx mdrun -v -deffnm eql runs well But, through qsub command, (with 8

[gmx-users] mpirun noticed that process rank 7 with PID 19160 on node compute-0-28.local exited on signal 11 (Segmentation fault).

My log file is provided in the link below Can you please look into it and let me know why the error arises? I am feeding my commands in SGE cluster. When I run it in my login node, gmx mdrun -v -deffnm eql runs well But, through qsub command, (with 8 processors) It says, mpirun noticed that