Re: [gmx-users] query for gromacs-4.5.4

2013-03-14 Thread Chaitali Chandratre
Hello Sir, The job runs for 8 processes given 1 , 2 or 8 nodes but not for more than that. 16 proceses : Segmentation fault and For 32 processes it gives : Fatal error : 467 particles communicated to PME node 4 are more than 2/3 times the cut off out of the domain decomposition cell of their

Re: [gmx-users] query for gromacs-4.5.4

2013-03-14 Thread Mark Abraham
One cannot run an arbitrary simulation on an arbitrary number of processors. The particles in the simulation have to get mapped to processors that handle them. This is done in small parcels called domains. The atoms move between domains, and so the responsibility moves too. If the velocities are

Re: [gmx-users] query for gromacs-4.5.4

2013-03-12 Thread Mark Abraham
They're just MPI error messages and don't provide any useful GROMACS diagnostics. Look in the end of the .log file, stderr and stdout for clues. One possibility is that your user's system is too small to scale effectively. Below about 1000 atoms/core you're wasting your time unless you've

Re: [gmx-users] query for gromacs-4.5.4

2013-03-12 Thread Chaitali Chandratre
Sir, Thanks for your reply But the same script runs on some other cluster with apprx same configuration but not on cluster on which I am doing set up. Also job hangs after some 16000 steps but not come out immediately. It might be problem with configuration or what? Thanks... Chaitali On

Re: [gmx-users] query for gromacs-4.5.4

2013-03-12 Thread Mark Abraham
It could be anything. But until we see some GROMACS diagnostic messages, nobody can tell. Mark On Tue, Mar 12, 2013 at 10:08 AM, Chaitali Chandratre chaitujo...@gmail.com wrote: Sir, Thanks for your reply But the same script runs on some other cluster with apprx same configuration but

Re: [gmx-users] query for gromacs-4.5.4

2013-03-11 Thread Chaitali Chandratre
Hello Sir, Actually I have been given work to setup gromacs-4.5.4 in our cluster which is being used by users.I am not gromacs user and not aware of its internal details. I have got only .tpr file from user and I need to test my installation using that .tpr file. It works fine for 2 nodes 8

[gmx-users] query for gromacs-4.5.4

2013-03-06 Thread Chaitali Chandratre
Dear Sir , I am new to this installation and setup area. I need some information for -stepout option for mdrun_mpi and also probable causes for segmentation fault in gromacs-4.5.4. (my node having 64 GB mem running with 16 processes, nsteps = 2000) Thanks in advance. -- With Regards,

Re: [gmx-users] query for gromacs-4.5.4

2013-03-06 Thread Justin Lemkul
On 3/6/13 4:20 AM, Chaitali Chandratre wrote: Dear Sir , I am new to this installation and setup area. I need some information for -stepout option for What more information do you need? mdrun_mpi and also probable causes for segmentation fault in gromacs-4.5.4. (my node having 64 GB mem