Re: Re: [gmx-users] mdrun mpi segmentation fault in high load situation

2010-12-24 Thread Wojtyczka , André
I'm not sure that PD has any advantage here. From memory it has to create a 128x1x1 grid, and you can direct that with DD also. See mdrun -h -hidden for -dd. Mark The contents of your .log file will be far more helpful than stdout in diagnosing what condition led to the problem. Mark

Re: [gmx-users] mdrun mpi segmentation fault in high load situation

2010-12-24 Thread Mark Abraham
On 24/12/2010 9:59 PM, Wojtyczka, André wrote: I'm not sure that PD has any advantage here. From memory it has to create a 128x1x1 grid, and you can direct that with DD also. See mdrun -h -hidden for -dd. Mark The contents of your .log file will be far more helpful than stdout in diagnosing

Re: [gmx-users] mdrun mpi segmentation fault in high load situation

2010-12-23 Thread Mark Abraham
On 23/12/2010 10:01 PM, Wojtyczka, André wrote: Dear Gromacs Enthusiasts. I am experiencing problems with mdrun_mpi (4.5.3) on a Nehalem cluster. Problem: This runs fine: mpiexec -np 72 /../mdrun_mpi -pd -s full031K_mdrun_ions.tpr This produces a segmentation fault: mpiexec -np 128