[gmx-users] MPI segmentation Fault

Xu Dong Huang xudongh at eden.rutgers.edu
Wed Jan 2 21:20:24 CET 2013

Dear gromac users,

after examining my nvt run outcome, I see that my molecule has half of the arm stuck outside of the box (I guess my run wasn't very successful). But I thought the jumping outside of the box would be corrected by periodic boundary? Should I run my nvt for longer since the structure itself did not seem to change much in the solute? (My initial 
Xu Dong Huangnvt nstep=10000, should I increase it to resolve the problem? if that resolves the problem at all that is)

Thanks for any input,

Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu 

On Jan 2, 2013, at 3:08 PM, Xu Dong Huang <xudongh at eden.rutgers.edu> wrote:

> Dear gromac users,
> after running a successful NVT, I was going to run NPT. (All ran with MPI), however when I attempt to run the NPT, I get the following segmentation error: 
> Getting Loaded...
> Reading file npt.tpr, VERSION 4.5.3 (single precision)
> Loaded with Money
> WARNING: This run will generate roughly 3890 Mb of data
> starting mdrun 'star'
> 1000000 steps,  20000.0 ps.
> step 0[Ultranode02:26884] *** Process received signal ***
> [Ultranode02:26884] Signal: Segmentation fault (11)
> [Ultranode02:26884] Signal code: Address not mapped (1)
> [Ultranode02:26884] Failing at address: 0x1f5acf020
> [Ultranode02:26884] [ 0] /lib/libpthread.so.0(+0xf8f0) [0x2b21605168f0]
> [Ultranode02:26884] [ 1] mdrun_mpi() [0x745509]
> [Ultranode02:26884] *** End of error message ***
> /usr/local/SGE/default/spool/Ultranode02/job_scripts/39346: line 38: 26884 Segmentation fault      mdrun_mpi -v -deffnm npt
> -----Is my system blowing up? Or there is something wrong with MPI ? (I requested 4 processors)
> Xu Dong Huang
> Chemical & Biochemical Engineering
> Rutgers School of Engineering 
> xudongh at eden.rutgers.edu 
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