[gmx-users] MPI segmentation Fault

Xu Dong Huang xudongh at eden.rutgers.edu
Wed Jan 2 21:08:12 CET 2013

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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