[gmx-users] Segmentation fault !
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 6 10:51:06 CEST 2002
On Tue, 2002-08-06 at 10:41, Satyan Sharma wrote:
> Hi all,
> I am doing simulations for 3ns in steps of 1ns each.
> Although the first 2 ns go very fine but I am
> encountering segmentation fault in the last lap..
> step 35820, will finish at Tue Aug 6 14:42:13 2002
> step 35830, will finish at Tue Aug 6 14:42:10 2002
> ERROR: 0031-250 task 0: Segmentation fault
> ERROR: 0031-250 task 5: Terminated
> ERROR: 0031-250 task 4: Terminated
> ERROR: 0031-250 task 1: Terminated
> ERROR: 0031-250 task 7: Terminated
> ERROR: 0031-250 task 6: Terminated
> ERROR: 0031-250 task 3: Terminated
> ERROR: 0031-250 task 2: Terminated
> Any suggestion about what should i check . I have been
> using the system and have done about 10ns simulations
> earlier. Basically in this 3ns simulation i took the
> structure from previous 10ns simulation and have added
> one more residue.
there are at least three possibilities:
- the sytem is out of equlibrium and large forces give problems. Check
the log file for messages
- something with your hardware: try to rerun the exact same simulation
and see if the problem is reproducible (it is only 35000 steps
apparenly). If the problem is not reproducible, you most likely have a
hardware problem. If you have athlon machines, check the temperature and
the system log files too...
- bug in gromacs...
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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