[gmx-users] which may caused this error

[Justin A. Lemkul]

lina wrote:
> Hi,
> 
> I have very high frequency meeting below error:
> 
> [hostname-c06:07555] *** Process received signal ***
> [hostname-c06:07555] Signal: Segmentation fault (11)
> [hostname-c06:07555] Signal code: Address not mapped (1)
> [hostname-c06:07555] Failing at address: 0x2aaab3248120
> [hostname-c06:07555] [ 0] /lib64/libpthread.so.0 [0x399440e7c0]
> [hostname-c06:07555] [ 1]
> /home/lina/lib/libgmx_mpi.so.6(nb_kernel_allvsallgb_sse2_single+0x1cc1)
> [0x2b7249a92d61]
> [hostname-c06:07555] [ 2]
> /home/lina/lib/libgmx_mpi.so.6(do_nonbonded+0xe8) [0x2b72499d99d8]
> [hostname-c06:07555] [ 3]
> /home/lina/lib/libmd_mpi.so.6(do_force_lowlevel+0x32f)
> [0x2b724931c7bf]
> [hostname-c06:07555] [ 4]
> /home/lina/lib/libmd_mpi.so.6(do_force+0xbf5) [0x2b72493766c5]
> [hostname-c06:07555] [ 5] mdrun_g_f(do_md+0x54ba) [0x41b1ca]
> [hostname-c06:07555] [ 6] mdrun_g_f(mdrunner+0x1169) [0x415ae9]
> [hostname-c06:07555] [ 7] mdrun_g_f(main+0x9c7) [0x41c027]
> [hostname-c06:07555] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
> [0x3993c1d994]
> [hostname-c06:07555] [ 9] mdrun_g_f(do_cg+0x191) [0x407e39]
> [hostname-c06:07555] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 52 with PID 7555 on node hostname-c06
> exited on signal 11 (Segmentation fault).
> 
> I have made a clear installation with 4.5.5.
> 
> just please feel free to give some wild guess about what's the possible reasons,
> 

Wild guesses are unproductive.  Please provide more information:

1. The OS, compilers used, etc.
2. What is the system? Does it run in serial or parallel?
3. Do other simulations work?
4. What is your .mdp file?
5. Are other error messages printed to stderr/stdout?

-Justin

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================