LAMMPS errors - Segmentation fault and address not mapped

Hi,

I was executing a very simple script on LAMMPS on my university’s supercomputer cluster to learn how to use the software. Unfortunately, every time I run the script, I receive the following error:

LAMMPS (10 Oct 2012)
Scanning data file …
1 = max bonds/atom
1 = max angles/atom
Reading data file …
orthogonal box = (0 0 -0.5) to (10 10 0.5)
1 by 1 by 1 MPI processor grid
3 atoms
3 bonds
[node013:15005] *** Process received signal ***
[node013:15005] Signal: Segmentation fault (11)
[node013:15005] Signal code: Address not mapped (1)
[node013:15005] Failing at address: (nil)
[node013:15005] [ 0] /lib64/libpthread.so.0 [0x2aaaab1a6be0]
[node013:15005] [ 1] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert [0x41c9ad]
[node013:15005] [ 2] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert [0x706bab]
[node013:15005] [ 3] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert [0x7083ab]
[node013:15005] [ 4] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert [0x56c4f2]
[node013:15005] [ 5] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert [0x56cb2e]
[node013:15005] [ 6] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert [0x57a1b6]
[node013:15005] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2aaaab8e0994]
[node013:15005] [ 8] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert(_ZNSt8ios_base4InitD1Ev+0x39) [0x40a6c9]
[node013:15005] *** End of error message ***

Hi,

I was executing a very simple script on LAMMPS on my university's
supercomputer cluster to learn how to use the software. Unfortunately,
every time I run the script, I receive the following error:

LAMMPS (10 Oct 2012)
Scanning data file ...
  1 = max bonds/atom
  1 = max angles/atom
Reading data file ...
  orthogonal box = (0 0 -0.5) to (10 10 0.5)
  1 by 1 by 1 MPI processor grid
  3 atoms
  3 bonds
[node013:15005] *** Process received signal ***
[node013:15005] Signal: Segmentation fault (11)
[node013:15005] Signal code: Address not mapped (1)
[node013:15005] Failing at address: (nil)
[node013:15005] [ 0] /lib64/libpthread.so.0 [0x2aaaab1a6be0]
[node013:15005] [ 1] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert
[0x41c9ad]
[node013:15005] [ 2] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert
[0x706bab]
[node013:15005] [ 3] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert
[0x7083ab]
[node013:15005] [ 4] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert
[0x56c4f2]
[node013:15005] [ 5] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert
[0x56cb2e]
[node013:15005] [ 6] /home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert
[0x57a1b6]
[node013:15005] [ 7] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x2aaaab8e0994]
[node013:15005] [ 8]
/home/auxetic/LAMMPS/lammps-10Oct12/src/lmp_albert(_ZNSt8ios_base4InitD1Ev+0x39)
[0x40a6c9]
[node013:15005] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 15005 on node node013 exited on
signal 11 (Segmentation fault).
--------------------------------------------------------------------------

together with a core file containing symbols within which I have no idea

it works for me, but i have not yet fully caught up with the latest code:

[[email protected]... tmp]$ mpirun -np 4 ../src/lmp_openmpi < in.test
LAMMPS (19 Sep 2012-ICMS)
Scanning data file ...
  1 = max bonds/atom
  1 = max angles/atom
Reading data file ...
  orthogonal box = (0 0 -0.5) to (10 10 0.5)
  2 by 2 by 1 MPI processor grid
  3 atoms
  3 bonds
  2 angles
Finding 1-2 1-3 1-4 neighbors ...
  2 = max # of 1-2 neighbors
  2 = max # of 1-3 neighbors
  4 = max # of 1-4 neighbors
  2 = max # of special neighbors

what it is. Also, interestingly enough, the log.lammps remains empty after
running the script.

that is to be expected. that file is block buffered.

I have included the contents of my input and data files below. Could someone
explain to me what I am doing wrong please?

apparently not. either there has been a change
that would require a change in the data/input, or
you have a miscompiled executable, or there has
been a bug introduced during the last month.

axel.

works for me with the current LAMMPS version.

Steve

Thank you all for your help. Probably lammps is not installed correctly on the cluster. I will be trying to run it on other computers. Thanks once again for your help and sorry if I have bothered you with my query.

Regards,

Joseph