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Re: [lammps-users] Fwd: Got "segmentation fault" error when using pari_style quip with gap potential file
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Re: [lammps-users] Fwd: Got "segmentation fault" error when using pari_style quip with gap potential file


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 31 Aug 2017 20:38:56 -0400



On Thu, Aug 31, 2017 at 7:34 PM, Tingyu Lu <tlu3@...1442...> wrote:
Hello,

I compiled the new version lammps: lammps-11Aug17. However when I tested the "in.gap" example, I got the same error in the output file:

​does it also segfault with the in.sw or in.molecular​ example input?

axel.

 

LAMMPS (11 Aug 2017)
Reading data file ...
  orthogonal box = (0 0 0) to (10.9685 10.9685 10.9685)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  64 atoms
Neighbor list info ...
  update every 1 steps, delay 10 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 4.3
  ghost atom cutoff = 4.3
  binsize = 2.15, bins = 6 6 6
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair quip, perpetual
      attributes: full, newton on
      pair build: full/bin/atomonly
      stencil: full/bin/3d
      bin: standard
Setting up Verlet run ...
  Unit style    : metal
  Current step  : 0
  Time step     : 0.001

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
~


Thanks,
Tingyu

---------- Forwarded message ----------
From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, Aug 30, 2017 at 4:34 PM
Subject: Re: [lammps-users] Got "segmentation fault" error when using pari_style quip with gap potential file
To: Tingyu Lu <tlu3@...1442...>
Cc: LAMMPS Users Mailing List <lammps-users@...429...96...sourceforge.net>




On Wed, Aug 30, 2017 at 4:21 PM, Tingyu Lu <tlu3@...1442...> wrote:
Hello lammps users,

- I compiled the lammps with quip and gap packages following the guidelines in http://libatoms.github.io/QUIP/install.html and the README files in lammps. The commands from quip and gap works well.

- Then I tested the example "in.sw" in the /lammps/examples/USER/quip/ folder, it worked well, which ensures that I compiled the quip package right. 

- However when I tried the example named "in.gap" which uses the potential from gap, I got the segmentation fault error in the output file. 

- The information in the output file is listed below:

LAMMPS (15 May 2015)
Reading data file ...
  orthogonal box = (0 0 0) to (10.9685 10.9685 10.9685)
  1 by 1 by 2 MPI processor grid
  reading atoms ...
  64 atoms
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 4.3
Setting up run ...

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

- My lammps version is "lammps-15May15".

Could you please kindly help me with the problem?

​this is *far* too old a LAMMPS version. there were some recent, incompatible changes in the LAMMPS-QUIP interface.
you need to install LAMMPS version 11Aug2017 or later.

axel.



 

Thanks,
Tingyu



--
Best Regards,
Tingyu Lu
Mechanical and Aerospace Engineering 
911 Oval Dr. - 3404 EBIII
North Carolina State University
Raleigh, NC 27695

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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.



--
Best Regards,
Tingyu Lu
Mechanical and Aerospace Engineering 
911 Oval Dr. - 3404 EBIII
North Carolina State University
Raleigh, NC 27695

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
lammps-users mailing list
lammps-users@...6297....sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users




--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.