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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: Tingyu Lu <tlu3@...1442...>
Date: Fri, 1 Sep 2017 10:40:59 -0400

Hello,

BTW, I got some warnings printed in the screen when running in.gap:

 WARNING: gpCoordinates_startElement_handler: covariance type is dot product, bu                                                                             t no zeta attribute is present. This may mean an XML generated by an older versi                                                                             on. If found, the single value from the theta element will be used, to ensure ba                                                                             ckwards compatibility
 WARNING: gpCoordinates_startElement_handler: covariance type is dot product, bu                                                                             t no zeta attribute is present. This may mean an XML generated by an older versi                                                                             on. If found, the single value from the theta element will be used, to ensure ba                                                                             ckwards compatibility
 WARNING: gpCoordinates_startElement_handler: covariance type is dot product, bu                                                                             t no zeta attribute is present. This may mean an XML generated by an older versi                                                                             on. If found, the single value from the theta element will be used, to ensure ba                                                                             ckwards compatibility
 WARNING: gpCoordinates_startElement_handler: covariance type is dot product, bu                                                                             t no zeta attribute is present. This may mean an XML generated by an older versi                                                                             on. If found, the single value from the theta element will be used, to ensure ba                                                                             ckwards compatibility
 WARNING: gpCoordinates_endElement_handler: dot product covariance is used, but                                                                              found a theta element in the XML. This may be a sign of an XML generated by an o                                                                             lder version. The first and only element of theta will be used as zeta.
 WARNING: gpCoordinates_endElement_handler: dot product covariance is used, but                                                                              found a theta element in the XML. This may be a sign of an XML generated by an o                                                                             lder version. The first and only element of theta will be used as zeta.
 WARNING: gpCoordinates_endElement_handler: dot product covariance is used, but                                                                              found a theta element in the XML. This may be a sign of an XML generated by an o                                                                             lder version. The first and only element of theta will be used as zeta.
 WARNING: gpCoordinates_endElement_handler: dot product covariance is used, but                                                                              found a theta element in the XML. This may be a sign of an XML generated by an o                                                                             lder version. The first and only element of theta will be used as zeta.


Thanks,
Tingyu

On Fri, Sep 1, 2017 at 10:36 AM, Tingyu Lu <tlu3@...1442...> wrote:
Hello,

Sorry, I don't quite understand it. Do you mean the libatoms in QUIP?
I did unarchived the GAP.tar.gz in /QUIP/src directory. Then I edited the Makefile.inc in the build directory and do "make" in /QUIP.
I checked the command "teach_sparse" in the build directory, and it worked. 
Does it mean that I compiled it with GAP support? 

Thanks,
Tingyu

On Fri, Sep 1, 2017 at 6:31 AM, Axel Kohlmeyer <akohlmey@...24...> wrote:


On Fri, Sep 1, 2017 at 12:08 AM, Tingyu Lu <tlu3@...1442...> wrote:
Hello,

It works well with the other examples.

​then i suspect you have compiled libatoms without GAP support.
please check the libatoms documentation. the GAP code has different licensing terms and has to be obtained separately.

at any rate, the interface is working and thus any segfault issue has to be on the side of libatoms.

axel.

 

Thanks,
Tingyu

On Thu, Aug 31, 2017 at 8:38 PM, Axel Kohlmeyer <akohlmey@...24...> wrote:


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@...42...e.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@...655....net
https://lists.sourceforge.net/lists/listinfo/lammps-users




--
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



--
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



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