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Re: [lammps-users] combining read_data and fix property/atom
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Re: [lammps-users] combining read_data and fix property/atom


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Tue, 8 May 2018 19:26:29 -0400

On Tue, May 8, 2018 at 7:19 PM, Quang Ha <quang.t.ha.20@...24...> wrote:
> Hi all,
>
> I am trying to use write_data and read_data to restart simulation. At the
> end of the first stage, I have:
>
> [...some simulation...]
> write_data      dump.data nofix
>
> Then, at the beginning of the second stage, I follow the instruction
> provided at http://lammps.sandia.gov/doc/fix_property_atom.html:
>
> # Adding a new property - need to be added before simulation box
> fix             prop all property/atom d_foo ghost yes
> read_data       dump.data
> [... more simulation...]
>
> The simulation seems to be working until the very end:
>
> MPI task timing breakdown:
> Section |  min time  |  avg time  |  max time  |%varavg| %total
> ---------------------------------------------------------------
> Pair    | 1.7229     | 1.81       | 1.9589     |   5.4 | 70.16
> Neigh   | 0.04775    | 0.04942    | 0.051717   |   0.7 |  1.92
> Comm    | 0.010183   | 0.16158    | 0.25001    |  18.2 |  6.26
> Output  | 0.51714    | 0.52038    | 0.52466    |   0.3 | 20.17
> Modify  | 0.029224   | 0.030705   | 0.033574   |   0.8 |  1.19
> Other   |            | 0.007594   |            |       |  0.29
>
> Nlocal:    7875.12 ave 7938 max 7772 min
> Histogram: 1 0 0 0 1 0 4 0 0 2
> Nghost:    1187.38 ave 1261 max 1158 min
> Histogram: 3 2 1 0 0 0 1 0 0 1
> Neighs:    102144 ave 104750 max 100667 min
> Histogram: 3 0 1 1 0 0 2 0 0 1
> FullNghs:  204288 ave 209003 max 201481 min
> Histogram: 3 0 0 1 1 2 0 0 0 1
>
> Total # of neighbors = 1634300
> Ave neighs/atom = 25.9409
> Neighbor list builds = 10
> Dangerous builds = 10
> [hyperion:20184] *** Process received signal ***
> [hyperion:20184] Signal: Segmentation fault (11)
> [hyperion:20184] Signal code: Address not mapped (1)
> [hyperion:20184] Failing at address: 0xa01bd1e78
> *** Error in `/home/qth20/Documents/lammps-sph/lammps/src/lmp_mpi':
> corrupted size vs. prev_size: 0x0000000002af2fd0 ***
> *** Error in `*** Error in `*** Error in
> `/home/qth20/Documents/lammps-sph/lammps/src/lmp_mpi[hyperion:20185] ***
> Process received signal ***
> *** Error in
> `/home/qth20/Documents/lammps-sph/lammps/src/lmp_mpi/home/qth20/Documents/lammps-sph/lammps/src/lmp_mpi':
> [hyperion:20185] Signal: Aborted (6)
> [hyperion:20185] Signal code:  (-6)
> corrupted size vs. prev_size[hyperion:20182] *** Process received signal ***
> /home/qth20/Documents/lammps-sph/lammps/src/lmp_mpi': munmap_chunk():
> invalid pointer: 0x0000000001dde9c0 ***
> [...]
>
> which is such a weird stage to fail. I tried to debug with valgrind, but the
> tool complained that I have way too many errors to report (!).

then you should fix those issues *first*.

the way to identify the location of the issue is to compile with the
-g flag included and to enable core dumps.
but then again, the error message indicates memory corruption, which
means, that likely the issue can be anywhere.

> Any suggestions on where I could look into? If further information is
> required please let me know.

you forgot the most basic info: the LAMMPS version you are using.
and it would be helpful to have a small demo input to reproduce it.

axel.


> Thanks,
> Quang
>
>
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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.