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


From: Quang Ha <quang.t.ha.20@...24...>
Date: Tue, 8 May 2018 19:19:35 -0400

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 (!). 

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

Thanks,
Quang