combining read_data and fix property/atom

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

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 LAMMPS Molecular Dynamics Simulator

# 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.

Hi Axel,

I fixed it! Or should I say I realised what was wrong…

Here for others to avoid this problem. Somehow I used a command create_atoms before the read_data. Removing the create_atoms get rid of the problem.

I guess it has something to do with duplicating IDs or some sort…

Thanks,
Quang

Thanks for reporting the solution, and glad you fixed it.
Nevertheless, if you can create a small test case which reproduces the problem (input script, small data file, short simulation duration), hopefully one of us will eventually figure out why it’s crashing. LAMMPS should at least print an error message.

Cheers
Andrew