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.