Signal code: Address not mapped

Hello,
I want to simulate a direct sear box test. I get the code for the test form anther user form the platform. But when I want to run the code I get the following error message:

[zieher@ifas-parallel lammps]$ '/usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora' < in.f0.4_90Kpa_0.7
LIGGGHTS 1.5.3 based on lammps-10Mar10
Created orthogonal box = (-0.2 -0.3 -0.1) to (0.2 0.8 0.1)
1 by 1 by 1 processor grid
0 atoms in group nve_group

Importing STL file 'upper_4.stl'
Solid body detected in STL file
End of solid body detected in STL file.
Mesh calculations running. This may take a while...finished!

Import of 44 triangles completed successfully!

Importing STL file 'lower_4_2.stl'
Solid body detected in STL file
End of solid body detected in STL file.
Mesh calculations running. This may take a while...finished!

Import of 28 triangles completed successfully!

Fix particledistribution/discrete (id pdd1): distribution based on mass%:
pts1: d=6.400000e-03 (max. bounding sphere) mass%=80.000000%
pts2: d=4.400000e-03 (max. bounding sphere) mass%=20.000000%
Fix particledistribution/discrete (id pdd1): distribution based on number%:
pts1: d=6.400000e-03 (max. bounding sphere) number%=56.518047%
pts2: d=4.400000e-03 (max. bounding sphere) number%=43.481953%
Particle packing insertion: trying 7920.006149 particles once
Setting up run ...
Memory usage per processor = 21.3395 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 0.088
1 7919 0 0 0.088
Loop time of 0.608468 on 1 procs for 1 steps with 7919 atoms

Pair time (%) = 0.000239849 (0.0394185)
Neigh time (%) = 0.0307679 (5.05662)
Comm time (%) = 0.000106096 (0.0174366)
Outpt time (%) = 0.000149012 (0.0244896)
Other time (%) = 0.577205 (94.862)

Nlocal: 7919 ave 7919 max 7919 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3623 ave 3623 max 3623 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3623
Ave neighs/atom = 0.457507
Neighbor list builds = 1
Dangerous builds = 0
7919 atoms in group exclude_pwall
Lattice spacing in x,y,z = 0.004 0.004 0.004
Created 480 atoms
480 atoms in group pwall
Setting atom values ...
480 settings made for diameter
480 settings made for density
1 rigid bodies with 480 atoms
Setting up run ...
[ifas-parallel:44132] *** Process received signal ***
[ifas-parallel:44132] Signal: Segmentation fault (11)
[ifas-parallel:44132] Signal code: Address not mapped (1)
[ifas-parallel:44132] Failing at address: 0xfffffffeb3678e50
[ifas-parallel:44132] [ 0] /lib64/libpthread.so.0() [0x39d620f500]
[ifas-parallel:44132] [ 1] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora(_ZN9LAMMPS_NS17FixContactHistory12pre_exchangeEv+0xee) [0x508d5c]
[ifas-parallel:44132] [ 2] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora(_ZN9LAMMPS_NS17FixContactHistory18setup_pre_exchangeEv+0x13) [0x508553]
[ifas-parallel:44132] [ 3] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora(_ZN9LAMMPS_NS6Modify18setup_pre_exchangeEv+0x36) [0x591930]
[ifas-parallel:44132] [ 4] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora(_ZN9LAMMPS_NS6Verlet5setupEv+0x4f) [0x63db29]
[ifas-parallel:44132] [ 5] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora(_ZN9LAMMPS_NS3Run7commandEiPPc+0x5b1) [0x6207a3]
[ifas-parallel:44132] [ 6] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora(_ZN9LAMMPS_NS5Input15execute_commandEv+0xc66) [0x5828d2]
[ifas-parallel:44132] [ 7] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora(_ZN9LAMMPS_NS5Input4fileEv+0x277) [0x582d0d]
[ifas-parallel:44132] [ 8] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora(main+0x5b) [0x588466]
[ifas-parallel:44132] [ 9] /lib64/libc.so.6(__libc_start_main+0xfd) [0x39d5e1ecdd]
[ifas-parallel:44132] [10] /usr/lib64/liggghts_1p5p3/liggghts_1p5p3/src/lmp_fedora() [0x4747f9]
[ifas-parallel:44132] *** End of error message ***

I did some tests to delimit the problem and found out that the error appears when I create atoms by pour/dev/packing and create_atoms in one script. If I create atom only either by pour/dev/packing or by create_atoms. Than it works. I can reproduce the error by any other script with this both commands.

I use RedHat and compiled LIGGGHTS by the lmp_fedora make file.

I tried to run the code on another workstation with fedora (also compiled by lmp_fedora) with the same problem. In addition I tried to run the code on several versions of LIGGGHS too.

And here the code for the SherBox test:

############################################
# LIGGGHTS version: 1-5-1
# Simulation of Direct Shear Box Test --- to test the effect of .....
# By Anson Liang
# The University of Hong Kong
# lzefeng@gmail.com
############################################
#Dimentions:
# upperbox: 2*1.27*0.1 m^3 cuole
# lowerbox: 2*1.00*0.1 m^3
#Particle size:
# Diameter: 3 cm
#========================Basic setting===============================
units si
atom_style granular
atom_modify map array
boundary f f f
newton off

region reg block -0.2 0.2 -0.3 0.8 -0.1 0.1 units box
create_box 3 reg
region bc block -0.08 0.08 -0.12 0.48 0 0.05 units box
group nve_group region reg

communicate single vel yes
neighbor 0.0008 bin
neigh_modify delay 0
timestep 5e-6

#========================Parameter setting===============================
#Material properties required for new pair styles
fix m1 all property/global youngsModulus peratomtype 8.e10 8.e9 8.e10
fix m2 all property/global poissonsRatio peratomtype 0.3 0.3 0.3
fix m3 all property/global coefficientRestitution peratomtypepair 3 &
0.2 0.3 0.05 &
0.1 0.3 0.1 &
0.05 0.3 0.2
fix m4 all property/global coefficientFriction peratomtypepair 3 &
0.0 0.0 0.0 &
0.0 0.435 0.0 &
0.0 0.0 0.0
fix m5 all property/global characteristicVelocity scalar 2.
# type 1 : walls of boxex
# type 2 : filled particles
# type 3 : pariticle-wall

#New pair style
pair_style gran/hertz/history 1 0 #Hertzian without cohesion
pair_coeff * *

#introduce granular walls as container (idealized, generated by Gmsh)
fix upper all mesh/gran/stressanalysis upper_4.stl 1 1 0. 0. 0. 0. 0. 0.
fix lower all mesh/gran/stressanalysis lower_4_2.stl 1 1 0. 0. 0. 0. 0. 0.

fix wall all wall/gran/hertz/history 1 0 mesh/gran 2 upper lower

#====================Particles insertion========================
fix pts1 all particletemplate/sphere 1 atom_type 2 density constant 6000000 radius constant 0.0032
fix pts2 all particletemplate/sphere 1 atom_type 2 density constant 6000000 radius constant 0.0022
fix pdd1 all particledistribution/discrete 1 2 pts1 0.8 pts2 0.2

#De the insertion

fix insert nve_group pour/dev/packing 1 distributiontemplate pdd1 vol 0.16 100 region bc #overlapcheck no

#apply NVE integration to all particles that are inserted as single particles

fix NVE all nve/sphere

#Output settings, include total thermal energy
compute 1 all erotate/sphere
compute CoordNum all coord/gran
compute Radius all property/atom radius
compute fc all pair/gran/local id pos force

thermo_style custom step atoms ke c_1 vol
thermo 100000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
fix ts_check all check/timestep/gran 100000 0.1 0.1
#insert the first particles so that dump is not empty
run 1

dump dmp1 all custom 100000 post/dump.f0.4_90Kpa_0.7_before id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius

unfix insert
group exclude_pwall region bc

#=========================Creat particle-wall & do radius expansion==========================
region pwall_region block -0.078 0.078 0.49 0.493 0.002 0.048 units box
lattice custom 0.004 a1 1 0 0 a2 0 1 0 a3 0 0 1 basis 0.5 0.5 0.5
create_atoms 3 region pwall_region
group pwall region pwall_region
set group pwall diameter 0.004 density 6000000
unfix NVE
fix NVE_new exclude_pwall nve/sphere

#Apply confining pressure
fix vertical pwall aveforce 0 -1.5 0
fix setrigid pwall rigid single force * off on off torque * off off off
neigh_modify exclude type 3 3
neigh_modify exclude type 1 3
dump dmp2 pwall custom 100000 post/dump.pwall_f0.4_90Kpa_0.7_before id x y z radius

run 200000

fix wiggle_1 all move/mesh/gran wiggle 0.001 0 0 0.1 upper
fix wiggle_2 all move/mesh/gran wiggle -0.002 0 0 0.1 lower

#do the radius expansion
variable D_grown atom 1.001*2*c_Radius
fix Grow_radius exclude_pwall adapt 20000 atom diameter D_grown

dump Coord exclude_pwall custom 50000 post/CoordNum_f0.4_90Kpa_0.7 c_CoordNum

run 3000000

unfix Grow_radius
unfix wiggle_1
unfix wiggle_2
run 700000

#========================do the shearing==========================
#Reset parameters
unfix m4
fix m4_new all property/global coefficientFriction peratomtypepair 3 &
0.0 0.0 0.0 &
0.0 0.7 0.0 &
0.0 0.0 0.0
unfix m3
fix m3_new all property/global coefficientRestitution peratomtypepair 3 &
0.2 0.3 0.05 &
0.3 0.3 0.3 &
0.05 0.3 0.2
#Set output
fix Force_of_mesh all ave/time 50 100 50000 f_lower[1] f_lower[2] f_lower[3] file Force_f0.4_90Kpa_0.7.txt
undump dmp2
dump dmp3 pwall custom 50000 post/dump.pwall_f0.4_90Kpa_0.7 id x y z radius
undump dmp1
dump dmp4 all custom 50000 post/dump.f0.4_90Kpa_0.7 id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius
dump forcechain exclude_pwall local 50000 post/dump.fc.*.liggghts c_fc[1] c_fc[2] c_fc[3] c_fc[4] c_fc[5] c_fc[6] c_fc[7] c_fc[8] c_fc[9] c_fc[10] c_fc[11] c_fc[12]