[lammps-users] segmentation fault. signal 11

LAMMPS LAMMPS Mailing List Mirror
1

Dear users, I get segmentation fault error.
My question is why this error occurs.

units metal # sets units to ‘metal’ units - Atomic units w/ ps timescale
dimension 3
boundary p p p # periodic BCs on x,y plane faces, z dimension fixed volume

atom_style atomic
neighbor 1.0 bin
neigh_modify delay 5 check yes

Create geometry using internal stuff

lattice diamond 5.43
region box block 0 50 0 50 0 50
create_box 1 box # initialize box
create_atoms 1 box

region rPKA sphere 25 24.5 49.5 0.1
mass 1 28.1 # type 2 = Si

Define potential

pair_style sw
pair_coeff * * Si.sw Si

Groups

region rallatoms block INF INF INF INF INF INF
region rinterior block 2 48 2 48 2 INF
region rexterior block 2 48 2 48 2 INF side out

group interior region rinterior
group exterior region rexterior
group PKA region rPKA

compute 1 all temp
compute 2 interior coord/atom 2.72
compute 3 interior ke/atom
compute 4 interior pe/atom

velocity all zero linear

fix 1 all nve
fix 2 exterior temp/rescale 1 0 0 0.5 1.20 region rexterior
fix 3 interior temp/rescale 1 0 0 0.5 1.0 region rinterior

timestep 0.001

thermo_style custom step temp pe etotal press
run 1000

unfix 3 # remove the rescaling fix from the interior
run 1000

set PKA velocity to correspond to ~ 10 keV - 2620.549 Ang/ps

set group PKA vx 100
set group PKA vy 200
set group PKA vz -2000

#set timestep to smaller value for initial phase of collisions (.01 fs for .2 ps)
timestep 0.00001

dump 2 PKA custom 1000 PKA_traj_init_col4.dump id x y z c_3 c_2 c_4

run 20000# run the collisional phase for .2 ps

run intermediate phase with intermediate timestep (.1 fs for 1 ps)

timestep 0.00001

#dump 3 interior custom 1000 test_inter_evolve4.dump id x y z c_3 c_2 c_4
dump 4 PKA custom 1000 PKA_traj_inter_evolve4.dump id x y z c_3 c_2 c_4

run 10000

after initial phase, let evolve for remainder of time using .001 ps timestep (1 fs for 10 ps)

undump 4

timestep .001

dump 5 interior custom 10000 test_final_evolve4.dump id x y z c_3 c_2 c_4
dump 6 PKA custom 1000 PKA_traj_final_evolve4.dump id x y z c_3 c_2 c_4
run 10000

2

2010/12/20 t t <[email protected]...>:

Dear users, I get segmentation fault error.
My question is why this error occurs.

a segmentation fault is a memory access error signaled by
the operating system. it can have many reasons.
you are using MPICH for parallel execution, right?
in that case the segmentation fault can be a followup
error from some other error exit. for example, if you
have a typo in your input script, one MPI rank may
terminate normally, but the others will terminate with
a segmentation fault. due to i/o buffering, you may
even lose the original error message for that.

the next step that you should do, is to identify the
part of your input script that causes the segmentation
fault. there are several hints in the lammps manual
that help with debugging failure conditions.

until you can prove that there is a specific facility
in lammps that is causing the segfault, it is most
likely that you have some problem in your input
script that that it is your job to identify that problem.

since it looks like you are running a fairly large problem,
you may also have a problem of running out of address
space, in case you are using a 32-bit binary. but that
is a stab in the dark, since you are not providing any
information about how and on what kind of machine
you are running this.

cheers,
    axel.