Signal 11 (Segmentation fault)

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1

Dear all

Good day.

I run few simulations for pristine graphene and polycrystalline. Recently I face problem in LAMMPS simulations in the cluster for the polycrystalline. When I run the jobs in cluster few simulation jobs from my all simulations stop automatically in between with the following error.

mpirun noticed that process rank 3 with PID 0 on node cph-cXX exited on signal 11 (Segmentation fault).

A part of the input file:

------------------------ INITIALIZATION ----------------------------

units metal
dimension 3
atom_style atomic
boundary p p p

-------------------- ATOM DEFINITION 10/17/13----------------------------

read_data coord_PCG.data
mass 1 12.0107

---------------------- FORCE FIELDS 9/23/13------------------------------

pair_style airebo 1.92 1 1
pair_coeff * * CH.airebo C

#################################### GROUP DEFINE #####################################

###################################### Computes ##########################################

some compute command

############################### Defining stress and strain variables ################################

some variable command

###################################### Thermo commands ####################################

thermo 1000
thermo_style custom step temp lx ly lz pxx pyy pzz time pe etotal v_Up1 v_Up2 v_Up3 v_Down1 v_Down2 v_Down3 v_p2 v_p3 v_p4 v_p5 v_p6 v_p7 v_p8 v_L1 v_L2 v_L3 v_R1 v_R2 v_R3
thermo_modify line one format float %20.10f
timestep 0.001

dump myDump all custom 10000 dump.lammpstrj id type x y z c_STRESS[1] c_STRESS[2] c_STRESS[3] c_STRESS[4] c_STRESS[5] c_STRESS[6]
dump_modify myDump append yes first yes

####################################### Minimization #########################################

min_style cg
fix 1 all box/relax iso 0.0 vmax 0.001
minimize 1e-25 1e-15 50000 10000
unfix 1

reset_timestep 0

####################################### DEFORMATION ##################################

fix lower Down setforce NULL 0.0 0.0 #freezing lower boundary atoms
fix upper Up setforce NULL 0.0 0.0 #Setting zero forces only in x and z directions
fix left2 left setforce 0.0 NULL 0.0 #freezing lower boundary atoms
fix right2 right setforce 0.0 NULL 0.0 #Setting zero forces only in x and z directions

############ Equilibrating the system ##############

############ Equilibrating the system ##############

velocity group2 create 500 9284155
fix 1 group2 nve
fix 2 group2 temp/berendsen 500 500 0.1
run 40000
unfix 1
unfix 2

velocity group2 create 300 9284155
fix 1 group2 nve
fix 2 group2 temp/berendsen 300 300 0.1
run 30000
unfix 1
unfix 2

fix 3 group2 npt temp 300 300 0.1 iso 1.0 1.0 1.0 #Tdamp is 100 times the timestep
run 100000
unfix 3

2

Dear all
Good day.

I run few simulations for pristine graphene and polycrystalline. Recently I face problem in LAMMPS simulations in the cluster for the polycrystalline. When I run the jobs in cluster few simulation jobs from my all simulations stop automatically in between with the following error.

mpirun noticed that process rank 3 with PID 0 on node cph-cXX exited on signal 11 (Segmentation fault).

signal 11 (segmentation fault) can have many causes (please google
it). this can range from hardware problems like overheating, broken
hardware (CPU, RAM), to memory leaks, or incorrect use of software (or
bad dynamics in MD codes due to bad force field parameters or bad
topology information) or using features that require a lot of RAM on
limited hardware.
it is next to impossible to determine which of these apply from
remote. if you can provide a simple, small input that will reliably
and quickly produce such a segfault, we can look into it. but at this
state of affairs, you are on your own.

axel.