Shear Cell example fails in 3.6

Submitted by Jagirhussan on Fri, 05/05/2017 - 13:24

Greetings,
I tried to run the shear cell example on a 3.6.0 build. Unfortunately, I am getting the following error. I would be extremely grateful if you could help me out with this.

Import and parallelization of mesh cad2 containing 720 triangle(s) successful
ERROR on proc 0: assertion failed (../region_neighbor_list_I.h:156)

I have listed the echo output below.

Cheers
Jagir

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.6.0, compiled 2017-04-27-15:40:37 by Jagir, git commit 18a96adf8688e0d46423c7d812001a8d9e0a9af0)
# Shear Cell example
### Initialization
# Preliminaries
units si
atom_style sphere
boundary f f f
newton off
communicate single vel yes
#processors 2 2 2

# Declare domain
region reg block -0.325 0.325 -0.325 0.325 -0.001 0.081 units box
create_box 2 reg
Created orthogonal box = (-0.325 -0.325 -0.001) to (0.325 0.325 0.081)
1 by 1 by 1 MPI processor grid

### Setup
# Material and interaction properties
fix m1 all property/global youngsModulus peratomtype 1.0e7 1.0e7
fix m2 all property/global poissonsRatio peratomtype 0.25 0.25
fix m3 all property/global coefficientRestitution peratomtypepair 2 0.5 0.5 0.5 0.5
fix m4 all property/global coefficientFriction peratomtypepair 2 0.5 0.5 0.5 0.5

# Physics
pair_style gran model hertz tangential history
pair_coeff * *

# Particle setup – insertions to be handled below
fix pts1 all particletemplate/sphere 49979687 atom_type 1 density constant 1000 radius constant 0.003
fix pdd1 all particledistribution/discrete 32452843 1 pts1 1.0
Fix particledistribution/discrete (id pdd1): distribution based on mass%:
pts1: d=6.000000e-03 (max. bounding sphere) mass%=100.000000%
Fix particledistribution/discrete (id pdd1): distribution based on number%:
pts1: d=6.000000e-03 (max. bounding sphere) number%=100.000000%
fix pts2 all particletemplate/sphere 49979693 atom_type 2 density constant 1000 radius constant 0.002
fix pdd2 all particledistribution/discrete 15485863 1 pts2 1.0
Fix particledistribution/discrete (id pdd2): distribution based on mass%:
pts2: d=4.000000e-03 (max. bounding sphere) mass%=100.000000%
Fix particledistribution/discrete (id pdd2): distribution based on number%:
pts2: d=4.000000e-03 (max. bounding sphere) number%=100.000000%

# Geometry
fix cad1 all mesh/surface/stress file shear_cell.stl type 1 scale 0.001 stress on

Reading STL file 'shear_cell.stl' (mesh processing step 1/3)
fix cad2 all mesh/surface/stress file bottom_plate.stl type 1 scale 0.001 stress on

Reading STL file 'bottom_plate.stl' (mesh processing step 1/3)
fix ins_mesh all mesh/surface/planar file factory.stl type 1 scale 0.001

Reading STL file 'factory.stl' (mesh processing step 1/3)
fix geometry all wall/gran model hertz tangential history mesh n_meshes 2 meshes cad1 cad2

### Detailed settings
# Integration
fix integrator all nve/sphere
# Gravity
fix grav all gravity 9.81 vector 0.0 0.0 -1.0
# Timestep
timestep 0.00002
# Thermodynamic output
thermo_style custom step atoms ke cpu
thermo 10000
thermo_modify lost ignore norm no
### Execution and further settings

# Particle insertion – large particles
fix ins1 all insert/stream seed 67867967 distributiontemplate pdd1 nparticles 5000 particlerate 10000 overlapcheck yes vel constant 0. 0. -2. all_in yes insertion_face ins_mesh extrude_length 0.01
run 50000
WARNING: It is heavily recommended to use 'neigh_modify delay 0' with granular pair styles (../pair_gran.cpp:236)
Setting up run at Fri May 5 23:17:24 2017

Import and parallelization of mesh cad1 containing 1440 triangle(s) successful
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Import and parallelization of mesh cad2 containing 720 triangle(s) successful
ERROR on proc 0: assertion failed (../region_neighbor_list_I.h:156)

AttachmentSize
Binary Data Mesh files and liggghts script47.86 KB

Jagirhussan | Fri, 05/05/2017 - 22:02

Many thanks for the prompt response.

I used make openmpi (Anaconda 2.7 mpi) with gnu 5.4 on ubuntu 16.04
The examples that shipped with the distribution run without any issues.

I have listed the contents of the Makefile.openmpi below
Cheers
Jagir

# openmpi = Fedora Core 6, mpic++, OpenMPI-1.1, FFTW2

SHELL = /bin/sh

# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler

CC = mpic++
CCFLAGS = -O2 \
-funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized
SHFLAGS = -fPIC
DEPFLAGS = -M

LINK = mpic++
LINKFLAGS = -O
LIB = -lstdc++
SIZE = size

ARCHIVE = ar
ARFLAGS = -rcsv
SHLIBFLAGS = -shared

# ---------------------------------------------------------------------
# LAMMPS-specific settings
# specify settings for LAMMPS features you will use
# if you change any -D setting, do full re-compile after "make clean"

# LAMMPS ifdef settings, OPTIONAL
# see possible settings in doc/Section_start.html#2_2 (step 4)

LMP_INC = -DLAMMPS_GZIP

# MPI library, REQUIRED
# see discussion in doc/Section_start.html#2_2 (step 5)
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library

MPI_INC =
MPI_PATH =
MPI_LIB =

# FFT library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 6)
# can be left blank to use provided KISS FFT library
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
# PATH = path for FFT library
# LIB = name of FFT library

FFT_INC = -DFFT_FFTW3
FFT_PATH =
FFT_LIB = -lfftw

# JPEG and/or PNG library, OPTIONAL
# see discussion in doc/Section_start.html#2_2 (step 7)
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
# INC = path(s) for jpeglib.h and/or png.h
# PATH = path(s) for JPEG library and/or PNG library
# LIB = name(s) of JPEG library and/or PNG library

JPG_INC =
JPG_PATH =
JPG_LIB =

# ---------------------------------------------------------------------
# build rules and dependencies
# no need to edit this section

include Makefile.package.settings
include Makefile.package

EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)

# Path to src files

vpath %.cpp ..
vpath %.h ..

# Link target

$(EXE): $(OBJ)
$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
$(SIZE) $(EXE)

# Library targets

lib: $(OBJ)
$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)

shlib: $(OBJ)
$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
$(OBJ) $(EXTRA_LIB) $(LIB)

# Compilation rules

%.o:%.cpp
$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<

%.d:%.cpp
$(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@

# Individual dependencies

DEPENDS = $(OBJ:.o=.d)
sinclude $(DEPENDS)

drheine | Wed, 07/19/2017 - 21:06

The factory mesh is wrong in the files that were attached. It is currently a circle that is out of the simulation box when it should be a ring that sits above the shear cell. Once I corrected this, it ran without the error.