ERROR IN TUTORISL PACKED BED

HELLO Everyone

while running packedbed tutorial it show an error

test@test-All-Series:~/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI$ ./Allrun.sh
/home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI
mesh needs to be built
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 4.1
Exec : blockMesh
Date : May 05 2017
Time : 12:42:50
Host : "test-All-Series"
PID : 16867
Case : /home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Creating block mesh from
"/home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD/constant/polyMesh/blockMeshDict"
Creating curved edges
Creating topology blocks
Creating topology patches

Reading patches section

Creating block mesh topology

Reading physicalType from existing boundary file

Default patch type set to empty

Check topology

Basic statistics
Number of internal faces : 0
Number of boundary faces : 6
Number of defined boundary faces : 6
Number of undefined boundary faces : 0
Checking patch -> block consistency

Creating block offsets
Creating merge list .

Creating polyMesh from blockMesh
Creating patches
Creating cells
Creating points with scale 1
Block 0 cell size :
i : 0.1 .. 0.1
j : 0.1 .. 0.1
k : 0.1 .. 0.1

Writing polyMesh
----------------
Mesh Information
----------------
boundingBox: (0 0 0) (1 1 4)
nPoints: 4961
nCells: 4000
nFaces: 12900
nInternalFaces: 11100
----------------
Patches
----------------
patch 0 (start: 11100 size: 100) name: inlet
patch 1 (start: 11200 size: 1600) name: wall
patch 2 (start: 12800 size: 100) name: outlet

End

Decomposing case.
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 4.1
Exec : decomposePar -force
Date : May 05 2017
Time : 12:42:50
Host : "test-All-Series"
PID : 16873
Case : /home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Decomposing mesh region0

Create mesh

Calculating distribution of cells
Selecting decompositionMethod simple

Finished decomposition in 0 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes

Processor 0
Number of cells = 1000
Number of faces shared with processor 1 = 200
Number of faces shared with processor 2 = 200
Number of processor patches = 2
Number of processor faces = 400
Number of boundary faces = 450

Processor 1
Number of cells = 1000
Number of faces shared with processor 0 = 200
Number of faces shared with processor 3 = 200
Number of processor patches = 2
Number of processor faces = 400
Number of boundary faces = 450

Processor 2
Number of cells = 1000
Number of faces shared with processor 0 = 200
Number of faces shared with processor 3 = 200
Number of processor patches = 2
Number of processor faces = 400
Number of boundary faces = 450

Processor 3
Number of cells = 1000
Number of faces shared with processor 1 = 200
Number of faces shared with processor 2 = 200
Number of processor patches = 2
Number of processor faces = 400
Number of boundary faces = 450

Number of processor faces = 800
Max number of cells = 1000 (0% above average 1000)
Max number of processor patches = 2 (0% above average 2)
Max number of faces between processors = 400 (0% above average 400)

Time = 0

Processor 0: field transfer
Processor 1: field transfer
Processor 2: field transfer
Processor 3: field transfer

End

do nothing.

// run_parallel_cfdemSolverIB_twoSpheresGlowinskiMPI_CFDDEM //

/home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD

rm: cannot remove 'couplingFiles/*': No such file or directory
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 4.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 4.1
Exec : cfdemSolverIB -parallel
Date : May 05 2017
Time : 12:42:51
Host : "test-All-Series"
PID : 16898
Case : /home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD
nProcs : 4
Slaves :
3
(
"test-All-Series.16899"
"test-All-Series.16900"
"test-All-Series.16901"
)

Pstream initialized with:
floatTransfer : 0
nProcsSimpleSum : 0
commsType : nonBlocking
polling iterations : 0
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Allowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0

Selecting dynamicFvMesh dynamicRefineFvMesh

PISO: Operating solver in PISO mode

Reading field p

Reading physical velocity field U
Note: only if voidfraction at boundary is 1, U is superficial velocity!!!

Reading physical velocity field U
Note: only if voidfraction at boundary is 1, U is superficial velocity!!!

Creating dummy density field rho = 1

Reading field phiIB

Reading field phiIB

Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian
Selecting turbulence model type laminar
Reading field interFace

Reading g
Selecting locateModel engineIB
Selecting dataExchangeModel twoWayMPI
Starting up LIGGGHTS for first time execution
Executing input script '../DEM/in.liggghts_run'
LIGGGHTS (Version LIGGGHTS-PUBLIC 3.6.0, compiled 2017-05-05-12:01:09 by test, git commit 18a96adf8688e0d46423c7d812001a8d9e0a9af0)
log ../DEM/log.liggghts
thermo_log ../DEM/post/thermo.txt

atom_style granular
atom_modify map array
communicate single vel yes

boundary f f f
newton off

units si
processors 2 2 1

region reg block 0. 1. 0. 1. 0. 4. units box
create_box 1 reg
Created orthogonal box = (0 0 0) to (1 1 4)
2 by 2 by 1 MPI processor grid

neighbor 0.3 bin
neigh_modify delay 0 binsize 0.01

# Material properties required for new pair styles

fix m1 all property/global youngsModulus peratomtype 5.e7
fix m2 all property/global poissonsRatio peratomtype 0.45
fix m3 all property/global coefficientRestitution peratomtypepair 1 0.9
fix m4 all property/global coefficientFriction peratomtypepair 1 0.5

# pair style
pair_style gran model hertz tangential history #Hertzian without cohesion
pair_coeff * *

# timestep, gravity
timestep 0.00003

fix gravi all gravity 981 vector 0.0 0.0 -1.0

# walls
fix xwalls1 all wall/gran model hertz tangential history primitive type 1 xplane 0.
fix xwalls2 all wall/gran model hertz tangential history primitive type 1 xplane 1.
fix ywalls1 all wall/gran model hertz tangential history primitive type 1 yplane 0.
fix ywalls2 all wall/gran model hertz tangential history primitive type 1 yplane 1.
fix zwalls1 all wall/gran model hertz tangential history primitive type 1 zplane 0.
fix zwalls2 all wall/gran model hertz tangential history primitive type 1 zplane 4.

# cfd coupling
fix cfd all couple/cfd couple_every 10 mpi
nevery as specified in LIGGGHTS is overriden by calling external program (../cfd_datacoupling_mpi.cpp:77)
fix cfd2 all couple/cfd/force

# create single partciles
create_atoms 1 single .5 .5 3.5 units box
Created 1 atoms
create_atoms 1 single .5 .5 3.16 units box
Created 1 atoms
set atom 1 diameter 0.167 density 1.5 vx 0 vy 0 vz 0
Setting atom values ...
1 settings made for diameter
1 settings made for density
1 settings made for vx
1 settings made for vy
1 settings made for vz
set atom 2 diameter 0.167 density 1.5 vx 0 vy 0 vz 0
Setting atom values ...
1 settings made for diameter
1 settings made for density
1 settings made for vx
1 settings made for vy
1 settings made for vz

variable vx1 equal vx[1]
variable vy1 equal vy[1]
variable vz1 equal vz[1]
variable vx2 equal vx[2]
variable vy2 equal vy[2]
variable vz2 equal vz[2]
variable x1 equal x[1]
variable y1 equal y[1]
variable z1 equal z[1]
variable x2 equal x[2]
variable y2 equal y[2]
variable z2 equal z[2]
variable time equal step*dt

fix extra1 all print 100 "${time} ${vx1} ${vy1} ${vz1}" file ../DEM/post/velocity_particle_1.txt title "%" screen no
fix extra2 all print 100 "${time} ${vx2} ${vy2} ${vz2}" file ../DEM/post/velocity_particle_2.txt title "%" screen no
fix extra3 all print 100 "${time} ${x1} ${y1} ${z1}" file ../DEM/post/position_particle_1.txt title "%" screen no
fix extra4 all print 100 "${time} ${x2} ${y2} ${z2}" file ../DEM/post/position_particle_2.txt title "%" screen no

# apply nve integration to all particles that are inserted as single particles
fix integr all nve/sphere #wenn das ausgeblendet, dann kein vel update

# screen output
compute rke all erotate/sphere
thermo_style custom step atoms ke c_rke vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:141)
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:141)
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:141)

# insert the first particles so that dump is not empty
dump dmp all custom 100 ../DEM/post/dump.liggghts_run id type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius
WARNING: Changing thermo_temp compute object. This object is deprecated and will be removed in the future. (../compute.cpp:141)

#force : f_couple_cfd[0] f_couple_cfd[1] f_couple_cfd[2]
#node : f_couple_cfd[6]
#cell id : f_couple_cfd[7]

run 1
Setting up run at Fri May 5 12:42:51 2017

Memory usage per processor = 51.8087 Mbytes
Step Atoms KinEng rke Volume
0 2 0 0 4
1 2 3.1682527e-06 0 4
Loop time of 4.4167e-05 on 4 procs for 1 steps with 2 atoms, finish time Fri May 5 12:42:51 2017

Pair time (%) = 1.19209e-06 (2.69906)
Neigh time (%) = 0 (0)
Comm time (%) = 3.09944e-06 (7.01754)
Outpt time (%) = 1.2219e-05 (27.6653)
Other time (%) = 2.76566e-05 (62.6181)

Nlocal: 0.5 ave 2 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 1.5 ave 2 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0.25 ave 1 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1

Total # of neighbors = 1
Ave neighs/atom = 0.5
Neighbor list builds = 0
Dangerous builds = 0

Selecting IOModel basicIO
Selecting probeModel off
Selecting voidFractionModel IB

W A R N I N G - do not use in combination with differentialRegion model!

Selecting averagingModel dilute
Selecting clockModel off
start clock measurement at t >0.0006
Selecting smoothingModel off
Selecting meshMotionModel noMeshMotion

CFDEMcoupling version: cfdem-3.6.1
, compatible to LIGGGHTS version: 3.6.0
, compatible to OF version and build: 3.0.x-commit-ac3f6c67e02f0aac3777c27f9fb7558fc3536e37

You are currently using:
OF version: 4.1
[1] [3] OF build: 4.1
CFDEM build: 3.6.1-dirty

cg is set to: 1
LIGGGHTS hosts 1 atom types.
If BC are important, please provide volScalarFields -imp/expParticleForces-
ignoring ddt(voidfraction)

[1]
[1] --> FOAM FATAL IO ERROR:
[1] 'functions' entry is not a dictionary
[1]
[1] file: /home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD/processor1/system/controlDict from line 0 to line 0.
[1]
[1] From function bool Foam::functionObjectList::read()
[1] in file db/functionObjects/functionObjectList/functionObjectList.C at line Selecting forceModel ShirgaonkarIB
582.
[1]
FOAM parallel run exiting
[1]

nrForceSubModels()=1
Selecting forceSubModel ImEx
[3]
[3] --> FOAM FATAL IO ERROR:
[3] 'functions' entry is not a dictionary
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 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.
--------------------------------------------------------------------------
[3]
[3] file: /home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD/processor3/system/controlDict from line 0 to line 0.
[3]
[3] From function bool Foam::functionObjectList::read()
[3] in file db/functionObjects/functionObjectList/functionObjectList.C at line 582.
[3]
FOAM parallel run exiting
[3]
[2]
[2]
[2] --> FOAM FATAL IO ERROR:
[2] 'functions' entry is not a dictionary
[2]
[2] file: /home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD/processor2/system/controlDict from line 0 to line 0.
[2]
[2] From function bool Foam::functionObjectList::read()
[2] in file db/functionObjects/functionObjectList/functionObjectList.C at line
reading switches for forceSubModel:ImEx
looking for treatForceExplicit ...
treatForceExplicit = false
looking for verbose ...
verbose = false

Selecting forceModel ArchimedesIB
582.
[2]
FOAM parallel run exiting
[2]
nrForceSubModels()=1
Selecting forceSubModel ImEx

reading switches for forceSubModel:ImEx
looking for treatForceExplicit ...
treatForceExplicit = true

accounting for Archimedes only on DEM side!
Selecting liggghtsCommandModel runLiggghts ,provide dicts, numbered from 0 to n

Starting time loop

[0]
[0]
[0] --> FOAM FATAL IO ERROR:
[0] 'functions' entry is not a dictionary
[0]
[0] file: /home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD/processor0/system/controlDict from line 18 to line 82.
[0]
[0] From function bool Foam::functionObjectList::read()
[0] in file db/functionObjects/functionObjectList/functionObjectList.C at line 582.
[0]
FOAM parallel run exiting
[0]
[test-All-Series:16895] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[test-All-Series:16895] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
error: load: unable to determine file format of '../../DEM/post/position_particle_1.txt'
error: called from
postproc.m at line 11 column 5

** (evince:16918): WARNING **: Error when getting information for file '/home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD/octave/pos_y_two_part_rec_glow.eps': No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16918): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error when getting information for file '/home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI/CFD/octave/vel_y_two_part_rec_glow.eps': No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory

** (evince:16933): WARNING **: Error setting file metadata: No such file or directory
deleting data at: /home/test/CFDEM/test-PUBLIC-4.1/run/tutorials/cfdemSolverIB/twoSpheresGlowinskiMPI ? otherwise press Ctrl-C:\n

regards
dinesh kumar