Can't start the paraview

Submitted by daye on Wed, 08/23/2017 - 05:19

Dear all
I just intalled the CFDEM and I try to run the tutorial case- fillCyliner, but the terminals shows that I can't start the paraview.It says:
trying to start paraview...
./Allrun.sh: line 81: /home/daye/software/ParaView-4.3.1-Linux-64bit/bin/paraview: No such file or directory
And the detail is:
daye@daye:~/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder$ ./Allrun.sh
mesh needs to be built
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 3.0.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 3.0.1-d8a290b55d28
Exec : blockMesh
Date : Aug 23 2017
Time : 19:06:34
Host : "daye"
PID : 2440
Case : /home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/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/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/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 : 8
Number of boundary faces : 14
Number of defined boundary faces : 14
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 : 0.001725 .. 0.001725
j : 0.001725 .. 0.001725
k : 0.00230417 .. 0.00230417

Block 1 cell size :
i : 0.001725 .. 0.001725
j : 0.00101048 .. 0.00101048
k : 0.00230417 .. 0.00230417

Block 2 cell size :
i : 0.00101048 .. 0.00101048
j : 0.00270527 .. 0.00270527
k : 0.00230417 .. 0.00230417

Block 3 cell size :
i : 0.00270527 .. 0.00270527
j : 0.00101048 .. 0.00101048
k : 0.00230417 .. 0.00230417

Block 4 cell size :
i : 0.00101048 .. 0.00101048
j : 0.001725 .. 0.001725
k : 0.00230417 .. 0.00230417

Writing polyMesh
----------------
Mesh Information
----------------
boundingBox: (-0.0138 -0.0138 0) (0.0138 0.0138 0.0553)
nPoints: 5225
nCells: 4608
nFaces: 14400
nInternalFaces: 13248
----------------
Patches
----------------
patch 0 (start: 13248 size: 192) name: inlet
patch 1 (start: 13440 size: 192) name: outlet
patch 2 (start: 13632 size: 768) name: wall

End

rm: cannot remove ‘/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/DEM/post/*’: No such file or directory

// run_liggghts_fillCylinder_DEM //

/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/DEM

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.7.0, compiled 2017-08-23-17:28:22 by daye, git commit c449f30b63c5eec5c8053a67dccd892fe2c5cef2)
atom_style granular
atom_modify map array
communicate single vel yes

boundary m m m
newton off

units si

region reg block -0.015 0.015 -0.015 0.015 -0.001 0.0554 units box
create_box 2 reg
Created orthogonal box = (-0.015 -0.015 -0.001) to (0.015 0.015 0.0554)
1 by 1 by 1 MPI processor grid

neighbor 0.001 bin
neigh_modify delay 0

#Material properties required for new pair styles

fix m1 all property/global youngsModulus peratomtype 5.e6 5.e6
fix m2 all property/global poissonsRatio peratomtype 0.45 0.45
fix m3 all property/global coefficientRestitution peratomtypepair 2 0.3 0.3 0.3 0.3
fix m4 all property/global coefficientFriction peratomtypepair 2 0.5 0.5 0.5 0.5

#pair style
pair_style gran model hertz tangential history
pair_coeff * *

#timestep, gravity
timestep 0.00001
fix gravi all gravity 9.81 vector 0.0 0.0 -1.0

#walls
fix zwalls1 all wall/gran model hertz tangential history primitive type 1 zplane 0.0
fix zwalls2 all wall/gran model hertz tangential history primitive type 1 zplane 0.0553
fix cylwalls all wall/gran model hertz tangential history primitive type 1 zcylinder 0.0138 0. 0.

#cfd coupling
#fix cfd all couple/cfd

#particle insertion
region bc cylinder z 0.0 0.0 0.012 0.02 0.03 units box
region bc2 cylinder z 0.0 0.0 0.012 0.01 0.02 units box
fix pts1 all particletemplate/sphere 49979687 atom_type 1 density constant 200 radius constant 0.001
fix pts2 all particletemplate/sphere 49979693 atom_type 2 density constant 200 radius constant 0.001
fix pdd1 all particledistribution/discrete 15485863 1 pts1 1.0
Fix particledistribution/discrete (id pdd1): distribution based on mass%:
pts1: d=2.000000e-03 (max. bounding sphere) mass%=100.000000%
Fix particledistribution/discrete (id pdd1): distribution based on number%:
pts1: d=2.000000e-03 (max. bounding sphere) number%=100.000000%
fix pdd2 all particledistribution/discrete 15485867 1 pts2 1.0
Fix particledistribution/discrete (id pdd2): distribution based on mass%:
pts2: d=2.000000e-03 (max. bounding sphere) mass%=100.000000%
Fix particledistribution/discrete (id pdd2): distribution based on number%:
pts2: d=2.000000e-03 (max. bounding sphere) number%=100.000000%

fix ins all insert/pack seed 32452843 distributiontemplate pdd1 vel constant 0. 0. -1. insert_every once overlapcheck yes all_in yes particles_in_region 1000 region bc
fix ins2 all insert/pack seed 32452867 distributiontemplate pdd2 vel constant 0. 0. -1. insert_every once overlapcheck yes all_in yes particles_in_region 1000 region bc2

#apply nve integration to all particles that are inserted as single particles
fix integr all nve/sphere

#screen output
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 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:159)

#insert the first particles so that dump is not empty
run 1
Setting up run at Wed Aug 23 19:06:35 2017

INFO: Resetting random generator for region bc
INFO: Particle insertion ins: inserting every 0 steps
INFO: Resetting random generator for region bc2
INFO: Particle insertion ins2: inserting every 0 steps
Memory usage per processor = 4.32251 Mbytes
Step Atoms KinEng 1 Volume
0 0 0 0 5.076e-05
insertion: proc 0 at 0 %
insertion: proc 0 at 10 %
insertion: proc 0 at 20 %
insertion: proc 0 at 30 %
INFO: Particle insertion ins: inserted 312 particle templates (mass 2.613805e-04) at step 1
- a total of 312 particle templates (mass 2.613805e-04) inserted so far.
WARNING: Particle insertion: Less insertions than requested (../fix_insert.cpp:814)
insertion: proc 0 at 0 %
insertion: proc 0 at 10 %
insertion: proc 0 at 20 %
insertion: proc 0 at 30 %
INFO: Particle insertion ins2: inserted 310 particle templates (mass 2.597050e-04) at step 1
- a total of 310 particle templates (mass 2.597050e-04) inserted so far.
WARNING: Particle insertion: Less insertions than requested (../fix_insert.cpp:814)
1 622 0.00026056831 0 5.076e-05
Loop time of 0.025511 on 1 procs for 1 steps with 622 atoms, finish time Wed Aug 23 19:06:36 2017

Pair time (%) = 3.00407e-05 (0.117756)
Neigh time (%) = 0.000547171 (2.14484)
Comm time (%) = 3.8147e-06 (0.0149531)
Outpt time (%) = 8.10623e-06 (0.0317754)
Other time (%) = 0.0249219 (97.6907)

Nlocal: 622 ave 622 max 622 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: 2205 ave 2205 max 2205 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2205
Ave neighs/atom = 3.54502
Neighbor list builds = 1
Dangerous builds = 0
dump dmp all custom/vtk 1000 post/liggghts_init*.vtk id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius

run 3000 upto
Setting up run at Wed Aug 23 19:06:36 2017

Memory usage per processor = 7.99319 Mbytes
Step Atoms KinEng 1 Volume
1 622 0.00026056831 0 5.076e-05
1000 622 0.00028439741 1.3344982e-06 5.076e-05
2000 622 1.0367323e-05 5.4297602e-06 5.076e-05
3000 622 1.0863057e-06 1.0389306e-06 5.076e-05
Loop time of 0.244699 on 1 procs for 2999 steps with 622 atoms, finish time Wed Aug 23 19:06:36 2017

Pair time (%) = 0.142473 (58.2236)
Neigh time (%) = 0.0231028 (9.4413)
Comm time (%) = 0.000406027 (0.165929)
Outpt time (%) = 0.0316901 (12.9507)
Other time (%) = 0.0470276 (19.2185)

Nlocal: 622 ave 622 max 622 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: 3262 ave 3262 max 3262 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 3262
Ave neighs/atom = 5.24437
Neighbor list builds = 51
Dangerous builds = 0
#write_restart liggghts.restart
rm: cannot remove ‘/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/0.*’: No such file or directory

// run_cfdemPostproc_fillCylinder_CFD //

/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD

/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 3.0.1 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 3.0.1-d8a290b55d28
Exec : cfdemPostproc
Date : Aug 23 2017
Time : 19:06:37
Host : "daye"
PID : 2468
Case : /home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/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

Create mesh for time = 0

Reading field p

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

Creating dummy density field rho

Reading voidfraction field voidfraction = (Vgas/Vparticle)

Reading particle velocity field Us

Reading/calculating face flux field phi

Selecting incompressible transport model Newtonian
Selecting turbulence model type laminar
Selecting locateModel standard
Selecting dataExchangeModel oneWayVTK
relativePath_"../DEM/post"
Selecting IOModel basicIO
--> FOAM Warning : IO model is in serial write mode, only data on proc 0 is written
Selecting probeModel off
Selecting voidFractionModel divided
Selecting averagingModel dense
Selecting clockModel off
start clock measurement at t >0.002
Selecting smoothingModel off
Selecting meshMotionModel noMeshMotion

CFDEMcoupling version: cfdem-3.7.0
, compatible to LIGGGHTS version: 3.7.0
, compatible to OF version and build: 3.0.x-commit-ac3f6c67e02f0aac3777c27f9fb7558fc3536e37

You are currently using:
OF version: 3.0.1
OF build: 3.0.1-d8a290b55d28
CFDEM build: 3.7.0-dirty

cg is set to: 1
If BC are important, please provide volScalarFields -imp/expParticleForces-
ignoring ddt(voidfraction)
Selecting momCoupleModel off
Selecting forceModel noDrag
Selecting forceSubModel ImEx
reading switches:
looking for treatForceExplicit ... not found in dict, using default. treatForceExplicit = false
looking for verbose ... not found in dict, using default. verbose = false

Starting time loop

Time = 0.001

debug: index is liggghts_init1000.vtk
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init1000.vtk"
debug: index is liggghts_init1000.vtk
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init1000.vtk"
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init1000.vtk"
createTimeDir(path_), path="./lagrangian"
lagPath_=createTimeDir(fileName(lagPath_/lagrangian)), lagPath="./lagrangian"
ExecutionTime = 0.21 s ClockTime = 0 s

Time = 0.002

debug: index is liggghts_init2000.vtk
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init2000.vtk"
debug: index is liggghts_init2000.vtk
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init2000.vtk"
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init2000.vtk"
createTimeDir(path_), path="./lagrangian"
lagPath_=createTimeDir(fileName(lagPath_/lagrangian)), lagPath="./lagrangian"
ExecutionTime = 0.35 s ClockTime = 0 s

Time = 0.003

debug: index is liggghts_init3000.vtk
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init3000.vtk"
debug: index is liggghts_init3000.vtk
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init3000.vtk"
opening file: "/home/daye/CFDEM/CFDEMcoupling-PUBLIC-3.0.1/tutorials/cfdemPostproc/fillCylinder/CFD/../DEM/post/liggghts_init3000.vtk"
createTimeDir(path_), path="./lagrangian"
lagPath_=createTimeDir(fileName(lagPath_/lagrangian)), lagPath="./lagrangian"
ExecutionTime = 0.5 s ClockTime = 1 s

End

trying to start paraview...
./Allrun.sh: line 81: /home/daye/software/ParaView-4.3.1-Linux-64bit/bin/paraview: No such file or directory

Thank you very much!
Daye

alice's picture

alice | Wed, 08/23/2017 - 08:01

Hello Daye,
please have a look at the mentioned directory:
/home/daye/software/ParaView-4.3.1-Linux-64bit/bin/paraview
The error message states that there is no such file or directory. Is the path correct?
Cheers,
Alice

daye | Wed, 08/23/2017 - 09:29

Dear Alice,
Thanks for your reply! The path is wrong , even the path /home/daye/software is not correct. I want to know how to change the path and the path should point to which file or directory.
Thank you very much!
Daye

alice's picture

alice | Thu, 08/24/2017 - 09:35

Hello Daye,
I just saw that the paraview path is hardcoded in that example. For changing it please open the Allrun.sh script and search for the keywprd paraview. In my case (and I guess also in your case) you 'll find the "bad command" that causes issues in your case in line 81. Please exchange the path with you paraview path. This should do the trick. Otherwise you can also open Paraview manually...
Cheers,
Alice

daye | Wed, 08/23/2017 - 15:04

Hi Alice,
I can't find the executable paraview in any directory but paraview has been installed in Ubuntu. I want know whether I can use the paraFoam instead of paraview.
Thanks
Daye

praveenapprasad | Sun, 03/18/2018 - 08:00

I had a similar issue.
You can fix it by changing the paraview path in line:81 in the Allrun.sh script as Alice pointed out.
The paraview executable can be found in : $HOME/OpenFOAM/ThirdParty-5.x/build/linux64Gcc/ParaView-5.4.0/bin/paraview
(if you had installed as instructed)