Installation of CFDEM

Hey Kun,
the first part of the message (i.e. the warning about the potentially missing solvers) is just meant to remind you that solvers you might hav added personally are not compiled with that command.
The real error occurs in the post processing, where octave claims not to find a certain data file (pressure information located in probes/0). Have a look there if the file exists, in case not: does the actual computation take place?
Cheers,
Alice

I'm going to piggy-back on this thread because I had similar problems to Kunzhang when I tried doing the CFDEM coupling last night. But I have also many others...

I'm going step-by-step with the installation manual but I keep having a problem when I edit my .bashrc file with this line in particular:

export CFDEM_PROJECT_DIR=$HOME/CFDEM/CFDEMcoupling-$CFDEM_VERSION-$WM_PROJECT_VERSION


When I did the git-pull command with $WM_PROJECT_VERSION, there was no problem and I made the directory "CFDEMcoupling-PUBLIC-2.2.0"

But now when I add that line above to my .bashrc file and start a new terminal, I get the first error that

bash: /home/jon/CFDEM/CFDEMcoupling-PUBLIC-/src/lagrangian/cfdemParticle/etc/bashrc: No such file or directory

You can see that the bash file isn't creating the string "2.2.0" to append to my path. So there's an error getting into that subdirectory where the src files are.

Last night I had changed the bash file to just erase any instance I saw "-$WM_PROJECT_VERSION" and it at least worked temporarily. But there's another etc/.bashrc in the lagrangian directory that I don't want to modify but it references more -$WM_PROJECT_VERSION directories -- so I think this is my problem. When I got to the point of running tutorials, my paths were all mixed up and errors were dropping from the sky like rain.

Can I do something to force my .bashrc to understand that $WM_... is 2.2.0? Am I doing something else wrong? If I just type $WM_PROJECT_VERSION into a terminal, it clearly relates this to 2.2.0 (and obviously says that it is not a command).

Many thanks for any advice.

Hi all,
I did the installing process according the " Install CFDEM.txt" in this page. when I run an example of liggghts in 3 steps, and changed the path to :"~/LIGGGHTS/LIGGGHTS-PUBLIC/examples/LIGGGHTS/Tutorials_public/conveyor", followed the next "liggghts < in.conveyor " line, some strange thing happened as shown in the following:
"liggghts: error while loading shared libraries: libmpi.so.1: cannot open shared object file: No such file or directory"
I googled this problem, but no any clue. somebody help me out of here. thanks a lot.

Hi yyu,

in OpenFOAM's /etc/bashrc you can set if you want to use SYSTEMOPENMPI or OPENMPI (this woud use those delivered with OpenFOAM third party), I'd recommend SYSTEMOPENMPI and see that mpi libraries are installed on the system.
On OpenCFD's installation guide you find some libraries that are necessary (http://www.openfoam.org/download/git.php).

Further when typing cfdemSysTest it will tell you which gcc, g++ etc. are used, as well as the mpi installed. You might install some openMPI-devel package to get the mpirun command.

Cheers,
Chris

I tried several ways, but just didnot work. from your reply, first I should set the path in OpenFOAM's /etc/bashrc
(export LD_LIBRARY_PATH=/usr/lib/openmpi/lib
export LD_LIBRARY_PATH:=$PATH:/usr/lib/openmpi/lib/)
and then download the libmpi.so.1 (openmpi-1.6.3-6.fc18.x86_64) from the OpenCFD's installation guide. and ran it again. still had the question. and ran cfdemSysTest command and got:
*******************
system settings:
*******************
CFDEM_VERSION=PUBLIC
couple to OF_VERSION=

check if paths are set correctly
valid:yes critical:yes - $CFDEM_PROJECT_DIR = /home/yyu/CFDEM/CFDEMcoupling-PUBLIC-
valid:yes critical:no - $CFDEM_PROJECT_USER_DIR = /home/yyu/CFDEM/yyu-PUBLIC-
valid:yes critical:yes - $CFDEM_SRC_DIR = /home/yyu/CFDEM/CFDEMcoupling-PUBLIC-/src/lagrangian/cfdemParticle
valid:yes critical:yes - $CFDEM_SOLVER_DIR = /home/yyu/CFDEM/CFDEMcoupling-PUBLIC-/applications/solvers
valid:yes critical:yes - $CFDEM_TUT_DIR = /home/yyu/CFDEM/CFDEMcoupling-PUBLIC-/tutorials
valid:yes critical:yes - $CFDEM_LIGGGHTS_SRC_DIR = /home/yyu/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_LPP_DIR = /home/yyu/LIGGGHTS/mylpp/src
valid:yes critical:no - $CFDEM_PIZZA_DIR = /home/yyu/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src
valid:yes critical:no - $CFDEM_TEST_HARNESS_PATH = /home/yyu/CFDEM/yyu-PUBLIC-/log/logFilesCFDEM-PUBLIC-

library names
$CFDEM_LIGGGHTS_LIB_NAME = lmp_fedora_fpic
$CFDEM_LIB_NAME = lagrangianCFDEM-PUBLIC-
$LD_LIBRARY_PATH =
*******************
g++:
/usr/bin/g++
g++ (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

gcc:
/usr/bin/gcc
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

mpic++:
/usr/bin/mpic++
g++ (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

mpirun:
/usr/bin/mpirun
mpirun (Open MPI) 1.4.3

Report bugs to http://www.open-mpi.org/community/help/
Please help me out of here, Chris. I'm really frustrated.

Hi every one,
I followed the order for installing CFDEM. When I almost finished it, last step: cfdemTestTUT and changed the path to :
path = '../postProcessing/probes/0/p';

path = '../postProcessing/probes/0/T';
and something happened. what can I do?? Thanks for attention. Looking forward to your replying.
For information about changes from previous versions, type `news'.

error: load: unable to find file ../../DEM/post/velocity.txt
error: called from:
error: settlingVelocity.m at line 9, column 6

** (evince:27862): WARNING **: Error when getting information for file '/home/yyu/CFDEM/CFDEMcoupling-PUBLIC-2.2.x/tutorials/cfdemSolverPiso/settlingTestMPI/CFD/octave/cfdemSolverPiso_settlingTestMPI.eps': No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

** (evince:27862): WARNING **: Error setting file metadata: No such file or directory

Hi,
I have correctly installed CFDEM coupling. But there is following error after running a tutorial example:
Unable to open document “file:///home/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemSolverPisoScalar/packedBedTemp/CFD/octave/cfdemSolverPisoScalar_pressureDrop.eps”.

I have made several changes in files that other mentioned in Forums. But I have still the same error.

Please let me know how I can fix these errors.

Best

Aneseh

Hello Aneseh,
this message just states that the file of type eps cannot be displayed. Is the document viewer "evince" installed on your system? Just have a look at one of the processor directories within the CFD folder. In case there are timestep folders (called 0.1, 0.2, ...) the calculation ran through and you can postprocess the data with paraview for example.
Best regards,
Alice

Dear Alice , thank you so much, there are no timestep folders (called 0.1, 0.2, ...) in my folder.
I have document viewer installed.
would you please take a look at my run process
-----------
aneseh@aneseh-OptiPlex-7010:~/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder$ ./Allrun.sh
mesh needs to be built
/*---------------------------------------------------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 2.4.0 |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
Build : 2.4.0-f0842aea0e77
Exec : blockMesh
Date : Apr 02 2016
Time : 13:10:48
Host : "aneseh-OptiPlex-7010"
PID : 15862
Case : /home/aneseh/CFDEMcoupling-PUBLIC-/run/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/aneseh/CFDEMcoupling-PUBLIC-/run/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/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder/DEM/post/*’: No such file or directory
/home/aneseh/CFDEM/CFDEMcoupling-PUBLIC-/src/lagrangian/cfdemParticle/etc/functions.sh: line 417: [: ==: unary operator expected
/home/aneseh/CFDEM/CFDEMcoupling-PUBLIC-/src/lagrangian/cfdemParticle/etc/functions.sh: line 419: [: ==: unary operator expected
rm: cannot remove ‘/home/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder/log_run_liggghts_fillCylinder_DEM’: No such file or directory

// run_liggghts_fillCylinder_DEM //

/home/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder/DEM

LIGGGHTS (Version LIGGGHTS-PUBLIC 3.3.1, compiled 2016-04-01-14:10:59 by aneseh, git commit 99507f5217ad4fd4be5107d6262bd7274c9a5c03 based on LAMMPS 23 Nov 2013)
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 1 atom_type 1 density constant 200 radius constant 0.001
fix pts2 all particletemplate/sphere 1 atom_type 2 density constant 200 radius constant 0.001
fix pdd1 all particledistribution/discrete 1. 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 1. 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 100001 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 100001 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

#insert the first particles so that dump is not empty
run 1
Setting up run ...
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 305 particle templates (mass 0.000256) at step 1
- a total of 305 particle templates (mass 0.000256) inserted so far.
WARNING: Particle insertion: Less insertions than requested (../fix_insert.cpp:734)
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 305 particle templates (mass 0.000256) at step 1
- a total of 305 particle templates (mass 0.000256) inserted so far.
WARNING: Particle insertion: Less insertions than requested (../fix_insert.cpp:734)
1 --------------------------------------------------------------------------
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.
--------------------------------------------------------------------------
610 0.00025554127 0 5.076e-05
Loop time of 0.0300939 on 1 procs for 1 steps with 610 atoms

Pair time (%) = 2.69413e-05 (0.0895241)
Neigh time (%) = 0.000457048 (1.51874)
Comm time (%) = 3.8147e-06 (0.012676)
Outpt time (%) = 1.40667e-05 (0.0467427)
Other time (%) = 0.029592 (98.3323)

Nlocal: 610 ave 610 max 610 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: 2169 ave 2169 max 2169 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2169
Ave neighs/atom = 3.55574
Neighbor list builds = 1
Dangerous builds = 0
dump dmp all custom 1000 post/dump.liggghts_init id type type x y z ix iy iz vx vy vz fx fy fz omegax omegay omegaz radius

run 3000 upto
ERROR on proc 0: Cannot open dump file (../dump.cpp:512)
./Allrun.sh: line 48: cd: /home/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder/DEM/post: No such file or directory
python: can't open file '/home/aneseh/LIGGGHTS/mylpp/src/lpp.py': [Errno 2] No such file or directory
rm: cannot remove ‘/home/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder/CFD/0.*’: No such file or directory
rm: cannot remove ‘/home/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder/log_run_cfdemPostproc_fillCylinder_CFD’: No such file or directory

// run_cfdemPostproc_fillCylinder_CFD //

/home/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder/CFD

/home/aneseh/CFDEM/CFDEMcoupling-PUBLIC-/src/lagrangian/cfdemParticle/etc/functions.sh: line 542: cfdemPostproc: command not found

trying to start paraview...
./Allrun.sh: line 81: /home/aneseh/software/ParaView-4.3.1-Linux-64bit/bin/paraview: No such file or directory
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Please let me know what is the problem,
Thanks,

Hi Aneseh,
the lines

ERROR on proc 0: Cannot open dump file (../dump.cpp:512)
./Allrun.sh: line 48: cd: /home/aneseh/CFDEMcoupling-PUBLIC-/run/cfdemPostproc/fillCylinder/DEM/post: No such file or directory

indicate that there might be no post-folder inside cou DEM folder. If thats the case, please just generate an empty folder called post, and within it an empty folder called restart.
Best regards,
Alice

Hi everyone,

I am facing the installation problem. Sorry for raising the context in this regard. I am raising it as everyone is here with the discussion of installation problem.
I have tried severe documentations (one is githubAccess_public.pdf from CFDEMCoupling download section & many others available in google) and step-by-step guidelines to install CFDEMCoupling-LIGGGHTS-OpenFOAM-Paraview on my Linux ubuntu 14.04LTS system, i.e. CFDEM full package. But unfortunately, i failed every time at any stage somehow during installation process.

Can you kindly help me by giving the exact proper step-by-step guidelines/tutorial to install that CFDEMCoupling package properly on my machine?

Thanks in advance
With regards,
Anirban