CFDEM Compiling Problems while OF and LIGGGHTS Work Well

Submitted by NTT1508 on Mon, 11/17/2014 - 00:06

Hi everybody,

I am a really new guy in Linux (Ubuntu) and coding as well. I have tried to compile CFDEM for my study for more than 2 months recently however it is really a tough job. I always get stucked on cfdemCompCFDEM step though I think I had followed strictly the instruction. After several removing and installing efforts, I decided to post my problem here and hope a support from some specialists here.

The result from cfdemSysTest is listed below (seems to be a perfect condition):

system settings:
*******************
CFDEM_VERSION=PUBLIC
couple to OF_VERSION=2.3.x
compile option=Opt

check if paths are set correctly
valid:yes critical:yes - $CFDEM_PROJECT_DIR = /home/thanh/CFDEM/CFDEMcoupling-PUBLIC-2.3.x
valid:yes critical:no - $CFDEM_PROJECT_USER_DIR = /home/thanh/CFDEM/thanh-PUBLIC-2.3.x
valid:yes critical:yes - $CFDEM_SRC_DIR = /home/thanh/CFDEM/CFDEMcoupling-PUBLIC-2.3.x/src
valid:yes critical:yes - $CFDEM_SOLVER_DIR = /home/thanh/CFDEM/CFDEMcoupling-PUBLIC-2.3.x/applications/solvers
valid:yes critical:yes - $CFDEM_TUT_DIR = /home/thanh/CFDEM/CFDEMcoupling-PUBLIC-2.3.x/tutorials
valid:yes critical:yes - $CFDEM_LIGGGHTS_SRC_DIR = /home/thanh/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_LPP_DIR = /home/thanh/LIGGGHTS/mylpp/src
valid:yes critical:no - $CFDEM_PIZZA_DIR = /home/thanh/LIGGGHTS/PIZZA/gran_pizza_17Aug10/src
valid:yes critical:no - $CFDEM_TEST_HARNESS_PATH = /home/thanh/CFDEM/thanh-PUBLIC-2.3.x/log/logFilesCFDEM-PUBLIC-2.3.x

library names
$CFDEM_LIGGGHTS_LIB_NAME = lmp_fedora_fpic
$CFDEM_LIB_NAME = lagrangianCFDEM-PUBLIC-2.3.x
$LD_LIBRARY_PATH = /home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64Gcc/CGAL-4.3/lib:/home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64Gcc/gperftools-svn/lib:/home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64Gcc/ParaView-4.1.0/lib/paraview-4.1:/home/thanh/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib/openmpi-1.6.5:/home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64GccDPOpt/lib/openmpi-1.6.5:/home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64Gcc/openmpi-1.6.5/lib:/home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64Gcc/openmpi-1.6.5/lib64:/home/thanh/OpenFOAM/thanh-2.3.x/platforms/linux64GccDPOpt/lib:/home/thanh/OpenFOAM/site/2.3.x/platforms/linux64GccDPOpt/lib:/home/thanh/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib:/home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64GccDPOpt/lib:/home/thanh/OpenFOAM/OpenFOAM-2.3.x/platforms/linux64GccDPOpt/lib/dummy
$WM_NCOMPPROCS =
*******************
g++:
/usr/bin/g++
g++ (Ubuntu 4.8.2-19ubuntu1) 4.8.2
Copyright (C) 2013 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 4.8.2-19ubuntu1) 4.8.2
Copyright (C) 2013 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++:
/home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64Gcc/openmpi-1.6.5/bin/mpic++
g++ (Ubuntu 4.8.2-19ubuntu1) 4.8.2
Copyright (C) 2013 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:
/home/thanh/OpenFOAM/ThirdParty-2.3.x/platforms/linux64Gcc/openmpi-1.6.5/bin/mpirun
mpirun (Open MPI) 1.6.5
----------------------------------------------------------------------------------------

When I tried to run cfdemTestTUT, the following problems appear,

----------------------------------------------------------------------------------------------
Unable to open document “file:///home/thanh/CFDEM/CFDEMcoupling-PUBLIC-2.3.x/tutorials/cfdemSolverPiso/settlingTestMPI/CFD/octave/cfdemSolverPiso_settlingTestMPI.eps”.

and

Unable to open document “file:///home/thanh/CFDEM/CFDEMcoupling-PUBLIC-2.3.x/tutorials/cfdemSolverPiso/ErgunTestMPI/CFD/octave/cfdemSolverPiso_ErgunTestMPI.eps”.

-----------------------------------------------------------------------------------------------------
I have read some nice discussions which had the same problems with me and tried their solutions but they donot work unfortunately.

I have successfully tested with tutorial for OpenFoam and LIGGGHTS, all work perfectly.

I am writing here and really expecting someone can give me a hint to solve my problem. I have read many problems and discussions here and are very impressive with strong and immediate support from specialist team. Thank very much for that.

Attachment is my log file of compiling.

Thank very much for concern.

Regards,

AttachmentSize
Binary Data Log file of compiling21.76 KB

Forums:

j-kerbl's picture

j-kerbl | Mon, 11/17/2014 - 11:01

Hi,
thanks for posting the logs!
It looks as the compilation of the CFDEM library worked fine, so there might be some issues with the solver.
What happens if you go to $CFDEM_SOLVER_DIR/cfdemSolverPiso
and execute
wclean all
rmdepall
wmake
?
Please share the output of the compiling.

What could be helpful for further compilations is when you set the WM_NCOMPPROCS variable in your .bashrc. This is the number of concurrent processes used for compiling.

Cheers
Josef

Dina | Wed, 12/16/2015 - 13:03

I'm new in CFDEM and i'm facing the same problem

Unable to open document
file:///home/dina/CFDEM/CFDEMcoupling-PUBLIC-2.3.1/tutorials/cfdemSolverPiso/ErgunTestMPI_cgs/CFD/octave/cfdemSolverPiso_ErgunTestMPI.eps

Should i also try to run the lines:
wclean all
rmdepall
wmake

In the directory:
dina@dina:~/CFDEM/CFDEMcoupling-PUBLIC-2.3.1/tutorials/cfdemSolverPiso$
right?

And could you please tell me how can i access to the file
bashrc. in order to change the WM_NCOMPPROCS variable

Should i also try that?

I have OpenFoam 2.3.1 and paraView 4.1.0

Thank you in advance

Dina | Sun, 12/20/2015 - 10:00

I already tried the lines

wclean all
rmdepall
wmake

In the directory:
dina@dina:~/CFDEM/CFDEMcoupling-PUBLIC-2.3.1/tutorials/cfdemSolverPiso$

And i got this error:
wmake: 'Make' directory does not exist in /home/dina/CFDEM/CFDEMcoupling-PUBLIC-2.3.1/tutorials/cfdemSolverPiso
Searching up directories tree for Make directory
wmake error: could not find Make directory
wmake error: file 'Make/files' does not exist in /home/dina

What should i do?

richti83's picture

richti83 | Mon, 11/17/2014 - 13:30

AFAIK the *.eps files are generated by octave (a gnu matlab alternative), maybe it is not installed on your system ?

I'm not an associate of DCS GmbH and not a core developer of LIGGGHTS®
ResearchGate | Contact

NTT1508 | Tue, 11/18/2014 - 00:51

Hi Josef and Rich,

Thank much for your responses.

I have compiled again several times for cfdemsolverpiso, cfdemsolverIB and cfdemSolverPisoScalar. However the problem is still existed. I think the reason might be from Octave which generates *.EPS file as mentioned by Rich. I actually installed Octave before compiling but might be missed somewhere. I types OCTAVE on terminal and the outcome is below.

/usr/local/bin/octave-cli-3.8.0: error while loading shared libraries: libcholmod.so.1.7.1: cannot open shared object file: No such file or directory

I am trying to fix this problem of Octave. It looks quite strange to me. Hope this is the major reason causing error of my compiling.

Regards

NTT1508 | Fri, 11/21/2014 - 04:35

Hi Josef and Rich,

After re-installing Ubuntu 14.04 and compiling CFDEM, I am finally able to get some figures from Tutorial test without any errors. I have some experiences after many trial and error in terms of CFDEM installation that might be helpful to some new-members here.

First, I stucked quite along time with MPIC++ wrapper which didnot enable me to do compiling successfully. It always came with a statement that MPIC++ wrapper unable to find Path for compiling while I installed everything fully and changed the PATH many time. The problem is due to that I installed ThirdParty and it automatically placed system-MPI. After change to system or global MPI, MPIC++ becomes able to compile well.

Secondly, During compiling work, I upgraded Ubuntu from 13.10 to 14.04 that resulted in a serious discontinuity of system. And my octacte didnot work properly and couldnot generate *.EPS files in tutorial cases (as suggested by Richti).

There is one thing I am still a bit confused that when I run tutorials, I cannot see any dump file generated in DEM folder. Normally there should be a number of dump files after LIGGGHTS processing. Do I have any problem on that?

Thank very much for your support.

j-kerbl's picture

j-kerbl | Mon, 11/24/2014 - 10:39

Hi,
thank you for sharing that information!
Usually the Allrun.sh scripts have an automated clean-up after the results are processed. You could either remove the clean-up from the script or run the simulation manually. It is a good idea to check the liggghts in-files, if the dumps are enabled.

Cheers
Josef

Shabby D | Wed, 11/26/2014 - 15:59

Hi NTT1508,

It is possible for you to give a detailed step-by-step guide on how you correctly installed OpenFOAM, LIGGGHTS, and CFDEMcoupling? I have been having trouble for some time now.

NTT1508 | Thu, 11/27/2014 - 21:38

Hi mate,

I actually follow exactly the step-by-step guide which was already uploaded on this page. The link for that can be found below

http://www.cfdem.com/system/files/Install%20CFDEM_0.txt

It depends on your current OS, so the trouble can be differrent. My problem and solution as well have been shared in previous comments. During your installaion, if you find any problem, you can post it in this forum and many active specialists are available to help.