CFDEM installation

Hi,
I have managed to install CFDEM on my local machine. I am trying to install CFDEM on university hpc. I have managed to compile liggghts code. As I am compiling CFEDEM i get log_compile_result_src_fail . I have attached log file for compileCFDEMcoupling_cfdemParticle. Also if I run solver with failed source log file I get following error (log file with name slurm-450370.txt as attached) after running in parallel. I am not sure where exactly I am doing wrong while compiling or running case. I am using OpenFOAM-3.0.0 as it is installed on hpc.

Thank you

Attachment	Size
log_compilecfdemcoupling_cfdemparticle.txt	287.55 KB
slurm-450370.txt	41.44 KB

Forums:

CFDEM®coupling - User Forum

j-kerbl | Tue, 01/30/2018 - 13:43

Hi,

Hi,

could you please load the environment and run cfdemSysTest and post the output of it?

The cfdemParticle library and the solver seem to have compiled, I am not sure yet what the issue might be.
But since its running on a cluster, there might be several possibilities :)

Cheers,
Josef

CFD_DEM | Tue, 01/30/2018 - 14:02

*****************************

*********************************************
* C F D E M (R) c o u p l i n g *
* *
* by DCS Computing GmbH *
* www.dcs-computing.com *
*********************************************

*********************************
CFDEM(R)coupling system settings:
*********************************
CFDEM_VERSION=PUBLIC
couple to OF_VERSION=3.0.0
compile option=Opt

check if paths are set correctly
valid:yes critical:yes - $CFDEM_PROJECT_DIR = /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0
valid:yes critical:no - $CFDEM_PROJECT_USER_DIR = /home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0
valid:yes critical:yes - $CFDEM_SRC_DIR = /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/src
valid:yes critical:yes - $CFDEM_SOLVER_DIR = /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/applications/solvers
valid:yes critical:yes - $CFDEM_TUT_DIR = /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/tutorials
valid:yes critical:yes - $CFDEM_LIGGGHTS_SRC_DIR = /home/eng/esrcqh/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_LIGGGHTS_LIB_PATH = /home/eng/esrcqh/LIGGGHTS/LIGGGHTS-PUBLIC/src
valid:yes critical:yes - $CFDEM_LPP_DIR = /home/eng/esrcqh/LIGGGHTS/lpp/src
valid:yes critical:yes - $CFDEM_ADD_LIBS_DIR = /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/src/lagrangian/cfdemParticle/etc/addLibs_universal
valid:yes critical:yes - $CFDEM_LIB_DIR = /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms//lib
valid:NO critical:yes - $CFDEM_APP_DIR = /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms//bin does not exist
valid:NO critical:no - $CFDEM_USER_LIB_DIR = /home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms//lib does not exist
valid:NO critical:no - $CFDEM_USER_APP_DIR = /home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms//bin does not exist
valid:yes critical:no - $CFDEM_TEST_HARNESS_PATH = /home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/log/logFilesCFDEM-PUBLIC-3.0.0
valid:NO critical:no - $C3PO_SRC_DIR = does not exist

library names
$CFDEM_LIGGGHTS_LIB_NAME = lmp_auto
$CFDEM_LIB_NAME = lagrangianCFDEM-PUBLIC-3.0.0
$LD_LIBRARY_PATH = /home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms//lib:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms//lib:/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms//lib:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms//lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/ThirdParty-3.0.0/platforms/linux64Icc/gperftools-svn/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/ParaView/4.4.0-mpi/lib/paraview-4.4:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/lib/mpi:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/ThirdParty-3.0.0/platforms/linux64IccDPInt32Opt/lib/mpi:/home/eng/esrcqh/OpenFOAM/esrcqh-3.0.0/platforms/linux64IccDPInt32Opt/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/site/3.0.0/platforms/linux64IccDPInt32Opt/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/ThirdParty-3.0.0/platforms/linux64IccDPInt32Opt/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/lib/dummy:/csc/tinis/software/Core/binutils/2.27/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/zlib/1.2.8/lib:/csc/tinis/software/Core/Bison/3.0.4/lib:/csc/tinis/software/Core/flex/2.6.0/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/CGAL/4.7-Python-2.7.11/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/Boost/1.58.0-Python-2.7.11/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/SCOTCH/6.0.4/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/imkl/11.2.4.223/mkl/lib/intel64:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/imkl/11.2.4.223/lib/intel64:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/ParaView/4.4.0-mpi/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/VTK/6.3.0-Python-2.7.11/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/METIS/5.1.0-32bitIDX/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/libGLU/9.0.0-Mesa-11.0.8/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/Qt/4.8.7-Python-2.7.11/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/Mesa/11.0.8-Python-2.7.11/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/LLVM/3.7.1/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/MPFR/3.1.3-GMP-6.1.0/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/GMP/6.1.0/lib:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/Python/2.7.11/lib:/csc/tinis/software/Compiler/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/lib64:/csc/tinis/software/Core/ifort/2015.5.223-GNU-4.9.3-2.25/lib/intel64:/csc/tinis/software/Core/ifort/2015.5.223-GNU-4.9.3-2.25/lib:/csc/tinis/software/Compiler/GCC/4.9.3/binutils/2.25/lib:/csc/tinis/software/Core/GCC/4.9.3-binutils-2.25/lib/gcc/x86_64-unknown-linux-gnu/4.9.3:/csc/tinis/software/Core/GCC/4.9.3-binutils-2.25/lib64:/csc/tinis/software/Core/GCC/4.9.3-binutils-2.25/lib:/csc/tinis/software/Core/icc/2015.5.223-GNU-4.9.3-2.25/lib/intel64:/csc/tinis/software/Core/icc/2015.5.223-GNU-4.9.3-2.25/lib:/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms/lib:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms/lib:/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms/lib:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms/lib:/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms/lib:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms/lib
$WM_NCOMPPROCS =
$WM_LABEL_SIZE = 32

Additional lib settings
CFDEM_ADD_LIBS_DIR/CFDEM_ADD_LIBS_NAME = /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/src/lagrangian/cfdemParticle/etc/addLibs_universal/additionalLibs_3.0.0
CFDEM_ADD_LIB_PATHS =
CFDEM_ADD_LIBS =

LIGGGHTS library link (created during compilation of CFDEM)
lrwxrwxrwx 1 esrcqh esrcqh 60 Jan 30 13:00 /home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms//lib/liblmp_auto.so -> /home/eng/esrcqh/LIGGGHTS/LIGGGHTS-PUBLIC/src/liblmp_auto.so
*******************
g++:
/csc/tinis/software/Core/GCC/4.9.3-binutils-2.25/bin/g++
g++ (GCC) 4.9.3
Copyright (C) 2015 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:
/csc/tinis/software/Core/GCC/4.9.3-binutils-2.25/bin/gcc
gcc (GCC) 4.9.3
Copyright (C) 2015 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++:
which: no mpic++ in (/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms//bin:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms//bin:/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms//bin:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms//bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/ThirdParty-3.0.0/platforms/linux64Icc/gperftools-svn/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/ParaView/4.4.0-mpi/bin:/home/eng/esrcqh/OpenFOAM/esrcqh-3.0.0/platforms/linux64IccDPInt32Opt/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/site/3.0.0/platforms/linux64IccDPInt32Opt/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/OpenFOAM-3.0.0/platforms/linux64IccDPInt32Opt/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/OpenFOAM-3.0.0/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/OpenFOAM/3.0.0-eb-deps-Python-2.7.11/OpenFOAM-3.0.0/wmake:/csc/tinis/software/Core/binutils/2.27/bin:/csc/tinis/software/Core/CMake/3.3.1/bin:/csc/tinis/software/Core/Bison/3.0.4/bin:/csc/tinis/software/Core/flex/2.6.0/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/CGAL/4.7-Python-2.7.11/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/SCOTCH/6.0.4/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/imkl/11.2.4.223/mkl/bin/intel64:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/imkl/11.2.4.223/mkl/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/imkl/11.2.4.223/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/VTK/6.3.0-Python-2.7.11/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/METIS/5.1.0-32bitIDX/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/Qt/4.8.7-Python-2.7.11/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/LLVM/3.7.1/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/libxml2/2.9.3-Python-2.7.11/bin:/csc/tinis/software/MPI/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/Python/2.7.11/bin:/csc/tinis/software/Compiler/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/bin64:/csc/tinis/software/Core/ifort/2015.5.223-GNU-4.9.3-2.25/bin:/csc/tinis/software/Compiler/GCC/4.9.3/binutils/2.25/bin:/csc/tinis/software/Core/GCC/4.9.3-binutils-2.25/bin:/csc/tinis/software/Core/icc/2015.5.223-GNU-4.9.3-2.25/bin:/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms/bin:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms/bin:/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms/bin:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms/bin:/home/eng/esrcqh/CFDEM/esrcqh-PUBLIC-3.0.0/platforms/bin:/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/platforms/bin:/Users/Alok/base:/usr/local/heroku/bin:/usr/local/bin:/opt/local/bin:/opt/local/sbin:/opt/scripts:/usr/lib64/qt-3.3/bin:/opt/moab/bin:/usr/lpp/mmfs/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/eng/esrcqh/bin)
/home/eng/esrcqh/CFDEM/CFDEMcoupling-PUBLIC-3.0.0/src/lagrangian/cfdemParticle/etc/cfdemSystemTest.sh: line 91: mpic++: command not found
mpirun:
/csc/tinis/software/Compiler/intel/2015.5.223-GNU-4.9.3-2.25/impi/5.0.3.049/bin64/mpirun
Intel(R) MPI Library for Linux* OS, Version 5.0 Update 3 Build 20150804 (build id: 12452)
Copyright (C) 2003-2015, Intel Corporation. All rights reserved.
**********************
additional packages...

CFD_DEM | Tue, 01/30/2018 - 14:10

Hello Josef,

Thank you for your reply. I think problem lies in while compilation as i get log for src file as fail and also while compiling i get following warning
In file included from lnInclude/momCoupleModel.H(44),
from ../cfdemParticle/cfdemCloud/cfdemCloudI.H(33),
from ../cfdemParticle/cfdemCloud/cfdemCloud.H(594),
from ../cfdemParticle/cfdemCloud/cfdemCloud.C(33):
lnInclude/dataExchangeModel.H(299): warning #173: floating-point value does not fit in required integral type
particleCloud_.setCG(lmp->force->cg(int(GREAT)));

Which i think leads to following error while running

#1 Foam::sigFpe::sigHandler(int) in "/lib64/libpthread.so.0"
[11] #3 Foam::twoWayMPI::setCG() const in "/lib64/libpthread.so.0"
[0] #3 Foam::twoWayMPI::setCG() const at ??:?

j-kerbl | Tue, 01/30/2018 - 16:11

Hi,

Hi,

from what I see you are using the intel compiler and mpi variant.

Can you edit $CFDEM_SRC_DIR/lagrangian/cfdemParticle/subModels/dataExchangeModel/dataExchangeModel/dataExchangeModel.H line 299
from particleCloud_.setCG(lmp->force->cg(int(GREAT)));
to particleCloud_.setCG(lmp->force->cg(INT_MAX));
recompile and test it?

I recently had i similar issue with an intel compiler. However I don't have one at hand and therefore can't test it.

Thanks,
Josef

CFD_DEM | Tue, 01/30/2018 - 19:06

Thank you Josef... It worked.

Thank you Josef... It worked...

j-kerbl | Fri, 02/02/2018 - 14:24

Hi,

Hi,

thanks for the confirmation!
This will be in the next release of CFDEM.

Happy simulations,
Josef

govind | Fri, 02/23/2018 - 14:21

ENVIRONMENT VARIABLE SETTING PROBLEM

Hi,

I have installed Openfoam , liggghts, cfdem but facing problem while setting environment variable. With this command:

mv CFDEMcoupling-PUBLIC CFDEMcoupling-PUBLIC-$WM_PROJECT_VERSION

CFDEMcoupling-PUBLIC name changes to CFDEMcoupling-PUBLIC-5.x. With following the further instructions to edit the my system bashrc file :

#- source cfdem env vars
export CFDEM_VERSION=PUBLIC
export CFDEM_PROJECT_DIR=$HOME/CFDEM/CFDEMcoupling-$CFDEM_VERSION-$WM_PROJECT_VERSION
export CFDEM_PROJECT_USER_DIR=$HOME/CFDEM/$LOGNAME-$CFDEM_VERSION-$WM_PROJECT_VERSION
export CFDEM_bashrc=$CFDEM_PROJECT_DIR/src/lagrangian/cfdemParticle/etc/bashrc
export CFDEM_LIGGGHTS_SRC_DIR=$HOME/LIGGGHTS/LIGGGHTS-PUBLIC/src
export CFDEM_LIGGGHTS_MAKEFILE_NAME=auto
export CFDEM_LPP_DIR=$HOME/LIGGGHTS/lpp/src
. $CFDEM_bashrc

I am getting error that "/home/govind/CFDEM/CFDEMcoupling-PUBLIC-: No such file or directory". A you see in the error that openfoam version isn't coming but directory name is changed with version name.

Govind

alice | Mon, 02/26/2018 - 10:45

Hi Govind,

it seems like the variable $WM_PRJECT_VERSION is just not set. Please make sure that the OpenFOAM version is sourced before all the CFDEM settings in your bashrc.

Cheers,

Alice

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