[Other] Error:Install LEMOS in openfoam2.3.0

mushtime · May 14, 2016, 03:15

Dear foamers,
I try to install LEMOS into openfoam2.3.0: http://www.lemos.uni-rostock.de/en/d.../cfd-software/

Quote:

1.move the Folder "LEMOS-2.3.x" into $FOAM_SRC
2.add the following line to your ~/.bashrc after ". ~/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc": . $FOAM_SRC/LEMOS-2.3.x/bashrc
3.parse your ~/.bashrc or open a new terminal
4.Execute applyPatches to install patches in $FOAM_SRC folder
5.Execute $LEMOSEXT/Allwmake to build the library and executables

But when I excute ./Allwmake under folder LEMOS-2.3.x, I got the following error.

Code:

/usr/bin/ld: cannot find -lgsl
collect2: error: ld returned 1 exit status
make: *** [/home/customer/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/libLEMOS-2.3.x.so] Error 1
+ cd applications
+ wmake all solvers
Making dependency list for source file scalarPimpleFoamLDMMS.C
Making dependency list for source file PODSolver.C
Making dependency list for source file scalarPimpleFoamMFM.C
Making dependency list for source file scalarPimpleFoam.C
could not open file PODODE.H for source file PODSolver.C due to No such file or directory
could not open file ODESolver.H for source file PODSolver.C due to No such file or directory
SOURCE=PODSolver.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/libLEMOS-2.3.x/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/meshTools/lnInclude  -IlnInclude -I. -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/PODSolver.o
SOURCE=scalarPimpleFoamLDMMS.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/turbulenceModels/incompressible/turbulenceModel -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/transportModels -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/incompressible/singlePhaseTransportModel -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/turbulenceModels/LES/LESfilters/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/meshTools/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/fvOptions/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/sampling/lnInclude -IlnInclude -I. -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/scalarPimpleFoamLDMMS.o
PODSolver.C:35:20: fatal error: PODODE.H: No such file or directory
 #include "PODODE.H"

Code:

compilation terminated.
SOURCE=scalarPimpleFoam.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/turbulenceModels/incompressible/turbulenceModel -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/transportModels -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/incompressible/singlePhaseTransportModel -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/turbulenceModels/LES/LESfilters/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/meshTools/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/fvOptions/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/sampling/lnInclude -IlnInclude -I. -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/scalarPimpleFoam.o
SOURCE=scalarPimpleFoamMFM.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/turbulenceModels/incompressible/turbulenceModel -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/transportModels -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/incompressible/singlePhaseTransportModel -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/turbulenceModels/LES/LESfilters/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/meshTools/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/fvOptions/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/sampling/lnInclude -IlnInclude -I. -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/scalarPimpleFoamMFM.o
make[2]: *** [Make/linux64GccDPOpt/PODSolver.o] Error 1
make[2]: Target `/home/customer/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/PODSolver' not remade because of errors.
make[1]: *** [PODSolver] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [basic] Error 2

Code:

compilation terminated.
make[3]: *** [Make/linux64GccDPOpt/postChannelExt.o] Error 1
make[3]: *** [Make/linux64GccDPOpt/vectorSnapshots.o] Error 1
make[3]: Target `/home/customer/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/vectorSnapshots' not remade because of errors.
make[2]: *** [vectorSnapshots] Error 2
make[3]: *** [Make/linux64GccDPOpt/scalarSnapshots.o] Error 1
make[3]: Target `/home/customer/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/scalarSnapshots' not remade because of errors.
make[2]: *** [scalarSnapshots] Error 2
make[2]: Target `application' not remade because of errors.
make[1]: *** [POD] Error 2
make[3]: Target `/home/customer/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/postChannelExt' not remade because of errors.
make[2]: *** [postChannelExt] Error 2
make[2]: Target `application' not remade because of errors.
make[1]: *** [miscellaneous] Error 2
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-100 -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/postProcessing/postCalc -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/meshTools/lnInclude -IlnInclude -I. -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/home/customer/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPOpt/LambdaCI.o -L/home/customer/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib \
     /home/customer/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/lib/postCalc.o -lfiniteVolume -lmeshTools -lgenericPatchFields -lOpenFOAM -ldl   -lm -o /home/customer/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64GccDPOpt/bin/LambdaCI
make[1]: Target `application' not remade because of errors.
make: *** [postProcessing] Error 2
make: Target `application' not remade because of errors.

Is this because LEMOS-2.3.x can only be used for Openfoam2.3.x not for Openfoam2.3.0?

Thanks.

mushtime · May 14, 2016, 10:26

Now I tried again to install LEMOS into Openfoam2.3.1. But the problem is till there.
Does anyone know why?

alexeym · May 15, 2016, 08:01

Hi,

This error

Code:

PODSolver.C:35:20: fatal error: PODODE.H: No such file or directory
 #include "PODODE.H"

means you did not set LEMOSEXT environment variable. Here is relevant piece from applications/solvers/basic/PODSolver/Make/options:

Code:

EXE_INC = \
    -I$(LEMOSEXT)/libLEMOS-2.3.x/lnInclude \
...

mushtime · May 16, 2016, 08:20

Thank you for your reply, Alexey.
I am new in OpenFOAM. I installed two versions of OF. So I add the path of bashrc of LEMOS-2.3.x to the bashrc of OpenFOAM2.3.1.
After I sourcing the bashrc of OpenFOAM2.3.1, and "echo LEMOSEXT,LIB_LEMOS_SRC" all give the right path.
But after that, the ./Allwmake still give the wrong message like this:

Code:

+ wmake libso libLEMOS-2.3.x
/usr/bin/ld: cannot find -lgsl
collect2: error: ld returned 1 exit status
make: *** [/home/customer/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64GccDPOpt/lib/libLEMOS-2.3.x.so] Error 1

Code:

/usr/bin/ld: cannot find -lLEMOS-2.3.x
collect2: error: ld returned 1 exit status
make[2]: *** [/home/customer/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64GccDPOpt/bin/PODSolver] Error 1
make[1]: *** [PODSolver] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [basic] Error 2

Code:

make[1]: *** [Make/linux64GccDPOpt/scalarPimpleFoamMFM.o] Error 1
make[1]: Target `/home/customer/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64GccDPOpt/bin/scalarPimpleFoamMFM' not remade because of errors.
make: *** [scalarPimpleFoamMFM] Error 2
make[1]: *** [Make/linux64GccDPOpt/scalarPimpleFoamLDMMS.o] Error 1
make[1]: Target `/home/customer/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64GccDPOpt/bin/scalarPimpleFoamLDMMS' not remade because of errors.
make: *** [scalarPimpleFoamLDMMS] Error 2
make: Target `application' not remade because of errors.

Code:

usr/bin/ld: cannot find -lLEMOS-2.3.x
collect2: error: ld returned 1 exit status
make[3]: *** [/home/customer/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64GccDPOpt/bin/vectorSnapshots] Error 1
make[2]: *** [vectorSnapshots] Error 2
/usr/bin/ld: cannot find -lLEMOS-2.3.x
collect2: error: ld returned 1 exit status
make[3]: *** [/home/customer/OpenFOAM/OpenFOAM-2.3.1/platforms/linux64GccDPOpt/bin/scalarSnapshots] Error 1
make[2]: *** [scalarSnapshots] Error 2
make[2]: Target `application' not remade because of errors.
make[1]: *** [POD] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [postProcessing] Error 2
make: Target `application' not remade because of errors.

alexeym · May 16, 2016, 08:30

The error causes all other errors is:

Code:

/usr/bin/ld: cannot find -lgsl

I GUESS it is GNU Scientific Library (or maybe Guidelines Support Library https://github.com/Microsoft/GSL

). Though the only place where -lgsl is mentioned is Make/options file, so maybe it is not used now.

mushtime · May 16, 2016, 08:42

Thanks Alexey,
Maybe I will try to remove the -lgsl to see whether it affects or look into the two libraries you mentioned.
Hope it works

mushtime · May 21, 2016, 11:36

Sorry that I forget to post the result.
After I remove the -lgsl. the compile of the libLEMOS-2.3.x.so just work fine. Though there is some mistakes when I compile the included solvers in LEMOS, but that's ok since I mainly use the Inflow-generator.

Giv · November 26, 2016, 08:04

Hi Qiaoling
I have the same problem in compiling LEMOS
how did you solve it?
thank you

wyldckat · December 3, 2016, 17:17

Quote:

Originally Posted by Giv

I have the same problem in compiling LEMOS

Quick question: Which version are you trying to install, namely which OpenFOAM version and LEMOS version?

Giv · December 4, 2016, 17:18

Hi Bruno

I solved my problem

I had not all the development tools installed

the OpenFOAM version is 2.3.1 with LEMOS 2.3.x

thank you

May 16, 2016, 08:30		#5
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	The error causes all other errors is: Code: /usr/bin/ld: cannot find -lgsl I GUESS it is GNU Scientific Library (or maybe Guidelines Support Library https://github.com/Microsoft/GSL ). Though the only place where -lgsl is mentioned is Make/options file, so maybe it is not used now. wyldckat likes this.

December 4, 2016, 17:18		#10
Giv New Member Join Date: Jul 2015 Posts: 5 Rep Power: 11	Hi Bruno I solved my problem I had not all the development tools installed the OpenFOAM version is 2.3.1 with LEMOS 2.3.x thank you wyldckat likes this.

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May 14, 2016, 10:26		#2
mushtime New Member Qiaoling Wang Join Date: Dec 2015 Posts: 18 Rep Power: 11	Now I tried again to install LEMOS into Openfoam2.3.1. But the problem is till there. Does anyone know why?

May 15, 2016, 08:01		#3
alexeym Senior Member Alexey Matveichev Join Date: Aug 2011 Location: Nancy, France Posts: 1,938 Rep Power: 39	Hi, This error Code: PODSolver.C:35:20: fatal error: PODODE.H: No such file or directory #include "PODODE.H" means you did not set LEMOSEXT environment variable. Here is relevant piece from applications/solvers/basic/PODSolver/Make/options: Code: EXE_INC = \ -I$(LEMOSEXT)/libLEMOS-2.3.x/lnInclude \ ...

May 16, 2016, 08:42		#6
mushtime New Member Qiaoling Wang Join Date: Dec 2015 Posts: 18 Rep Power: 11	Thanks Alexey, Maybe I will try to remove the -lgsl to see whether it affects or look into the two libraries you mentioned. Hope it works

May 21, 2016, 11:36		#7
mushtime New Member Qiaoling Wang Join Date: Dec 2015 Posts: 18 Rep Power: 11	Sorry that I forget to post the result. After I remove the -lgsl. the compile of the libLEMOS-2.3.x.so just work fine. Though there is some mistakes when I compile the included solvers in LEMOS, but that's ok since I mainly use the Inflow-generator.

November 26, 2016, 08:04		#8
Giv New Member Join Date: Jul 2015 Posts: 5 Rep Power: 11	Hi Qiaoling I have the same problem in compiling LEMOS how did you solve it? thank you