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[Other] Problem with compiling a third party code that relies on OF1606+

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Old   September 23, 2019, 20:08
Default Problem with compiling a third party code that relies on OF1606+
  #1
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Artur
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Hi everyone,

I'm new to both openfoam and ubuntu, I am trying to compile a code that relies on openfoam 1606+, but it's giving me an error. To be honest as far as I can see this might not even be an OF related issue, but I hope that maybe some here can help me anyway even if it is not.



Full log from running Allmake for that package twice:
Quote:
surfaceRoughness
wmake
make[1]: Entering directory '/home/artur/works/apps/contactAngle/surfaceRoughness'
make[1]: '/home/artur/works/bin-v16/bin/surfaceRoughness' is up to date.
make[1]: Leaving directory '/home/artur/works/apps/contactAngle/surfaceRoughness'
surfaceAddLayerToCL
wmake
make[1]: Entering directory '/home/artur/works/apps/contactAngle/surfaceAddLayerToCL'
make[1]: '/home/artur/works/bin-v16/bin/surfaceAddLayerToCL' is up to date.
make[1]: Leaving directory '/home/artur/works/apps/contactAngle/surfaceAddLayerToCL'
surfaceSmoothVP
wmake
make[1]: Entering directory '/home/artur/works/apps/contactAngle/surfaceSmoothVP'
make[1]: '/home/artur/works/bin-v16/bin/surfaceSmoothVP' is up to date.
make[1]: Leaving directory '/home/artur/works/apps/contactAngle/surfaceSmoothVP'
voxelImage
g++ -std=c++0x -c sphereToRaw.cpp
g++ -o /home/artur/works/bin-v16/bin/sphereToRaw sphereToRaw.o
g++ -c -fPIC imageReader.cpp -o imageReader.o
g++ -c -fPIC voxelMesh.cpp -o voxelMesh.o
g++ -shared voxelMesh.o imageReader.o -o /home/artur/works/bin-v16/bin/libvoxelMesh.so
g++ -c imageFileConvert.cpp
g++ -fPIC -L/home/artur/works/bin-v16/bin/ imageFileConvert.o -lvoxelMesh -o /home/artur/works/bin-v16/bin/imageFileConvert
g++ -fPIC -c rawToFoam.cpp
g++ -fPIC -o /home/artur/works/bin-v16/bin/rawToFoam -L/home/artur/works/bin-v16/bin rawToFoam.o -lvoxelMesh
rm -f *.o
voxelImageNew
g++ -O3 -Wall writeRaCLInds.o -o /home/artur/works/bin-v16/bin/writeRaCLInds
/usr/bin/ld: writeRaCLInds.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:66: recipe for target 'writeRaCLInds' failed
make: *** [writeRaCLInds] Error 1
voxelToSurfaceML
wmake
make[1]: Entering directory '/home/artur/works/apps/contactAngle/voxelToSurfaceML'
make[1]: '/home/artur/works/bin-v16/bin/voxelToSurfaceML' is up to date.
make[1]: Leaving directory '/home/artur/works/apps/contactAngle/voxelToSurfaceML'
Specifically the error seems to be here:


Quote:
voxelImage
g++ -std=c++0x -c sphereToRaw.cpp
g++ -o /home/artur/works/bin-v16/bin/sphereToRaw sphereToRaw.o
g++ -c -fPIC imageReader.cpp -o imageReader.o
g++ -c -fPIC voxelMesh.cpp -o voxelMesh.o
g++ -shared voxelMesh.o imageReader.o -o /home/artur/works/bin-v16/bin/libvoxelMesh.so
g++ -c imageFileConvert.cpp
g++ -fPIC -L/home/artur/works/bin-v16/bin/ imageFileConvert.o -lvoxelMesh -o /home/artur/works/bin-v16/bin/imageFileConvert
g++ -fPIC -c rawToFoam.cpp
g++ -fPIC -o /home/artur/works/bin-v16/bin/rawToFoam -L/home/artur/works/bin-v16/bin rawToFoam.o -lvoxelMesh
rm -f *.o
voxelImageNew
g++ -O3 -Wall writeRaCLInds.o -o /home/artur/works/bin-v16/bin/writeRaCLInds
/usr/bin/ld: writeRaCLInds.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
Makefile:66: recipe for target 'writeRaCLInds' failed
make: *** [writeRaCLInds] Error 1
Can anyone direct me on how to fix this?
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Old   September 23, 2019, 21:11
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Artur
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I seem to have solved this problem by adding -no-pie in the relevant section of the make file, in case it will help someone. The following stackoverflow question didn't pop up on my goggle search for some reason:


https://stackoverflow.com/questions/...-object-recomp

I still have another problem, where I am following a guide for the code, where I have to use the commands:

Quote:
voxelToSurfaceML && surfaceAddLayerToCL && surfaceSmoothVP && more contactAngles.txt
but my terminal says that there is no such command. Does it mean there were still errors during the compilation that I do not see?

log.make is below:

Quote:
surfaceRoughness
wmake
make[1]: Entering directory '/home/artur/works/apps/contactAngle/surfaceRoughness'
make[1]: '/home/artur/works/bin-v16/bin/surfaceRoughness' is up to date.
make[1]: Leaving directory '/home/artur/works/apps/contactAngle/surfaceRoughness'
surfaceAddLayerToCL
wmake
make[1]: Entering directory '/home/artur/works/apps/contactAngle/surfaceAddLayerToCL'
make[1]: '/home/artur/works/bin-v16/bin/surfaceAddLayerToCL' is up to date.
make[1]: Leaving directory '/home/artur/works/apps/contactAngle/surfaceAddLayerToCL'
surfaceSmoothVP
wmake
make[1]: Entering directory '/home/artur/works/apps/contactAngle/surfaceSmoothVP'
make[1]: '/home/artur/works/bin-v16/bin/surfaceSmoothVP' is up to date.
make[1]: Leaving directory '/home/artur/works/apps/contactAngle/surfaceSmoothVP'
voxelImage
g++ -std=c++0x -c sphereToRaw.cpp
g++ -o /home/artur/works/bin-v16/bin/sphereToRaw sphereToRaw.o
g++ -c -fPIC imageReader.cpp -o imageReader.o
g++ -c -fPIC voxelMesh.cpp -o voxelMesh.o
g++ -shared voxelMesh.o imageReader.o -o /home/artur/works/bin-v16/bin/libvoxelMesh.so
g++ -c imageFileConvert.cpp
g++ -fPIC -L/home/artur/works/bin-v16/bin/ imageFileConvert.o -lvoxelMesh -o /home/artur/works/bin-v16/bin/imageFileConvert
g++ -fPIC -c rawToFoam.cpp
g++ -fPIC -o /home/artur/works/bin-v16/bin/rawToFoam -L/home/artur/works/bin-v16/bin rawToFoam.o -lvoxelMesh
rm -f *.o
voxelImageNew
g++ -O3 -Wall -no-pie writeRaCLInds.o -o /home/artur/works/bin-v16/bin/writeRaCLInds
ln -f -s /home/artur/works/bin-v16/bin/writeRaCLInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie writeRaPoreInds.o -o /home/artur/works/bin-v16/bin/writeRaPoreInds
ln -f -s /home/artur/works/bin-v16/bin/writeRaPoreInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie writepAreaPoreInds.o -o /home/artur/works/bin-v16/bin/writepAreaPoreInds
ln -f -s /home/artur/works/bin-v16/bin/writepAreaPoreInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie writeCAThroatInds.o -o /home/artur/works/bin-v16/bin/writeCAThroatInds
ln -f -s /home/artur/works/bin-v16/bin/writeCAThroatInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie writeRcThroatInds.o -o /home/artur/works/bin-v16/bin/writeRcThroatInds
ln -f -s /home/artur/works/bin-v16/bin/writeRcThroatInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie writeCAPoreInds.o -o /home/artur/works/bin-v16/bin/writeCAPoreInds
ln -f -s /home/artur/works/bin-v16/bin/writeCAPoreInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie writeRcPoreInds.o -o /home/artur/works/bin-v16/bin/writeRcPoreInds
ln -f -s /home/artur/works/bin-v16/bin/writeRcPoreInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie writeCACornerInds.o -o /home/artur/works/bin-v16/bin/writeCACornerInds
ln -f -s /home/artur/works/bin-v16/bin/writeCACornerInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie writeRcCornerInds.o -o /home/artur/works/bin-v16/bin/writeRcCornerInds
ln -f -s /home/artur/works/bin-v16/bin/writeRcCornerInds /home/artur/works/bin-v16/bin/imageFileConvert
g++ -O3 -Wall -no-pie Ufraw2Ucdat.o -o /home/artur/works/bin-v16/bin/Ufraw2Ucdat
g++ -no-pie -O3 -Wall -std=c++0x -o /home/artur/works/bin-v16/bin/rawToFoamPar rawToFoamPar.o
g++ -no-pie -std=c++0x -o /home/artur/works/bin-v16/bin/rawToFoam rawToFoam.o
g++ -O3 -Wall -no-pie voxelImageConvert.o -o /home/artur/works/bin-v16/bin/voxelImageConvert
ln -f -s /home/artur/works/bin-v16/bin/voxelImageConvert /home/artur/works/bin-v16/bin/imageFileConvert
voxelToSurfaceML
wmake
make[1]: Entering directory '/home/artur/works/apps/contactAngle/voxelToSurfaceML'
make[1]: '/home/artur/works/bin-v16/bin/voxelToSurfaceML' is up to date.
make[1]: Leaving directory '/home/artur/works/apps/contactAngle/voxelToSurfaceML'
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Old   September 23, 2019, 22:26
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  #3
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Artur
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Managed to fix this one as well by adding the proper source into bashrc manually. Sorry for spamming!
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