[Attesz]

Yes I added #include <stddef.h> to a file, so the compilation doesn't stop at 5% but at 49%.

Otherwise I'm still getting error:

SOURCE=manualDecomp/manualDecomp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-40 -IlnInclude -I. -I/home/attila/OpenFOAM/OpenFOAM-1.6-ext/src/OpenFOAM/lnInclude -I/home/attila/OpenFOAM/OpenFOAM-1.6-ext/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/manualDecomp.o
/usr/bin/ld: cannot find -lscotchDecomp
collect2: ld returned 1 exit status
make: *** [/home/attila/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt/libdecompositionMethods.so] Error 1
+ wmake libso lagrangian/basic
wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file passiveParticle/passiveParticleCloud.C
Making dependency list for source file indexedParticle/indexedParticleCloud.C

The compilation hasn't finished yet. Maybe if I compile again, it will work.

Regards,
Attila

[Attesz]

Unfortunately the compilation doesn't still work. I attach the log file.

The errors are:

linux64GccDPOpt/options:8: *** missing separator. Stop.
wmake error: file 'Make/linux64GccDPOpt/objectFiles' could not be created

and after that:

This is my options file:

EXE_INC = -I$(SCOTCH_INCLUDE_DIR) -I../decompositionMethods/lnInclude



LIB_LIBS = -L$(SCOTCH_LIB_DIR) -lscotch -L$(SCOTCH_LIB_DIR) -lscotcherrexit


-lrt

Where is the missing separator? The line8 is the '-lrt'.

/usr/bin/ld: cannot find -lscotchDecomp
collect2: ld returned 1 exit status
make: *** [/home/attila/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt/libdecompositionMethods.so] Error 1

What is true, this file can't be found in that directory. Why? Is it a ThirdParty compilation error?


The 'cannot find' files are:

lmeshTools
ldynamicMesh
lfiniteVolume
ldynamicMesh
lfaceDecompositionMotionSolver
lfvMotionSolver
lRBFMotionSolver
lmesquiteMotionSolver
lsolidBodyMotion
lsampling
lbasicThermophysicalModels
lreactionThermophysicalModels
lODE
lcompressibleTurbulenceModel

and so on...

log_Allwmake_secondRun.zip

Regards,
Attila

[Attesz]

2) When I used the scotch from the ThirdParty directory (which compiled OK), the OF compilation complained about an undefined reference to 'clock_gettime'. I used the Ubuntu provided scotch, libscotch-5.1 and libscotch-dev packages to get it to build.

Hi,
how can I do this? I'm getting the same error message...

Thanks,
Attila

[Attesz]

Well.. I forget to add / to the end of line 7

COMPILED!! Can't believe it!

I will write the instructions to prevent the other beginners to waste a lot of time for this!

So David, thank you very much for your help!

I wish you the best,
Attila

[marupio]

Yay! That's a relief. Quite an ordeal - I'm glad you got it up and running. Now, go do some good science with it!

-Dave

[diego_angeli]

Hello FOAMers,

I've been configuring my new flaming laptop these days and I went through the usual pains of compiling both the vanilla and extend OF versions on a Kubuntu 11.10 64 bit system.
I thought it would be good to share my experience with the build of 1.6-ext, so I'm revamping this useful thread and bringing forth some status update with respect to what it was discussed before.

Luckily enough, and thanks to this and other threads scattered around the CFD-online and the OF-extend forums, I managed to sort out the compilation of both the ThirdParty tools and 99% of all the 1.6-ext package. Although there is only a minor glitch still unsolved, I'm fine with the result. Here are some comments on what I did

0) First of all, let me say that Bruno's tutorial is very useful for setting up both dependencies and the environment.
Also this guide from Hakan Nilsson

After cloning the git repository I also created my own git branch to keep the master copy clean and do my tricks safely:

 git checkout -b myFixes

1) The porting to gcc-4.6 seems to be quite OK now, so the compiler works fine with both ThirdParty tools and FOAM apps and libs.
I had to modify the $WM_DIR/rules/linux64Gcc/c++ file according to the instruction at
this link
And, as David suggested here I modified the Make/options file for the scotchDecomp library

Originally Posted by marupio

You also need to add -lrt to linker options for scotch.

File: src/decompositionMethods/scotchDecomp/Make/options:
 LIB_LIBS = \
     -L$(SCOTCH_LIB_DIR) -lscotch \
     -L$(SCOTCH_LIB_DIR) -lscotcherrexit \
     -lrt

Compilation then went on flawlessly and without errors

2) The only issue regarding gcc-4.6 was on the mesquite library, which was rather well known.
Rather than following the advice of Chris (on this thread)
who suggested to revert to gcc-4.5 for compilation of mesquite, I followed the advice on
this post of the extend forum

Mesquite-2.1.2 source-code gave some compilation errors. Thus, I have used the latest available version, updating the mesquite version in:

~/OpenFOAM®®/OpenFOAM®®-1.6-ext/ThirdParty/AllMake.stage3: rpm_make -p mesquite-2.99 -s mesquite-2.99.spec -u software.sandia.gov/~jakraft/mesquite-2.99.tar.gz

in /OpenFOAM®®/OpenFOAM®®-1.6-ext/etc/settings.sh :
[ -z "$MESQUITE_SYSTEM" ] && [ -e $WM_THIRD_PARTY_DIR/packages/mesquite-2.99/platforms/$WM_OPTIONS ] && { _foamSource $WM_THIRD_PARTY_DIR/packages/mesquite-2.99/platforms/$WM_OPTIONS/etc/mesquite-2.99.sh }

and in ~/OpenFOAM®®/OpenFOAM®®-1.6-ext/ThirdParty/rpmBuild/SPECS/ :
mv mesquite-2.1.2.spec mesquite-2.99.spec
vim mesquite-2.99.spec : replace mesquite-2.1.2 with mesquite-2.99 ~/OpenFOAM®® $ cd OpenFOAM®®-1.6-ext/ ./Allwmake

And everything went fine

3) I managed to compile and install Paraview: here are three key tips:
a) Initially, the compilation of ParaView typically stops at 5%. As also explained by David for other packages (for which seemingly now all problems are fixed), the AllMake.stage4 script fails, but it will have downloaded all the necessary .tar.gz files to ThirdParty/rpmBuild/SOURCES. When AllMake runs, it unpacks these .tar.gz files into source directories in ThirdParty/rpmBuild/BUILD.
The hack to be done here is then quite ugly: one has to edit the tar.gz archive itself! Here it is:
- open the $WM_PROJECT_DIR/ThirdParty/rpmBuild/SOURCES/ParaView-3.10.1.tar.gz
- extract (or directly edit, if the archiving program allows for it) the file ParaView-3.10.1/VTK/Utilities/vtkmetaio/metaUtils.cxx
- added

#include <stddef.h>

at line 21
- (if needed) add the modified file to the archive, being careful to place it in the right position
- save the archive.
When the AllMake script is run again, the compilation now (as many of you reported) stops at 49%
b) as Stanislav suggests in this thread , in the /opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/rpmBuild/SPECS/ParaView-3.10.1.spec file, line 153, statement

addCMakeVariable  OPENGL_gl_LIBRARY:STRING=

should be commented out. This brings compilation to full completion.
c) Two posts after, Stanislav offers the solution to the third and last issue: the AllMake.stage4 script exits with errors and no rpm is built.
One should go manually into the ParaView build directory and do the following:

./AllMake.stage4 # first try
cd rpmBuild/BUILD/ParaView-3.10.1/buildObj/
make install
cd ../../../../
./AllMake.stage4

This does the trick, even if the procedure starts over again. However, the whole package must then be installed manually, by copying the build directory:

cp -r rpmBuild/BUILDROOT/ParaView-3.10.1-linux64GccDPOpt.x86_64/opt/OpenFOAM/OpenFOAM-1.6.ext/ThirdParty/packages/ParaView-3.10.1/platforms/linux64GccDPOpt/*    ./packages/ParaView-3.10.1/platforms/linux64GccDPOpt/

One important thing about ParaView is that, currently, the etc/settings.sh file is still set to source the environment variable PARAVIEW_DIR by looking for ParaView 3.8.1, while, by default, the 3rd party script installs ParaView 3.10.1. Hence, one should open file etc/settings.sh, go to line 536, uncomment these two lines:

# [ -z "$PARAVIEW_SYSTEM" ] && [ -e $WM_THIRD_PARTY_DIR/packages/ParaView-3.10.1/platforms/$WM_OPTIONS ] && {
#    _foamSource $WM_THIRD_PARTY_DIR/packages/ParaView-3.10.1/platforms/$WM_OPTIONS/etc/ParaView-3.10.1.sh

and comment these two lines:

 [ -z "$PARAVIEW_SYSTEM" ] && [ -e $WM_THIRD_PARTY_DIR/packages/ParaView-3.8.1/platforms/$WM_OPTIONS ] && {
    _foamSource $WM_THIRD_PARTY_DIR/packages/ParaView-3.8.1/platforms/$WM_OPTIONS/etc/ParaView-3.8.1.sh

and this sets up correctly the environment.

4) Once I finally ran the cavity tutorial to test the installation, the only annoying thing was that the PV3FoamReader (correctly compiled and built) does not actually work: in fact, I had to select manually the reader to be used for the cavity.OpenFOAM file in a dialog when opening the results with ParaView.
I wanted to dig more into this, so I opened the Plugins->Manage Plugins menu in ParaView and I discovered that there was a problem in the libPV3FoamReader_SM plugin. Here it is

 libPV3FoamReader_SM Error
/opt/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt/paraview_plugins/libPV3FoamReader_SM.so
Load Error, Plugin verification data mismatch in '/opt/OpenFOAM/OpenFOAM-1.6-ext/lib/linux64GccDPOpt/paraview_plugins/libPV3FoamReader_SM.so'
/opt/OpenFOAM/OpenFOAM-1.6-ext/ThirdParty/packages/ParMetis-3.1.1/platforms/linux64GccDPOpt/lib/libparmetis.so: undefined symbol: ompi_mpi_comm_world

It is very likely to be a problem with the ParMetis installation, but at this point I decided to stop and circumvent the issue by modifying the $WM_PROJECT_DIR/bin/paraFoam file in order for it to create the dummy case file with the .foam extension rather than with the .OpenFOAM one.

sed -i -e 's=\.OpenFOAM=\.foam=' $WM_PROJECT_DIR/bin/paraFoam

Finally, I've got everything in the right place, except from this minor "problem" which I'll leave pending. I hope that this summary of "tips" can be useful for anyone tackling the installation of OpenFOAM-1.6-ext in the near future.

Regards,

diego