OpenFOAM 1.6 package - CentOS 5.3 x86_64

7islands · August 17, 2009, 02:02

Hi Jean-Peer,

Here: http://www.paraview.org/pipermail/pa...st/013278.html

Takuya

wersoe · August 20, 2009, 08:29

Hi linnemann,

I tried to compile the 1.6.x version with CentOS 64bit.
Unfortunately, I got lots of errors when compiling ../src only.
Attached you will find the output.
Actually, I do not know which libraries needed by OpenFOAM to compile, find an helpful installation instruction is quit difficult.
I would be happy for every hint you can give me, so that I can compile 1.6.x and later maybe 1.6-dev as well.
Maybe you can describe the steps you have done for setting up the system to compile without errors. Hopefully, it is not that much to explain...

Thanks for your time, regards Sören

$LD_LIBRARY_PATH:

Code:

/usr/local/OpenFOAM/ThirdParty-1.6/libraries/lib:
/usr/local/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linux64Gcc/bin:
/usr/local/OpenFOAM/OpenFOAM-1.6/lib/linux64GccDPOpt/openmpi-1.3.3:
/usr/local/OpenFOAM/ThirdParty-1.6/openmpi-1.3.3/platforms/linux64GccDPOpt/lib:
/usr/local/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib64:
/usr/local/OpenFOAM/ThirdParty-1.6/gcc-4.3.3/platforms/linux64/lib:
/usr/local/OpenFOAM/ThirdParty-1.6/gmp-4.2.4/platforms/linux64/lib:
/usr/local/OpenFOAM/ThirdParty-1.6/mpfr-2.4.1/platforms/linux64/lib:
/root/OpenFOAM/root-1.6/lib/linux64GccDPOpt:
/usr/local/OpenFOAM/site/1.6/lib/linux64GccDPOpt:
/usr/local/OpenFOAM/OpenFOAM-1.6/lib/linux64GccDPOpt

Output:

Code:

 [root@PC-1775 src]# ./Allwmake > error.log
+ wmakePrintBuild -check
+ wmakeLnInclude OpenFOAM
+ wmakeLnInclude OSspecific/POSIX
+ Pstream/Allwmake
+ wmake libso dummy
+ case "$WM_MPLIB" in
+ set +x
+ WM_OPTIONS=linux64GccDPOptOPENMPI
+ wmake libso mpi
+ wmake libo OSspecific/POSIX
+ wmake libso OpenFOAM
+ wmake libso lagrangian/basic
+ wmake libso triSurface
+ wmake libso edgeMesh
+ wmake libso surfMesh
+ decompositionMethods/Allwmake
+ wmake libso decompositionMethods
scotchDecomp/scotchDecomp.C:72:20: error: module.h: Datei oder Verzeichnis nicht gefunden
scotchDecomp/scotchDecomp.C:73:20: error: common.h: Datei oder Verzeichnis nicht gefunden
scotchDecomp/scotchDecomp.C:74:20: error: scotch.h: Datei oder Verzeichnis nicht gefunden
scotchDecomp/scotchDecomp.C: In member function ‘Foam::label Foam::scotchDecomp::decompose(const Foam::List<int>&, const Foam::List<int>&, Foam::List<int>&)’:
scotchDecomp/scotchDecomp.C:136: error: ‘SCOTCH_Strat’ was not declared in this scope
scotchDecomp/scotchDecomp.C:136: error: expected `;' before ‘stradat’
scotchDecomp/scotchDecomp.C:137: error: ‘stradat’ was not declared in this scope
scotchDecomp/scotchDecomp.C:137: error: ‘SCOTCH_stratInit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:152: error: ‘SCOTCH_stratGraphMap’ was not declared in this scope
scotchDecomp/scotchDecomp.C:163: error: ‘SCOTCH_Graph’ was not declared in this scope
scotchDecomp/scotchDecomp.C:163: error: expected `;' before ‘grafdat’
scotchDecomp/scotchDecomp.C:164: error: ‘grafdat’ was not declared in this scope
scotchDecomp/scotchDecomp.C:164: error: ‘SCOTCH_graphInit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:179: error: ‘SCOTCH_graphBuild’ was not declared in this scope
scotchDecomp/scotchDecomp.C:182: error: ‘SCOTCH_graphCheck’ was not declared in this scope
scotchDecomp/scotchDecomp.C:234: error: ‘SCOTCH_Arch’ was not declared in this scope
scotchDecomp/scotchDecomp.C:234: error: expected `;' before ‘archdat’
scotchDecomp/scotchDecomp.C:235: error: ‘archdat’ was not declared in this scope
scotchDecomp/scotchDecomp.C:235: error: ‘SCOTCH_archInit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:254: error: ‘SCOTCH_archCmpltw’ was not declared in this scope
scotchDecomp/scotchDecomp.C:262: error: ‘SCOTCH_archCmplt’ was not declared in this scope
scotchDecomp/scotchDecomp.C:294: error: ‘SCOTCH_graphMap’ was not declared in this scope
scotchDecomp/scotchDecomp.C:318: error: ‘SCOTCH_graphExit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:320: error: ‘SCOTCH_stratExit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:322: error: ‘SCOTCH_archExit’ was not declared in this scope
make: *** [Make/linux64GccDPOpt/scotchDecomp.o] Fehler 1
+ '[' -d /usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/openmpi-1.3.3 ']'
+ WM_OPTIONS=linux64GccDPOptOPENMPI
+ wmake libso parMetisDecomp
parMetisDecomp.C:41:25: error: parmetis.h: Datei oder Verzeichnis nicht gefunden
parMetisDecomp.C: In member function ‘Foam::label Foam::parMetisDecomp::decompose(Foam::Field<int>&, Foam::Field<int>&, const Foam::pointField&, Foam::Field<int>&, Foam::Field<int>&, const Foam::List<int>&, Foam::List<int>&)’:
parMetisDecomp.C:282: warning: use of old-style cast
parMetisDecomp.C:282: warning: use of old-style cast
parMetisDecomp.C:310: error: ‘ParMETIS_V3_PartGeomKway’ was not declared in this scope
make: *** [Make/linux64GccDPOptOPENMPI/parMetisDecomp.o] Fehler 1
+ wmake libso meshTools
/usr/bin/ld: cannot find -ldecompositionMethods
collect2: ld returned 1 exit status
make: *** [/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libmeshTools.so] Fehler 1
.
.
.
+ fvAgglomerationMethods/Allwmake
+ wmake libso MGridGenGamgAgglomeration
/usr/bin/ld: cannot find -lMGridGen
collect2: ld returned 1 exit status
make: *** [/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libMGridGenGAMGAgglomeration.so] Fehler 1
[root@PC-1775 src]#

Anyway, the file I wrote the output of ./Allwmake looks different:

Code:

same version as previous build
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/dummy/libPstream.so' is up to date.

Note: ignore spurious warnings about missing mpicxx.h headers
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/openmpi-1.3.3/libPstream.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libOSspecific.o' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libOpenFOAM.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/liblagrangian.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libtriSurface.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libedgeMesh.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libsurfMesh.so' is up to date.
SOURCE=scotchDecomp/scotchDecomp.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-40 -I/usr/local/OpenFOAM/ThirdParty-1.6.x/scotch_5.1/src/libscotch/lnInclude -I/usr/local/OpenFOAM/ThirdParty-1.6.x/metis-5.0pre2/include -IlnInclude -I. -I/usr/local/OpenFOAM/OpenFOAM-1.6.x/src/OpenFOAM/lnInclude -I/usr/local/OpenFOAM/OpenFOAM-1.6.x/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/scotchDecomp.o
SOURCE=parMetisDecomp.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-40 -DOMPI_SKIP_MPICXX -I/usr/local/OpenFOAM/ThirdParty-1.6.x/openmpi-1.3.3/platforms/linux64GccDPOpt/include -I/usr/local/OpenFOAM/ThirdParty-1.6.x/ParMetis-3.1/ParMETISLib -I/usr/local/OpenFOAM/ThirdParty-1.6.x/ParMetis-3.1 -I../decompositionMethods/lnInclude -IlnInclude -I. -I/usr/local/OpenFOAM/OpenFOAM-1.6.x/src/OpenFOAM/lnInclude -I/usr/local/OpenFOAM/OpenFOAM-1.6.x/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOptOPENMPI/parMetisDecomp.o
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libODE.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libspecie.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libthermophysicalFunctions.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libliquids.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libliquidMixture.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libsolids.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libsolidMixture.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libpdf.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libbarotropicCompressibilityModel.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/liblagrangian.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libmolecularMeasurements.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libmolecule.so' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/postCalc.o' is up to date.
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libfoamCalcFunctions.so' is up to date.

linnemann · August 20, 2009, 08:39

Hi

Have you copied or symlinked the Thirdparty-1.6 to Thirdparty-1.6.x?

This is where the 1.6.x looks for the libraries and also these lines need too be in the OpenFOAM bashrc or your own .bashrc in order for it to find the right libraries.

LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/libraries/lib:$LD_LIBRARY_PATH

linnemann · August 20, 2009, 08:51

Hi again.

I'm looking into the problem and I will post my results later.

EDIT:

Apparently it needs some header files from the Thirdparty sources so unpack them to your Thirdparty dir, just overwrite it the precompiled libraries/binary files are retained.

You also needs bison, so yum install bison

See how this works you for you, Im compiling 1.6.x now, and when that is done I will upload that to the sourceforge page with the Thirdparty sources included (except the gcc source files, those aren't needed).

I'm planing on uploading a new recompiled every month or so and when 1.6-dev is fully ported I will use that instead.

Regards

wersoe · August 20, 2009, 09:18

Hi Linneman,

I linked the Thirdparty-1.6 to 1.6.x
The LD_LIBRARY_PATH was set to 1.6
However, I changed it right now and the errors still occur.

Actually, I tried to compile the 1.6.x while waiting for the dev release.
With not so much success as you can see.

Since I am not sure, how much effort it cost to write down what you have done to compile on CentOS I asked for it. I guess, RedHat and its clones will be used quite often in scientific environment, so it would be helpful for other users to be able to compile it too. Anyway, I would write it, help you write it - after I got it all :-)

OpenFOAM is great code, anyway, the documentation and even the installation instruction is little useful to new users like me. This i quite a problem in my eyes, on the other hand I understand its quite hard to give install instruction for thousand of different system...
However, the erros is described here: http://openfoamwiki.net/index.php/Ho...mpile_OpenFOAM
but the described solution does not work...

Appreciate your help, Sören

linnemann · August 20, 2009, 09:22

To answer some of you questions.

The libraries needed for a succesfull compile in CentOS is the following

yum install gcc gcc-c++ bison

Then you need to build mpfr gmp and flex from source.

This should make you able to build gcc-4.3.3

When that is done you need to compile Qt either with Gcc-4.3.3 or the std system gcc.

when that is done you need to compile the Thirdparty and paraview

after this you should be able to compile OpenFOAM

Ive just made my life simpler and installed flex gmp mpfr ffmpeg (avi support for paraview) to the same library folder and copied the relevant libraries from Qt and VTK there to make Meshlab and engrid work, for gmesh you need to compile fltk from source. This way I dont screw my system up since I can just uncomment the line in my .bashrc again and my system wont be affected.

But I will update the sourceforge page and make it possibly for any user to do a git pull and recompile in an easier manner.

wersoe · August 20, 2009, 09:42

HI linnemann,

thanks.
I found, that the missing libraries, eg libMGridGen.so are in the ../OpenFOAM-1.6/lib but not in ../OpenFOAM-1.6.x/lib after git pull.
So, I understood it always, that .x is a complete OpenFOAM src anyway.
Now, I unpack 1.6, after that copy 1.6.x over 1.6 and compile again!?
Sounds kinda strange to me...

The full compilation including thirdparty I will try later :-) Thanks for the describtion.

Regards, Sören

linnemann · August 20, 2009, 09:52

Hi

yep .x is always src so no libMGridGen.so should be present since this is a compiled library (like a dll).

No you just need to unpack the Thirdparty-1.6-general from the official download page and unpack that into the already present Thirdparty-1.6 folder.

wersoe · August 20, 2009, 10:45

Well, thats what I understand too...
However, I copied the whole Thirdparty-1.6 from OpenCFD to the ThirdParty-1.6 from your package, but the error remains.
The first missing library is libscotch.so as you may see below.

Code:

+ decompositionMethods/Allwmake
+ wmake libso decompositionMethods
/usr/bin/ld: cannot find -lscotch
collect2: ld returned 1 exit status
make: *** [/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libdecompositionMethods.so] Fehler 1

Does it means I need to compile scotch again first?
This should be done already...

linnemann · August 20, 2009, 11:18

you could just go into the Thirdparty folder and run ./Allwmake but I think everything should be compiled since its compiling here.

wersoe · August 20, 2009, 14:16

Hi,

I now used complete new files, did the git pull, linked the Thirdparty dirs.
However, there is a problem with scotch as you can see in the output.
./Allwmake in Thirdparty brings nothing than all is up to date...

"scotchDecomp/scotchDecomp.C:72:20: error: module.h: Datei oder Verzeichnis nicht gefunden" means file not found...

Has anybody hints?

Regards, Sören

Code:

[root@PC-1775 src]# ./Allwmake 
+ wmakePrintBuild -check
same version as previous build
+ wmakeLnInclude OpenFOAM
+ wmakeLnInclude OSspecific/POSIX
+ Pstream/Allwmake
+ wmake libso dummy
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/dummy/libPstream.so' is up to date.
+ case "$WM_MPLIB" in
+ set +x

Note: ignore spurious warnings about missing mpicxx.h headers
+ WM_OPTIONS=linux64GccDPOptOPENMPI
+ wmake libso mpi
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/openmpi-1.3.3/libPstream.so' is up to date.
+ wmake libo OSspecific/POSIX
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libOSspecific.o' is up to date.
+ wmake libso OpenFOAM
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libOpenFOAM.so' is up to date.
+ wmake libso lagrangian/basic
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/liblagrangian.so' is up to date.
+ wmake libso triSurface
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libtriSurface.so' is up to date.
+ wmake libso edgeMesh
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libedgeMesh.so' is up to date.
+ wmake libso surfMesh
'/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libsurfMesh.so' is up to date.
+ decompositionMethods/Allwmake
+ wmake libso decompositionMethods
SOURCE=scotchDecomp/scotchDecomp.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-40 -I/usr/local/OpenFOAM/ThirdParty-1.6.x/scotch_5.1/src/libscotch/lnInclude -I/usr/local/OpenFOAM/ThirdParty-1.6.x/metis-5.0pre2/include -IlnInclude -I. -I/usr/local/OpenFOAM/OpenFOAM-1.6.x/src/OpenFOAM/lnInclude -I/usr/local/OpenFOAM/OpenFOAM-1.6.x/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOpt/scotchDecomp.o
scotchDecomp/scotchDecomp.C:72:20: error: module.h: Datei oder Verzeichnis nicht gefunden
scotchDecomp/scotchDecomp.C:73:20: error: common.h: Datei oder Verzeichnis nicht gefunden
scotchDecomp/scotchDecomp.C:74:20: error: scotch.h: Datei oder Verzeichnis nicht gefunden
scotchDecomp/scotchDecomp.C: In member function ‘Foam::label Foam::scotchDecomp::decompose(const Foam::List<int>&, const Foam::List<int>&, Foam::List<int>&)’:
scotchDecomp/scotchDecomp.C:136: error: ‘SCOTCH_Strat’ was not declared in this scope
scotchDecomp/scotchDecomp.C:136: error: expected `;' before ‘stradat’
scotchDecomp/scotchDecomp.C:137: error: ‘stradat’ was not declared in this scope
scotchDecomp/scotchDecomp.C:137: error: ‘SCOTCH_stratInit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:152: error: ‘SCOTCH_stratGraphMap’ was not declared in this scope
scotchDecomp/scotchDecomp.C:163: error: ‘SCOTCH_Graph’ was not declared in this scope
scotchDecomp/scotchDecomp.C:163: error: expected `;' before ‘grafdat’
scotchDecomp/scotchDecomp.C:164: error: ‘grafdat’ was not declared in this scope
scotchDecomp/scotchDecomp.C:164: error: ‘SCOTCH_graphInit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:179: error: ‘SCOTCH_graphBuild’ was not declared in this scope
scotchDecomp/scotchDecomp.C:182: error: ‘SCOTCH_graphCheck’ was not declared in this scope
scotchDecomp/scotchDecomp.C:234: error: ‘SCOTCH_Arch’ was not declared in this scope
scotchDecomp/scotchDecomp.C:234: error: expected `;' before ‘archdat’
scotchDecomp/scotchDecomp.C:235: error: ‘archdat’ was not declared in this scope
scotchDecomp/scotchDecomp.C:235: error: ‘SCOTCH_archInit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:254: error: ‘SCOTCH_archCmpltw’ was not declared in this scope
scotchDecomp/scotchDecomp.C:262: error: ‘SCOTCH_archCmplt’ was not declared in this scope
scotchDecomp/scotchDecomp.C:294: error: ‘SCOTCH_graphMap’ was not declared in this scope
scotchDecomp/scotchDecomp.C:318: error: ‘SCOTCH_graphExit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:320: error: ‘SCOTCH_stratExit’ was not declared in this scope
scotchDecomp/scotchDecomp.C:322: error: ‘SCOTCH_archExit’ was not declared in this scope
make: *** [Make/linux64GccDPOpt/scotchDecomp.o] Fehler 1
+ '[' -d /usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/openmpi-1.3.3 ']'
+ WM_OPTIONS=linux64GccDPOptOPENMPI
+ wmake libso parMetisDecomp
SOURCE=parMetisDecomp.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3  -DNoRepository -ftemplate-depth-40 -DOMPI_SKIP_MPICXX -I/usr/local/OpenFOAM/ThirdParty-1.6.x/openmpi-1.3.3/platforms/linux64GccDPOpt/include -I/usr/local/OpenFOAM/ThirdParty-1.6.x/ParMetis-3.1/ParMETISLib -I/usr/local/OpenFOAM/ThirdParty-1.6.x/ParMetis-3.1 -I../decompositionMethods/lnInclude -IlnInclude -I. -I/usr/local/OpenFOAM/OpenFOAM-1.6.x/src/OpenFOAM/lnInclude -I/usr/local/OpenFOAM/OpenFOAM-1.6.x/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64GccDPOptOPENMPI/parMetisDecomp.o
parMetisDecomp.C:41:25: error: parmetis.h: Datei oder Verzeichnis nicht gefunden
parMetisDecomp.C: In member function ‘Foam::label Foam::parMetisDecomp::decompose(Foam::Field<int>&, Foam::Field<int>&, const Foam::pointField&, Foam::Field<int>&, Foam::Field<int>&, const Foam::List<int>&, Foam::List<int>&)’:
parMetisDecomp.C:282: warning: use of old-style cast
parMetisDecomp.C:282: warning: use of old-style cast
parMetisDecomp.C:310: error: ‘ParMETIS_V3_PartGeomKway’ was not declared in this scope
make: *** [Make/linux64GccDPOptOPENMPI/parMetisDecomp.o] Fehler 1
+ wmake libso meshTools
/usr/bin/ld: cannot find -ldecompositionMethods
collect2: ld returned 1 exit status
make: *** [/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libmeshTools.so] Fehler 1

linnemann · August 20, 2009, 16:01

Hi

I'm sorry I cant help you since I am unable to reproduce the error.

have you checked manually that the files don't exists?

Have you copied the source files from the official ThirdParty onto the one I have supplied? when I installed bison and copied the sources everything was working here with regards to OpenFOAM-1.6.x compilation.

What happens if you use Allwmake from the OpenFOAM-1.6.x directory and not the src folder.

Regards

wersoe · August 25, 2009, 07:47

Hi linnemann,

first, thanks for the 1.6.x release.

In the meanwhile, I tried to compile the 1.5-dev and encountered the same errors as written above.
After a while, I found out, the the flex -c++ is not working with older version of flex. You need to use flex++ instead. Since your own compiled flex in the Thirdparty is not in the PATH, I think this causes the errors. I will try it again with adding it to PATH later this day and write about it...

One more thing, in CentOS the ncurses-devel is not installed by default, so this is a library you need to install as well for compiling OpenFOAM.

Regards, Sören

linnemann · August 25, 2009, 12:26

Hi Sören

Okay I didnt know you had the system flex installed, I've never installed it and have never added my compiled version to the PATH but maybe it locates the binaries from the libraries, just maybe.

Also try and delete the OpenFOAM bashrc and get a new one and add these to the very end this will overwrite any default installed versions of the needed binaries.

export PATH=$PATH:$WM_THIRD_PARTY_DIR/gmsh-2.3.1/bin
export PATH=$PATH:$WM_THIRD_PARTY_DIR/meshlab-1.2.1
export PATH=$PATH:$WM_THIRD_PARTY_DIR/engrid-1.0.1
export PATH=$PATH:$WM_THIRD_PARTY_DIR/libraries/bin

export LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/paraview-3.6.1/platforms/linux64Gcc/bin:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/libraries/lib:$LD_LIBRARY_PATH

With regards to ncurses I will add this to the default dependencies

Best Regards

Linnemann

piccinini · September 2, 2009, 13:16

Hello,

I've tried it but I have the following problem with Paraview:

/cluster/apps/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linux64Gcc/bin/paraview-real: error while loading shared libraries: libavformat.so.50: cannot open shared object file: No such file or directory

Should I install something else?

enGrid won't run either:

./engrid: error while loading shared libraries: libQVTK.so.5.4: cannot open shared object file: No such file or directory

linnemann · September 2, 2009, 13:23

Hi it seems that the library path is not correctly initialized,

what happens when you run.

cd $WM_THIRD_PARTY_DIR/libraries/lib

and then run

ls

do the same for

$WM_THIRD_PARTY_DIR/paraview-3.6.1/platforms/linux64Gcc/bin
Please post the output.

If there is no output something is incorrectly initialized and you could try putting these lines in you own .bashrc after the . OpenFOAM/etc.. entry

export LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/paraview-3.6.1/platforms/linux64Gcc/bin:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/libraries/lib:$LD_LIBRARY_PATH

piccinini · September 2, 2009, 13:46

The library path is correct:

# echo $WM_THIRD_PARTY_DIR
/cluster/apps/OpenFOAM/ThirdParty-1.6

I've added the paths to LD_LIBRARY_PATH after the OpenFOAM entry and then it worked. Thanks

August 20, 2009, 08:51		#24
linnemann Senior Member Niels Nielsen Join Date: Mar 2009 Location: NJ - Denmark Posts: 556 Rep Power: 27	Hi again. I'm looking into the problem and I will post my results later. EDIT: Apparently it needs some header files from the Thirdparty sources so unpack them to your Thirdparty dir, just overwrite it the precompiled libraries/binary files are retained. You also needs bison, so yum install bison See how this works you for you, Im compiling 1.6.x now, and when that is done I will upload that to the sourceforge page with the Thirdparty sources included (except the gcc source files, those aren't needed). I'm planing on uploading a new recompiled every month or so and when 1.6-dev is fully ported I will use that instead. Regards Last edited by linnemann; August 20, 2009 at 09:08.

August 20, 2009, 10:45		#29
wersoe Member Soeren Werner Join Date: Mar 2009 Location: Wädenswil, Switzerland Posts: 32 Rep Power: 17	Well, thats what I understand too... However, I copied the whole Thirdparty-1.6 from OpenCFD to the ThirdParty-1.6 from your package, but the error remains. The first missing library is libscotch.so as you may see below. Code: + decompositionMethods/Allwmake + wmake libso decompositionMethods /usr/bin/ld: cannot find -lscotch collect2: ld returned 1 exit status make: *** [/usr/local/OpenFOAM/OpenFOAM-1.6.x/lib/linux64GccDPOpt/libdecompositionMethods.so] Fehler 1 Does it means I need to compile scotch again first? This should be done already...

September 2, 2009, 13:16	Paraview and enGrid problems	#35
piccinini New Member Join Date: Mar 2009 Location: Sao Jose dos Campos, Brazil Posts: 29 Rep Power: 17	Hello, I've tried it but I have the following problem with Paraview: /cluster/apps/OpenFOAM/ThirdParty-1.6/paraview-3.6.1/platforms/linux64Gcc/bin/paraview-real: error while loading shared libraries: libavformat.so.50: cannot open shared object file: No such file or directory Should I install something else? enGrid won't run either: ./engrid: error while loading shared libraries: libQVTK.so.5.4: cannot open shared object file: No such file or directory

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August 17, 2009, 02:02		#21
7islands Super Moderator Takuya OSHIMA Join Date: Mar 2009 Location: Niigata City, Japan Posts: 518 Blog Entries: 1 Rep Power: 20	Hi Jean-Peer, Here: http://www.paraview.org/pipermail/pa...st/013278.html Takuya

August 20, 2009, 08:39		#23
linnemann Senior Member Niels Nielsen Join Date: Mar 2009 Location: NJ - Denmark Posts: 556 Rep Power: 27	Hi Have you copied or symlinked the Thirdparty-1.6 to Thirdparty-1.6.x? This is where the 1.6.x looks for the libraries and also these lines need too be in the OpenFOAM bashrc or your own .bashrc in order for it to find the right libraries. LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/libraries/lib:$LD_LIBRARY_PATH

August 20, 2009, 09:18		#25
wersoe Member Soeren Werner Join Date: Mar 2009 Location: Wädenswil, Switzerland Posts: 32 Rep Power: 17	Hi Linneman, I linked the Thirdparty-1.6 to 1.6.x The LD_LIBRARY_PATH was set to 1.6 However, I changed it right now and the errors still occur. Actually, I tried to compile the 1.6.x while waiting for the dev release. With not so much success as you can see. Since I am not sure, how much effort it cost to write down what you have done to compile on CentOS I asked for it. I guess, RedHat and its clones will be used quite often in scientific environment, so it would be helpful for other users to be able to compile it too. Anyway, I would write it, help you write it - after I got it all :-) OpenFOAM is great code, anyway, the documentation and even the installation instruction is little useful to new users like me. This i quite a problem in my eyes, on the other hand I understand its quite hard to give install instruction for thousand of different system... However, the erros is described here: http://openfoamwiki.net/index.php/Ho...mpile_OpenFOAM but the described solution does not work... Appreciate your help, Sören

August 20, 2009, 09:22		#26
linnemann Senior Member Niels Nielsen Join Date: Mar 2009 Location: NJ - Denmark Posts: 556 Rep Power: 27	To answer some of you questions. The libraries needed for a succesfull compile in CentOS is the following yum install gcc gcc-c++ bison Then you need to build mpfr gmp and flex from source. This should make you able to build gcc-4.3.3 When that is done you need to compile Qt either with Gcc-4.3.3 or the std system gcc. when that is done you need to compile the Thirdparty and paraview after this you should be able to compile OpenFOAM Ive just made my life simpler and installed flex gmp mpfr ffmpeg (avi support for paraview) to the same library folder and copied the relevant libraries from Qt and VTK there to make Meshlab and engrid work, for gmesh you need to compile fltk from source. This way I dont screw my system up since I can just uncomment the line in my .bashrc again and my system wont be affected. But I will update the sourceforge page and make it possibly for any user to do a git pull and recompile in an easier manner.

August 20, 2009, 09:42		#27
wersoe Member Soeren Werner Join Date: Mar 2009 Location: Wädenswil, Switzerland Posts: 32 Rep Power: 17	HI linnemann, thanks. I found, that the missing libraries, eg libMGridGen.so are in the ../OpenFOAM-1.6/lib but not in ../OpenFOAM-1.6.x/lib after git pull. So, I understood it always, that .x is a complete OpenFOAM src anyway. Now, I unpack 1.6, after that copy 1.6.x over 1.6 and compile again!? Sounds kinda strange to me... The full compilation including thirdparty I will try later :-) Thanks for the describtion. Regards, Sören

August 20, 2009, 09:52		#28
linnemann Senior Member Niels Nielsen Join Date: Mar 2009 Location: NJ - Denmark Posts: 556 Rep Power: 27	Hi yep .x is always src so no libMGridGen.so should be present since this is a compiled library (like a dll). No you just need to unpack the Thirdparty-1.6-general from the official download page and unpack that into the already present Thirdparty-1.6 folder.

August 20, 2009, 11:18		#30
linnemann Senior Member Niels Nielsen Join Date: Mar 2009 Location: NJ - Denmark Posts: 556 Rep Power: 27	you could just go into the Thirdparty folder and run ./Allwmake but I think everything should be compiled since its compiling here.

August 20, 2009, 16:01		#32
linnemann Senior Member Niels Nielsen Join Date: Mar 2009 Location: NJ - Denmark Posts: 556 Rep Power: 27	Hi I'm sorry I cant help you since I am unable to reproduce the error. have you checked manually that the files don't exists? Have you copied the source files from the official ThirdParty onto the one I have supplied? when I installed bison and copied the sources everything was working here with regards to OpenFOAM-1.6.x compilation. What happens if you use Allwmake from the OpenFOAM-1.6.x directory and not the src folder. Regards

August 25, 2009, 07:47		#33
wersoe Member Soeren Werner Join Date: Mar 2009 Location: Wädenswil, Switzerland Posts: 32 Rep Power: 17	Hi linnemann, first, thanks for the 1.6.x release. In the meanwhile, I tried to compile the 1.5-dev and encountered the same errors as written above. After a while, I found out, the the flex -c++ is not working with older version of flex. You need to use flex++ instead. Since your own compiled flex in the Thirdparty is not in the PATH, I think this causes the errors. I will try it again with adding it to PATH later this day and write about it... One more thing, in CentOS the ncurses-devel is not installed by default, so this is a library you need to install as well for compiling OpenFOAM. Regards, Sören

August 25, 2009, 12:26		#34
linnemann Senior Member Niels Nielsen Join Date: Mar 2009 Location: NJ - Denmark Posts: 556 Rep Power: 27	Hi Sören Okay I didnt know you had the system flex installed, I've never installed it and have never added my compiled version to the PATH but maybe it locates the binaries from the libraries, just maybe. Also try and delete the OpenFOAM bashrc and get a new one and add these to the very end this will overwrite any default installed versions of the needed binaries. export PATH=$PATH:$WM_THIRD_PARTY_DIR/gmsh-2.3.1/bin export PATH=$PATH:$WM_THIRD_PARTY_DIR/meshlab-1.2.1 export PATH=$PATH:$WM_THIRD_PARTY_DIR/engrid-1.0.1 export PATH=$PATH:$WM_THIRD_PARTY_DIR/libraries/bin export LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/paraview-3.6.1/platforms/linux64Gcc/bin:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/libraries/lib:$LD_LIBRARY_PATH With regards to ncurses I will add this to the default dependencies Best Regards Linnemann

September 2, 2009, 13:23		#36
linnemann Senior Member Niels Nielsen Join Date: Mar 2009 Location: NJ - Denmark Posts: 556 Rep Power: 27	Hi it seems that the library path is not correctly initialized, what happens when you run. cd $WM_THIRD_PARTY_DIR/libraries/lib and then run ls do the same for $WM_THIRD_PARTY_DIR/paraview-3.6.1/platforms/linux64Gcc/bin Please post the output. If there is no output something is incorrectly initialized and you could try putting these lines in you own .bashrc after the . OpenFOAM/etc.. entry export LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/paraview-3.6.1/platforms/linux64Gcc/bin:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=$WM_THIRD_PARTY_DIR/libraries/lib:$LD_LIBRARY_PATH

September 2, 2009, 13:46		#37
piccinini New Member Join Date: Mar 2009 Location: Sao Jose dos Campos, Brazil Posts: 29 Rep Power: 17	The library path is correct: # echo $WM_THIRD_PARTY_DIR /cluster/apps/OpenFOAM/ThirdParty-1.6 I've added the paths to LD_LIBRARY_PATH after the OpenFOAM entry and then it worked. Thanks