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-   -   OpenFOAM 1.7.x on Fedora 13 (http://www.cfd-online.com/Forums/openfoam-installation/78360-openfoam-1-7-x-fedora-13-a.html)

nuovodna July 19, 2010 17:42

OpenFOAM 1.7.x on Fedora 13
 
Hi, i m trying to compile OF 1.7.x but i have some problems.

This is the first of error on output


-lfiniteVolume -lOpenFOAM -liberty -ldl -lm -o /home/sheldon/OpenFOAM/OpenFOAM-1.7.x/applications/bin/linux64GccDPOpt/potentialFoam
/usr/bin/ld: Make/linux64GccDPOpt/potentialFoam.o: undefined reference to symbol 'Foam::OPstream::write(Foam::Pstream::commsTypes, int, char const*, long)'
/usr/bin/ld: note: 'Foam::OPstream::write(Foam::Pstream::commsTypes, int, char const*, long)' is defined in DSO /home/sheldon/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libPstream.so so try adding it to the linker command line
/home/sheldon/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/openmpi-1.4.1/libPstream.so: could not read symbols: Invalid operation
collect2: ld returned 1 exit status
make[2]: *** [/home/sheldon/OpenFOAM/OpenFOAM-1.7.x/applications/bin/linux64GccDPOpt/potentialFoam] Error 1
make[2]: Leaving directory `/home/sheldon/OpenFOAM/OpenFOAM-1.7.x/applications/solvers/basic/potentialFoam'
make[1]: *** [potentialFoam] Error 2

chnrdu July 19, 2010 21:22

Please add the line to the EXE_LIBS option in the file ./Make/options in the solver directory.

$(FOAM_MPI_LIBBIN)/libPstream.so

and this option should be

EXE_LIBS = -lfiniteVolume \
$(FOAM_MPI_LIBBIN)/libPstream.so


then remake it.

Some other errors like this should be edit the options file like the above.

Because the DSO link library should be declared explicitly in Fedora 13.

Does any one have other solutions?

nuovodna July 20, 2010 07:45

It works!! Thanks

It should be great to set up a script that add the line on all files interested by the issue

lewisb2 July 20, 2010 13:22

Question
 
Where exaclty are the files that need to be changed?

nuovodna July 20, 2010 13:28

I guess they are in applications/solvers directories

~/OpenFOAM/OpenFOAM-1.7.x/applications/solvers/*/*/Make/options

Example:

~/OpenFOAM/OpenFOAM-1.7.x/applications/solvers/compressible/sonicFoam/Make/options

ashishnedungadi July 20, 2010 17:45

Is the libPstream.so the only error you get? I am trying to compile on Fedora 13 and I get many, many complaints about libCompressibleTurbulenceModel , and libIncompressibleTurbulenceModel, etc. etc.

I don't think this is so simple to find all the places where the LINK_EXE needs to be changed.

Does anyone know a better fix for this? It is a Fedora 13 issue. Anyone else running across this problem?

Thanks!

Ashish

nuovodna July 20, 2010 17:56

Following this guide (made by chnrdu) i have only libPstream.so problem

http://www.idurun.com/?p=544

l_r_mcglashan July 29, 2010 08:26

I found it easier to just edit the wmake/rules/linux64Gcc/general file than edit all the options files:

Code:

PROJECT_LIBS = -l$(WM_PROJECT) -liberty -ldl $(FOAM_MPI_LIBBIN)/libPstream.so

nuovodna July 29, 2010 10:28

Thanks!! Great tip!!

tawhiri July 30, 2010 17:43

Following on from Laurence's post, the other libraries that gave me problems when trying to compile openFOAM 1.7.0 on Fedora 13 were libcompressibleTurbulenceModel.so, libincompressibleTurbulenceModel.so, and libmeshTools.so.

The fix was to also add these to the wmake/rules/linuxGcc/general file, as per Laurence's post, using $(FOAM_LIBBIN)/libcompressibleTurbulenceModel.so, etc.

l_r_mcglashan July 30, 2010 19:18

I never had problems with those libraries. Can you post the error messages that they generated up? Was it the git repository or the source packs?

Aurelien Thinat August 6, 2010 09:35

Hi everybody,

I have to install OF 1.7 on a cluster running with red hat. I have a problem with the "zlib" library.

When I'm running the command "wmake libso OpenFOAM" I get :

Quote:

SOURCE=db/IOstreams/IOstreams/IOstream.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/IOstream.o
SOURCE=db/IOstreams/IOstreams/Istream.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/Istream.o
SOURCE=db/IOstreams/IOstreams/Ostream.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/Ostream.o
SOURCE=db/IOstreams/Sstreams/ISstream.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/ISstream.o
SOURCE=db/IOstreams/Sstreams/OSstream.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/OSstream.o
SOURCE=db/IOstreams/Sstreams/SstreamsPrint.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/SstreamsPrint.o
SOURCE=db/IOstreams/Sstreams/readHexLabel.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/readHexLabel.o
SOURCE=db/IOstreams/Sstreams/prefixOSstream.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/prefixOSstream.o
SOURCE=db/IOstreams/gzstream/gzstream.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/home_crash/thinata/OpenFOAM/ThirdParty-1.7.0/zlib-1.2.3 -IlnInclude -I. -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home_crash/thinata/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/gzstream.o
In file included from db/IOstreams/gzstream/gzstream.C:29:
db/IOstreams/gzstream/gzstream.h:35:18: error: zlib.h: No such file or directory
In file included from db/IOstreams/gzstream/gzstream.C:29:
db/IOstreams/gzstream/gzstream.h:62: error: ‘gzFile’ does not name a type
db/IOstreams/gzstream/gzstream.C: In member function ‘gzstreambuf* gzstreambuf::open(const char*, int)’:
db/IOstreams/gzstream/gzstream.C:61: error: ‘file’ was not declared in this scope
db/IOstreams/gzstream/gzstream.C:61: error: ‘gzopen’ was not declared in this scope
db/IOstreams/gzstream/gzstream.C: In member function ‘gzstreambuf* gzstreambuf::close()’:
db/IOstreams/gzstream/gzstream.C:72: error: ‘file’ was not declared in this scope
db/IOstreams/gzstream/gzstream.C:72: error: ‘gzclose’ was not declared in this scope
db/IOstreams/gzstream/gzstream.C:72: error: ‘Z_OK’ was not declared in this scope
db/IOstreams/gzstream/gzstream.C: In member function ‘virtual int gzstreambuf::underflow()’:
db/IOstreams/gzstream/gzstream.C:90: error: ‘file’ was not declared in this scope
db/IOstreams/gzstream/gzstream.C:90: error: ‘gzread’ was not declared in this scope
db/IOstreams/gzstream/gzstream.C: In member function ‘int gzstreambuf::flush_buffer()’:
db/IOstreams/gzstream/gzstream.C:107: error: ‘file’ was not declared in this scope
db/IOstreams/gzstream/gzstream.C:107: error: ‘gzwrite’ was not declared in this scope
make: *** [Make/linux64GccDPOpt/gzstream.o] Error 1
Does anyone have any idea ? Thank you for your help.

l_r_mcglashan August 11, 2010 05:36

Can you 'locate zlib'? If it's not on your system, then install zlib; either ask whoever admins that cluster or install it locally.

Aurelien Thinat August 11, 2010 06:04

Thank you Laurence, I already fixed this problem. Anyway you are right, it was the problem.

jaber_6010 August 19, 2010 10:00

Another Problem in compiling OF-1.7.0 in Fedora 13
 
Hi
I get errors when compiling OF-1.7.0 in Fedora 13.
I have all required tools to proceed to the installation and already set the environment variables
when I run:
Code:

wmake ./applications/solvers/basic/laplacianFoam/
I get the following:
Code:

g++ -m32 -Dlinux -DWM_DP -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -O3  -DNoRepository -ftemplate-depth-40 -I/home/jaber/OpenFOAM/OpenFOAM-1.7.0/src/finiteVolume/lnInclude -IlnInclude -I. -I/home/jaber/OpenFOAM/OpenFOAM-1.7.0/src/OpenFOAM/lnInclude -I/home/jaber/OpenFOAM/OpenFOAM-1.7.0/src/OSspecific/POSIX/lnInclude  -fPIC Make/linuxGccDPOpt/laplacianFoam.o -L/home/jaber/OpenFOAM/OpenFOAM-1.7.0/lib/linuxGccDPOpt \
        -lfiniteVolume -lOpenFOAM -liberty -ldl /home/jaber/OpenFOAM/OpenFOAM-1.7.0/lib/linuxGccDPOpt/openmpi-1.4.1/libPstream.so  -lm -o /home/jaber/OpenFOAM/OpenFOAM-1.7.0/applications/bin/linuxGccDPOpt/laplacianFoam
/usr/bin/ld: cannot find -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/home/jaber/OpenFOAM/OpenFOAM-1.7.0/applications/bin/linuxGccDPOpt/laplacianFoam] Error 1


I already included the suggestion of Laurence. I alsa set the environment variables.

Any ideas?

Many thanks,
Jaber

l_r_mcglashan August 19, 2010 12:00

The finiteVolume library probably hasn't been built. Go to src/finiteVolume and try wmake libso. Post the error up here.

jaber_6010 August 19, 2010 15:08

Thank you Laurence
I tried your idea and this is the error I get after a long compilation output which I can not include here:
Code:

/usr/bin/ld: cannot find -ltriSurface
collect2: ld returned 1 exit status
make: *** [/home/jaber/OpenFOAM/OpenFOAM-1.7.0/lib/linuxGccDPOpt/libfiniteVolume.so] Error 1

By the way, the compilation does last a long time, more than one hour I would say. Is that normal?

l_r_mcglashan August 20, 2010 10:48

Yes. You can speed it up by running it on multiple processors if you have them by setting the environment variable WM_NCOMPPROCS to however many processors you have.

Your compilation is failing very early. The start is like:

'/home/userspace/lrm29/OpenFOAM/OpenFOAM-1.7.x/lib/linux64GccDPOpt/dummy/libPstream.so' is up to date.

Note: ignore spurious warnings about missing mpicxx.h headers
/openmpi-system/libPstream.so' is up to date.
/libOSspecific.o' is up to date.
/libOpenFOAM.so' is up to date.
/liblagrangian.so' is up to date.
/libtriSurface.so' is up to date.

Pipe Allwmake to a file and grep for the error.

l_r_mcglashan September 2, 2010 09:23

For everyone's information, this Fedora Gcc issue has been fixed in the Git repository of OpenFOAM:

http://www.openfoam.com/bugs/ See Issue 15

and

http://lrm29.github.com/openfoam/fed...sue-fixed.html

nuovodna October 9, 2010 06:54

OF 1.7.x in Fedora 14
 
Hi, i m compiling OF 1.7.x on Fedora 14 and everything work fine except the genericPatchFields part.

I have this error:
http://pastebin.com/40G1CpCD

Gcc version:
Name : gcc
Arch : x86_64
Version : 4.5.1
Release : 4.fc14

EDIT: solved deleting and renewing the ThirdyParty package


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