CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > OpenFOAM Installation

OpenFOAM 1.7.x on Fedora 13

Register Blogs Members List Search Today's Posts Mark Forums Read

Reply
 
LinkBack Thread Tools Display Modes
Old   July 19, 2010, 17:42
Default OpenFOAM 1.7.x on Fedora 13
  #1
Senior Member
 
Emanuele
Join Date: Mar 2009
Posts: 110
Rep Power: 7
nuovodna is on a distinguished road
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
nuovodna is offline   Reply With Quote

Old   July 19, 2010, 21:22
Default
  #2
New Member
 
Martin/Run DU
Join Date: Mar 2009
Location: Hong Kong
Posts: 25
Rep Power: 7
chnrdu is on a distinguished road
Send a message via Skype™ to chnrdu
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?
chnrdu is offline   Reply With Quote

Old   July 20, 2010, 07:45
Default
  #3
Senior Member
 
Emanuele
Join Date: Mar 2009
Posts: 110
Rep Power: 7
nuovodna is on a distinguished road
It works!! Thanks

It should be great to set up a script that add the line on all files interested by the issue
nuovodna is offline   Reply With Quote

Old   July 20, 2010, 13:22
Unhappy Question
  #4
New Member
 
Bryan Lewis
Join Date: Jul 2010
Posts: 5
Rep Power: 6
lewisb2 is on a distinguished road
Where exaclty are the files that need to be changed?
lewisb2 is offline   Reply With Quote

Old   July 20, 2010, 13:28
Default
  #5
Senior Member
 
Emanuele
Join Date: Mar 2009
Posts: 110
Rep Power: 7
nuovodna is on a distinguished road
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
nuovodna is offline   Reply With Quote

Old   July 20, 2010, 17:45
Default
  #6
New Member
 
Ashish Nedungadi
Join Date: Mar 2009
Location: Laurel, Maryland, USA
Posts: 13
Rep Power: 7
ashishnedungadi is on a distinguished road
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
ashishnedungadi is offline   Reply With Quote

Old   July 20, 2010, 17:56
Default
  #7
Senior Member
 
Emanuele
Join Date: Mar 2009
Posts: 110
Rep Power: 7
nuovodna is on a distinguished road
Following this guide (made by chnrdu) i have only libPstream.so problem

http://www.idurun.com/?p=544
nuovodna is offline   Reply With Quote

Old   July 29, 2010, 08:26
Default
  #8
Senior Member
 
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 13
l_r_mcglashan will become famous soon enough
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
__________________
Laurence R. McGlashan :: Website
l_r_mcglashan is offline   Reply With Quote

Old   July 29, 2010, 10:28
Default
  #9
Senior Member
 
Emanuele
Join Date: Mar 2009
Posts: 110
Rep Power: 7
nuovodna is on a distinguished road
Thanks!! Great tip!!
nuovodna is offline   Reply With Quote

Old   July 30, 2010, 17:43
Default
  #10
New Member
 
Craig Miller
Join Date: Jul 2010
Posts: 1
Rep Power: 0
tawhiri is on a distinguished road
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.
tawhiri is offline   Reply With Quote

Old   July 30, 2010, 19:18
Default
  #11
Senior Member
 
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 13
l_r_mcglashan will become famous soon enough
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?
__________________
Laurence R. McGlashan :: Website
l_r_mcglashan is offline   Reply With Quote

Old   August 6, 2010, 09:35
Default
  #12
Senior Member
 
Aurelien Thinat
Join Date: Jul 2010
Posts: 152
Rep Power: 6
Aurelien Thinat is on a distinguished road
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:pen(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.
Aurelien Thinat is offline   Reply With Quote

Old   August 11, 2010, 05:36
Default
  #13
Senior Member
 
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 13
l_r_mcglashan will become famous soon enough
Can you 'locate zlib'? If it's not on your system, then install zlib; either ask whoever admins that cluster or install it locally.
__________________
Laurence R. McGlashan :: Website
l_r_mcglashan is offline   Reply With Quote

Old   August 11, 2010, 06:04
Default
  #14
Senior Member
 
Aurelien Thinat
Join Date: Jul 2010
Posts: 152
Rep Power: 6
Aurelien Thinat is on a distinguished road
Thank you Laurence, I already fixed this problem. Anyway you are right, it was the problem.
Aurelien Thinat is offline   Reply With Quote

Old   August 19, 2010, 10:00
Default Another Problem in compiling OF-1.7.0 in Fedora 13
  #15
New Member
 
Join Date: Aug 2010
Posts: 2
Rep Power: 0
jaber_6010 is on a distinguished road
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
jaber_6010 is offline   Reply With Quote

Old   August 19, 2010, 12:00
Default
  #16
Senior Member
 
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 13
l_r_mcglashan will become famous soon enough
The finiteVolume library probably hasn't been built. Go to src/finiteVolume and try wmake libso. Post the error up here.
__________________
Laurence R. McGlashan :: Website
l_r_mcglashan is offline   Reply With Quote

Old   August 19, 2010, 15:08
Default
  #17
New Member
 
Join Date: Aug 2010
Posts: 2
Rep Power: 0
jaber_6010 is on a distinguished road
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?
jaber_6010 is offline   Reply With Quote

Old   August 20, 2010, 10:48
Default
  #18
Senior Member
 
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 13
l_r_mcglashan will become famous soon enough
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.
__________________
Laurence R. McGlashan :: Website
l_r_mcglashan is offline   Reply With Quote

Old   September 2, 2010, 09:23
Default
  #19
Senior Member
 
Laurence R. McGlashan
Join Date: Mar 2009
Posts: 370
Rep Power: 13
l_r_mcglashan will become famous soon enough
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
__________________
Laurence R. McGlashan :: Website
l_r_mcglashan is offline   Reply With Quote

Old   October 9, 2010, 06:54
Default OF 1.7.x in Fedora 14
  #20
Senior Member
 
Emanuele
Join Date: Mar 2009
Posts: 110
Rep Power: 7
nuovodna is on a distinguished road
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

Last edited by nuovodna; October 9, 2010 at 07:22. Reason: problem solved
nuovodna is offline   Reply With Quote

Reply

Tags
1.7.x, fedora, installation

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
install openfoam in fedora Ahmed Khattab OpenFOAM Installation 32 September 23, 2011 12:11
Qt installation in Fedora for OpenFOAM......Required Urgently...... devesh.baghel OpenFOAM 1 November 17, 2009 10:08
Openfoam Installtion on Linux Fedora devesh.baghel OpenFOAM 1 November 16, 2009 18:43
Installation of OpenFOAM on Fedora 11 jits_aps90 OpenFOAM Installation 0 August 20, 2009 03:23
Modified OpenFOAM Forum Structure and New Mailing-List pete Site News & Announcements 0 June 29, 2009 06:56


All times are GMT -4. The time now is 15:41.