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-   -   OpenFOAM-1.6 installation on Centos5.4 x86_64 Cluster (http://www.cfd-online.com/Forums/openfoam-installation/74736-openfoam-1-6-installation-centos5-4-x86_64-cluster.html)

dhoom April 7, 2010 11:58

OpenFOAM-1.6 installation on Centos5.4 x86_64 Cluster
 
1 Attachment(s)
Hello Friends,

By quirk of fate I am now an admin on a small univ. cluster eventhough I am a newbie with Linux and Clustering.

I am trying to install OpenFOAM-1.6 on the head-node of a cluster based on Centos5.4 x86_64. The directory in NSF shared. I downloaded the 2 source files named 1) OpenFOAM-1.6.General.gtgz and 2) ThirdParty-1.6.General.gtgz .

I have changed the bashrc and settings file to include mpi as I am using NSF shared MPICH2. I am getting error during ./Allwmake and I have attached the log file for review.

Thanks,

Dhoom

gschaider April 8, 2010 05:16

Quote:

Originally Posted by dhoom (Post 253600)
Hello Friends,

By quirk of fate I am now an admin on a small univ. cluster eventhough I am a newbie with Linux and Clustering.

I am trying to install OpenFOAM-1.6 on the head-node of a cluster based on Centos5.4 x86_64. The directory in NSF shared. I downloaded the 2 source files named 1) OpenFOAM-1.6.General.gtgz and 2) ThirdParty-1.6.General.gtgz .

I have changed the bashrc and settings file to include mpi as I am using NSF shared MPICH2. I am getting error during ./Allwmake and I have attached the log file for review.

Thanks,

Dhoom

Obviously the compiler doesn't find mpio.h (don't have MPICH so I can't help you where to find it). Check the wmake/rules/YourArchitecture/mpiYourImplementation that the paths there are correct.

About the second error: strange. Which g++ are you using? The one that comes with CentOS is 4.1 (which might not work with OF 1.6) BUT you can install 4.4 from the standard-repositories (but the best guess would be to use the 4.3 that comes in ThirdParty)

Bernhard

dhoom April 8, 2010 09:53

Bernhard,

I will check the paths to mpio.h are correct. I am using the third party module I guess for g++ as I have not specified anywhere to use system compilers.

Thanks for the feedback.

dhoom April 12, 2010 02:30

1 Attachment(s)
I have changed the settings.sh option to use Openfoam compilers and it seems I am getting a libPstream.so error and also errors in the Scotch package. Please find a log file attached.

hmm... where is my Johny Walker, I need it now...

gschaider April 12, 2010 06:41

Quote:

Originally Posted by dhoom (Post 254232)
I have changed the settings.sh option to use Openfoam compilers and it seems I am getting a libPstream.so error and also errors in the Scotch package. Please find a log file attached.

hmm... where is my Johny Walker, I need it now...

I think it's rather obvious: mpich.a was not compiles -fPIC to make it reloacatable and therefor the linker refuses to link it.

Bernhard

dhoom April 14, 2010 02:21

any solutions?

Thanks,

D

gschaider April 14, 2010 12:39

Quote:

Originally Posted by dhoom (Post 254515)
any solutions?

Thanks,

D

Recompile MPICH or use the OpenMPI that comes with OF

dhoom April 15, 2010 01:31

Quote:

Originally Posted by gschaider (Post 254612)
Recompile MPICH or use the OpenMPI that comes with OF

Thanks, OK will do, do I need to recompile MPICH with any particular options, in the past I used ch3:ssm.

Dhoom

gschaider April 15, 2010 04:42

Quote:

Originally Posted by dhoom (Post 254689)
Thanks, OK will do, do I need to recompile MPICH with any particular options, in the past I used ch3:ssm.

Keep that. The thing you have to make sure is that everything is compiled with the -fPIC-option.

This is the relevant section from your log:
Code:

/usr/bin/ld: /usr/cluster/mpich2-1.2.1/lib/libmpich.a(allreduce.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC


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