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OpenFOAM-1.6 installation on Centos5.4 x86_64 Cluster

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Old   April 7, 2010, 11:58
Default OpenFOAM-1.6 installation on Centos5.4 x86_64 Cluster
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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
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Old   April 8, 2010, 05:16
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Originally Posted by dhoom View Post
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
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Old   April 8, 2010, 09:53
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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.
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Old   April 12, 2010, 02:30
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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...
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Old   April 12, 2010, 06:41
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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.

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Old   April 14, 2010, 02:21
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any solutions?

Thanks,

D
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Old   April 14, 2010, 12:39
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any solutions?

Thanks,

D
Recompile MPICH or use the OpenMPI that comes with OF
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Old   April 15, 2010, 01:31
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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.

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Old   April 15, 2010, 04:42
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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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