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Compilation OpenFOAM 2.2.1 on BG/Q

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Old   October 14, 2013, 07:32
Default Compilation OpenFOAM 2.2.1 on BG/Q
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Vincent Keller
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Hi all,

I face a problem that I don't understand in order to compile OpenFOAM 2.2.1 on a BG/Q using the GCC suite (ver 4.4.7).

- the libraries have been (cross-)compiled (+Thirdpartypack). I created the special wmake rules + setting-sh + bashrc files in order to have the right paths to the BG/Q compilers :

Code:
 [vince@bluegeneq lib]$ pwd
/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/platforms/linuxBGQGccBGDPOpt/lib
[vince@bluegeneq lib]$ ll
total 207872
drwxr-xr-x 2 vince vince-group 4096 9 oct 15:50 dummy
-rwxr-xr-x 1 vince vince-group 2624095 9 oct 16:38 libautoMesh.so
-rwxr-xr-x 1 vince vince-group 337611 9 oct 16:20 libbarotropicCompressibilityModel.so
(...)
[vince@bluegeneq lib]$
and I think in the right way:
Code:
[vince@bluegeneq lib]$ file libautoMesh.so
libautoMesh.so: ELF 64-bit MSB shared object, 64-bit PowerPC or cisco 7500, version 1 (SYSV), dynamically linked, not stripped
[vince@bluegeneq lib]$
- I am not able to produce any executable against these libraries. The linking fail with a lib not found error (I only copy paste the first autoRefineMesh call):
Code:
[vince@bluegeneq autoRefineMesh]$ pwd
/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/applications/utilities/mesh/advanced/autoRefineMesh
[vince@bluegeneq autoRefineMesh]$ mpicxx -I/usr/include -DlinuxBGQ -DWM_DP -O3 -DNoRepository -I/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/src/dynamicMesh/lnInclude -I/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/src/meshTools/lnInclude -I/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/src/triSurface/lnInclude -I/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/src/lagrangian/basic/lnInclude -IlnInclude -I. -I/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/src/OpenFOAM/lnInclude -I/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/src/OSspecific/POSIX/lnInclude -Xlinker --add-needed -Xlinker -z -Xlinker nodefs Make/linuxBGQGccBGDPOpt/autoRefineMesh.o -L/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/platforms/linuxBGQGccBGDPOpt/lib -ldynamicMesh -lmeshTools -ltriSurface -llagrangian -lOpenFOAM -ldl -lm -o /bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/platforms/linuxBGQGccBGDPOpt/bin/autoRefineMesh
/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/bin/ld: cannot find -ldynamicMesh
/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/bin/ld: cannot find -lmeshTools
/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/bin/ld: cannot find -ltriSurface
/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/bin/ld: cannot find -llagrangian
/bgsys/drivers/toolchain/V1R2M1_base/gnu-linux/lib/gcc/powerpc64-bgq-linux/4.4.6/../../../../powerpc64-bgq-linux/bin/ld: cannot find -lOpenFOAM
collect2: ld a retourné 1 code d'état d'exécution
My LD_LIBRARY_PATH contains the right path to the libs:
Code:
[vince@bluegeneq autoRefineMesh]$ echo $LD_LIBRARY_PATH
/bgscratch/vince/OpenFOAM/ThirdParty-2.2.1-GNU/platforms/linuxBGQGccBG/gperftools-svn/lib:/bgscratch/vince/OpenFOAM/ThirdParty-2.2.1-GNU/platforms/linuxBGQGccBG/paraview-3.12.0/lib/paraview-3.12:/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/platforms/linuxBGQGccBGDPOpt/lib/mpi:/bgscratch/vince/OpenFOAM/ThirdParty-2.2.1-GNU/platforms/linuxBGQGccBGDPOpt/lib/mpi:/bgsys/drivers/ppcfloor/comm/lib:/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/platforms/linuxBGQGccBGDPOpt/lib:/bgscratch/vince/OpenFOAM/ThirdParty-2.2.1-GNU/platforms/linuxBGQGccBGDPOpt/lib:/bgscratch/vince/OpenFOAM/OpenFOAM-2.2.1-GNU/platforms/linuxBGQGccBGDPOpt/lib/dummy:/home/vince/scratch/bgq_soft_releases/hdf5-release/lib:/bgsys/local/zlib/1.2.7/lib:/home/vince/scratch/bgq_soft_releases/szlib-release/lib:/home/vince/scratch/bgq_soft_releases/netcdf-release/lib
Do you have any idea ? Do I forgot something important ?

Kind regards
Vince

Last edited by wyldckat; October 14, 2013 at 16:24. Reason: Added [CODE][/CODE]
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Old   October 14, 2013, 16:29
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Bruno Santos
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Greetings Vince and welcome to the forum!

Problem is that OpenFOAM 2.2 will only build with GCC 4.5 and above: http://www.openfoam.org/download/source.php#x6-32000 (section "Checking the System")
Quote:
In particular your system will need to include a recent version of a C++ compiler. Compilation has been tested with the following compilers and versions:
  • GCC: 4.5.0 and above
  • LLVM Clang: 3.1
  • Intel ICC: 12.1.0 and 13.1.0
As for having building problems with OpenFOAM, usually the first errors tell all of the story as to why it's not building. Therefore, to more easily keep track of such errors, run Allwmake like this:
Code:
./Allwmake > make.log 2>&1
Then check the file "make.log" when it finishes and search for the first occurrence of a build error. That will tell the whole story. And most likely, you'll find this problem:
Quote:
Originally Posted by Ohbuchi View Post
Code:
primitives/triad/triad.C:36: error: expected initializer before '<' token
primitives/triad/triad.C:39: error: expected initializer before '<' token
Which is due to using GCC 4.4.

Best regards,
Bruno
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Old   October 15, 2013, 04:11
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Vincent Keller
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Dear Bruno,

Many thanks for the reply. Sorry to haven't see it....

I'll check with our sysadmins if it is possible to upgrade the gcc suite to 4.5 and come back here.

(I must admit that I modify the sources in order to be compiled with 4.5 and face a new problem at linking)

Kind regards
Vince
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Old   October 30, 2015, 12:52
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Haomin Yuan
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Hi, Vincent,

I am not sure if you have solved your problem or not. I am quite new to HPC and BGQ system. But I need to compile OpenFOAM on BGQ system now.

I know I should change some settings in openfoam source code. But could you provide me more detail about how to do it?
Thanks.
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Old   October 30, 2015, 16:47
Default compile openfoam on BG/Q architecture
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Haomin Yuan
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Hi, foamers,

I am recently need to run openfoam on a BGQ system. However, in order to compile openfoam, several settings should be changed. But I really have no idea where and what to change.

If anyone of you have experience on this, please let me know.
Thanks in advance.
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Old   October 31, 2015, 08:06
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Bruno Santos
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Quick answer: As far as I know, IBM has a support section for their supercomputers. I say this due to two reasons:
  1. This post from 2010:
    Quote:
    Originally Posted by matteoL View Post
    thanks to the support of a person at IBM working on openFoam on Bluegene, I managed to install it correctly (i.e. two version, one 32 bit for the nodes, one 64 bit for the cluster..).
  2. This recent bug report: http://www.openfoam.org/mantisbt/view.php?id=1846 - if you take a look at the person who placed and attributed the bounty, this person seems to work at/for IBM: https://www.bountysource.com/people/20899-edelsohn - and seems responsible for making sure software is building with their platforms.
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