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Building OpenFoAm on SGI Altix 64bits

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Old   June 12, 2006, 11:25
Default Hello, Up to now I have run
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anne dejoan
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Hello,

Up to now I have runned OpenFoam on
my PC linux and only used the binary packages of OpenFoam.

I now want to use OpenFoam on a more performant
SGI Altix 3700, RedHat 7.2, 64 bits cluster and
I need help (I am quite bad in the installing stuff ...)

I have done the first steps, which are to download
the sources and read the README file ...

Here are the following points I would like to be helped:

1) it is said that a gcc version should be installed in the WM_project directory: is it compulsory to use a gcc version in WM_project, and
not the already installed version ??

The versions already available on the cluster are the following:
Can I use one of them, and if yes, how to correctely declare the environment variables ?
-----------
dot intel-mkl-7.2 ncarg.4.3.1.Intel
gcc-3.2.2 mm5.3.6.0 ncarg.4.4.1.Intel
hdf-4.1r5 mm5.3.6.1 netcdf-3.5.0
hdf-4.2 module-cvs null
histx-1.1 module-info pvm3
intel-compilers.7.1.014 modules sgi-mpt-1.8.1
intel-compilers.8.0 nag_smp sgi-mpt-1.9.1
intel-compilers.8.1 nag_smp-8.1 sgi-scsl-1.5.0.0
intel-compilers.9.0 nagfl totalview.6.5.0-2
intel-ipp-3.0 nagfl90 use.own
intel-mkl-6.0 ncarg.4.3.1
------------

2) I want to use MPI and not LAM.
The version MPI installed on the SGI Altix is:

sgi-mpt-1.7.1

Here again, I have to compile and declare the MPI
environment in ./OpenFoam/bashrc (The SHELL used
is bash) and /OpenFoam/.bashrc.

I had tried to do it on a PC cluster but I
finally was not successfull in making it work and
would like more explicit information.

3) The WM_64 variable has to be declared "on" before
building OpenFoam or can it be done after ?

I will really apreciate some help

Anne
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Old   June 12, 2006, 12:17
Default 1) it is said that a gcc versi
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stefan
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1) it is said that a gcc version should be installed in the WM_project directory: is it compulsory to use a gcc version in WM_project, and
not the already installed version ??

It is not compulsatory but it is strongly recommended to use the compiler shipped with OpenFOAM (current version gcc4.1)!

btw: according to the release notes you should be able to use the Intel C++ 9.0 compiler

2) I want to use MPI and not LAM.

Same thing, use the MPI versions which are delivered with OpenFOAM. For unsupported mpi implementations you have to dig yourself through the installation.

3) The WM_64 variable has to be declared "on" before
building OpenFoam or can it be done after ?

You have to switch on this flag and then rebuild OpenFOAM.
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Old   June 13, 2006, 03:13
Default Thank you Stefan for your answ
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anne dejoan
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Thank you Stefan for your answer,

just one question:
For the MPI, could you let me know
which is the version well supported by MPI ?

Also, do you know how
well to declare the MPI varibles environment ++in files .OpenFoam/bashrc and /openFoan/bashrc


Thanks you,

Anne
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Old   June 13, 2006, 03:45
Default OpenFOAM is shipped with OpenM
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OpenFOAM is shipped with OpenMPI and LAM support (but the current release is compiled with lam-MPI). The choice is controlled by the setting of the $WM_MPLIB environment variable.
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Old   June 13, 2006, 05:27
Default Any version of MPI is supporte
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Mattijs Janssens
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Any version of MPI is supported with a little bit of effort. All it takes is a recompilation of the libPstream library.

Easiest way:
- make sure that $WM_MPLIB is set to MPI. Change the .OpenFOAM-1.3/bashrc file to do so.
- cd $FOAM_SRC/Pstream/mpi
- wclean
- wmake libso

See what include files and link libraries it uses and change the compilation and link flags in $WM_DIR/rules/xxx/mplibMPI until it does the right thing.
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Old   June 13, 2006, 07:45
Default Hello Mattis, I have a ques
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anne dejoan
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Hello Mattis,

I have a question about the compiler gcc.
I wanted to build the version ggc4 in the $WM_project but it appears to me a little complicated. Also, I would prefer to
use the c++ compilators already installed on the
cluster, as far as it is possible.

Stefan, and I also saw it on the forum, mentioned that the intel-compilers.9. could be used.

It is the case, could you let me know where I have to specify the variables of intel compiler so that
the installation building of OpenFoam be OK,

Thanks You,

Anne
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Old   June 13, 2006, 11:17
Default Anne, the compilation of gc
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stefan
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Anne,

the compilation of gcc is pretty straighforward job. If you are not familiar with these things please consult the following webpages form the OpenFOAM-Wiki:
http://openfoamwiki.net/index.php/Howto_compile_O penFOAM#Compiling_and_installing_GNU_Gcc

The intel compiler 9 is definitly supported by FOAM! The choice of compiler is controlled by the setting of the $WM_COMPILER and $WM_COMPILER_ARCH environment variables.

I think you should have a look at the release notes, a lot of your questions are answered there!

cheers
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Old   June 14, 2006, 05:09
Default Thanks you stefan ... Indee
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anne dejoan
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Thanks you stefan ...

Indeed, I forgot to look at the OpenFoam kiwi,
(well, I become easily lost in som many
informations as well )

But, anyway,

I thank you a lot and next I will try to keep
patience in looking at the forum and wiki ,

anne
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Old   June 15, 2006, 09:27
Default Hello again, I have noew do
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anne dejoan
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Hello again,

I have noew downloaded all the packages and follow the
wiki instructions for the biuntils and gcc4.1.0 installation.

The full installation of biutils is apparently OK,
I ahve the good pointer when I tape "which ld",
in my case: ~/OpenFOAM/linuxSGI64/binutils-2.16.1/bin/ld

However, when building gcc 4.1.0 I have the
following error after having executed:

make bootstrap:

---------------------------------------
libgcc/./fde-glibc_s.o libgcc/./unwind-ia64_s.o -lc && rm -f ./libunwind.so && if [ -f ./libunwind.so.7 ]; then mv -f ./libunwind.so.7 ./libunwind.so.7.backup; else true; fi && mv ./libunwind.so.7.tmp ./libunwind.so.7 && ln -s libunwind.so.7 ./libunwind.so
/lib/libc.so.6.1: undefined reference to `_dl_loaded@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_map_object@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_out_of_memory@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_lookup_address@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_dst_substitute@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_clktck@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_lookup_versioned_symbol@GLIBC_2.2'/lib/libc.so.6.1: undefined reference to `_dl_fpu_control@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_start_profile@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_origin_path@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_unload_cache@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_lookup_symbol@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_map_object_deps@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_argv@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_check_map_versions@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `__libc_stack_end@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_debug_mask@GLIBC_2.2.3'
/lib/libc.so.6.1: undefined reference to `_dl_load_lock@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_init_all_dirs@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_signal_error@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_platformlen@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_mcount@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_initial_searchlist@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_global_scope_alloc@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_debug_printf@GLIBC_2.2.3'
/lib/libc.so.6.1: undefined reference to `_dl_lazy@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_profile@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_symbol_address@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_init@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_profile_map@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `__libc_enable_secure@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_lookup_symbol_skip@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_debug_state@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_all_dirs@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_catch_error@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_nloaded@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_pagesize@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_unmap@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_r_debug@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_profile_output@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_relocate_object@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_dst_count@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_lookup_versioned_symbol_skip@GLIBC_2.2'
/lib/libc.so.6.1: undefined reference to `_dl_main_searchlist@GLIBC_2.2'
collect2: ld returned 1 exit status
make[3]: *** [libunwind.so] Error 1
make[3]: Leaving directory `/disco06/c_fosiles/u5303/OpenFOAM/linuxSGI64/tmp/gcc-4.1.0/gcc-4.1.0-obj/gcc'
make[2]: *** [libgcc.a] Error 2
make[2]: Leaving directory `/disco06/c_fosiles/u5303/OpenFOAM/linuxSGI64/tmp/gcc-4.1.0/gcc-4.1.0-obj/gcc'
make[1]: *** [stage1_build] Error 2
make[1]: Leaving directory `/disco06/c_fosiles/u5303/OpenFOAM/linuxSGI64/tmp/gcc-4.1.0/gcc-4.1.0-obj/gcc'
make: *** [bootstrap] Error 2

------------------------------------


I know I ask a lot, but I am quite lost,
so I can get some help, thanks you


Anne
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