Install several versions and compile with Salome and Syrthes

[zihenwuming]

Hi everyone,
I'm totally new for Linux and Code Saturne, my system is Ubuntu 14.04 LTS, and I'm trying to install Salome, Code Saturne and Syrthes, and compile them together. However there are so many tutorials, each one is different and some really a little confuse me, it's really hard to find one to do all.
Now I'v installed :
----3 times Salomes, one from Wizard (7.4.0), one from universal binary(7.4.0) and one from Ubuntu Software Center(Salome kernel6.5.0-7)
----Code Saturne from Ubuntu Software Center (3.2.1-1build1)
----And several pre-required packages separately.
I know the situation seems exaggerated and it's really too complex, unnecessary and a waste of the computer space. (I'm really ignorant of Linux)
So could anyone tell me how to uninstall the useless ones and re-install the useful ones and a concise way to compile them together ?
Thank you very much.

[Yvan Fournier]

Hello,

For the pre-required software, I would stick to that from Ubuntu (except for PT-Scotch, which has a buggy build, or at least is built with incompatible options, so I you want to use it, build it with the options recommended in the Code_Saturne installation manual).

Salome 6.5 is obsolete, so I would get rid of that. Between the universal binary or the Wizard version, I have no preference (maybe people on the salome-platform.org forum could recommend one over the other).

Code Saturne 3.2 is obsolete, and not supported anymore, so I recommend installing 4.0 beta (or 3.0 for an older, but fully validated long-term support version).

A common packaging is in the works, but for now, install Salome first, then see the Code_Saturne install documentation (or older threads on this forum) to install Code_Saturne with Salome support (basically, adding --with-salome=<path_to_salome_directory> to Code_Saturne's configure command).

Regards,

Yvan

[zihenwuming]

Thank you. Now the question is, do I need to uninstall all the things that I've installed ? And for the packages that pre-required, as I've installed several times, is it ok to have them repetitively ?

Kindly regardness,

Wei

Hello,

For the pre-required software, I would stick to that from Ubuntu (except for PT-Scotch, which has a buggy build, or at least is built with incompatible options, so I you want to use it, build it with the options recommended in the Code_Saturne installation manual).

Salome 6.5 is obsolete, so I would get rid of that. Between the universal binary or the Wizard version, I have no preference (maybe people on the salome-platform.org forum could recommend one over the other).

Code Saturne 3.2 is obsolete, and not supported anymore, so I recommend installing 4.0 beta (or 3.0 for an older, but fully validated long-term support version).

A common packaging is in the works, but for now, install Salome first, then see the Code_Saturne install documentation (or older threads on this forum) to install Code_Saturne with Salome support (basically, adding --with-salome=<path_to_salome_directory> to Code_Saturne's configure command).

Regards,

Yvan

[zihenwuming]

Hi I just did the configure for Code_Saturne with

Code: Select all

>..//..//code_saturne-4.0-beta/configure \
> --prefix=/home/wei/code_saturne/saturne_build \
> --with-libxml2=/home/wei/salome/Salome-V7_4_0-LGPL-x86_64/prerequisites/Libxml2_290 \
> --with-metis=/home/wei/salome/Salome-V7_4_0-LGPL-x86_64/prerequisites/Metis_40 \
> --with-scotch=/home/wei/salome/Salome-V7_4_0-LGPL-x86_64/prerequisites/Scotch_5111 \
> --with-hdf5=/home/wei/salome/Salome-V7_4_0-LGPL-x86_64/prerequisites/Hdf5_1810 \
> --with-cgns=/home/wei/salome/Salome-V7_4_0-LGPL-x86_64/prerequisites/Cgnslib_3134 \
> --with-med=/home/wei/salome_7.4.0/med-3.0.7 \
> --with-salome=/home/wei/salome/Salome-V7_4_0-LGPL-x86_64/modules \
> --without-salome-med \
> --enable-debug \
> CC=mpicc FC=gfortran

.
There was some warnings who said that

Code: Select all

configure: WARNING: no MED file MPI support

and

Code: Select all

checking whether we can link with omniORB... yes
checking omniORBpy... yes
for omniORBpy: yes
for omniORB: yes
checking whether we have double and CORBA::Double compatibility... yes
checking whether we have int and CORBA::Long compatibility... yes
 unknown orb
configure: WARNING: no MEDCoupling support
configure: WARNING: no MEDCoupling support

Do they effect the following installation for Saturne and Syrthes ? And how could I deal with it ?

[zihenwuming]

Hello Yvan, I'm sorry that I have so many questions. I just ignored the warnings and do the make, however there were errors that appeared as follow:

../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:1501:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
# pragma omp parallel for reduction(+:n_no_adj_halo)
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:1538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
# pragma omp parallel for
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:1580:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
# pragma omp parallel for
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c: In function ‘_renum_face_multipass’:
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:2390:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
# pragma omp parallel for private(c_id_0, c_id_1)
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:2406:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
# pragma omp parallel for private(c_id_0, c_id_1)
^
In file included from ../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:78:0:
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c: In function ‘_part_scotch’:
/usr/include/scotch/ptscotch.h:63:24: error: floating constant in preprocessor expression
#define SCOTCH_VERSION 5.1
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:4285:5: note: in expansion of macro ‘SCOTCH_VERSION’
#if SCOTCH_VERSION >= 6
^
/usr/include/scotch/ptscotch.h:63:24: error: floating constant in preprocessor expression
#define SCOTCH_VERSION 5.1
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:4325:5: note: in expansion of macro ‘SCOTCH_VERSION’
#if SCOTCH_VERSION >= 6
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c: In function ‘_renumber_i_test’:
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:5077:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
# pragma omp parallel for private(f_id, c_id_0, c_id_1)
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:5144:0: warning: ignoring #pragma dir nodep [-Wunknown-pragmas]
# pragma dir nodep
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:5145:0: warning: ignoring #pragma GCC ivdep [-Wunknown-pragmas]
# pragma GCC ivdep
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c: In function ‘_renumber_b_test’:
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:5245:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
# pragma omp parallel for private(f_id, c_id)
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:5303:0: warning: ignoring #pragma dir nodep [-Wunknown-pragmas]
# pragma dir nodep
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:5304:0: warning: ignoring #pragma GCC ivdep [-Wunknown-pragmas]
# pragma GCC ivdep
^
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c: At top level:
../../..//..//code_saturne-4.0-beta/src/base/cs_renumber.c:1129:1: warning: ‘_csr_graph_create’ defined but not used [-Wunused-function]
_csr_graph_create(cs_lnum_t n_cells_ext,
^
make[3]: *** [libcsrenumber_la-cs_renumber.lo] Error 1
make[3]: Leaving directory `/home/wei/code_saturne/saturne_build/dbg/src/base'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/home/wei/code_saturne/saturne_build/dbg/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/wei/code_saturne/saturne_build/dbg'
make: *** [all] Error 2

So how could I solve these problems ?
Thanks very much for your help.

Wei

[Yvan Fournier]

Hello,

In your previous post, it seems your --with-salome option is incorrect: you need to remove:

/modules

from the --with-salome option.

Also, warnings about OpenMp are not important when it is not enabled.

But you have an error with scotch.

Scotch < 6.0 is not supported with Code_Saturne 4. The installation manual provides recommendations for Scotch. Or more simply, disable it with --without-scotch.

Regards,

Yvan

[koch]

Dear Yvan

I tried install Code saturne with scotch from syrthes 4.3 built (scotch 6.03) but there is still the smae error like in zihenwuming situation. I tired install from source scotch 6.04 but with the same result.

Do you maybe think that it is because of scotch 5.12 I got instaled from repository? there are no new verions of scotch in repositories of ubuntu.

Have You maybe any idea how to fix that?

here is some text froom last lines from terminal:
http://pastebin.com/qc25T2mb

[Yvan Fournier]

Hello,

Could you also post your config.log ? It will help me check if the intended scotch version is used. Also, could you remind me which compiler versions (or Ubuntu version) you are using ?

Regards,

Yvan

[koch]

Sure it is in attachment.

I tried with version that was compiled with syrthes 4.3, then I tried with standalone scotch 6.0.4, because last version in repository is scotch 5.12 (saturne should work > 6.0)

I tried with automatical instalation - results was the same like early.

Finally I instaled it without scotch - I deleted my packages from sinaptic, CS was installed but there was error during analysis - that Folder of schotch 5.12 is empty - I suppose that I showed path to scotch 6.0.3 but it was taken something from main directories where was 5.12 reposiitory version.

Funny thing is that after I reinstalled repositoory 5.12 calculations started, bu I can suppose to that i will not work with syrthes in coupling analysis - but I try verify that tomorow.

Thanks for so quick support.

[koch]

I checked coupling with syrthes and unfortunetly it doesn't work. I got this message:

[mw-workstation:04224] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file ess_env_module.c at line 358
[mw-workstation:04221] tcp_peer_recv_connect_ack: invalid header type: 109051904
[mw-workstation:04224] [[INVALID],INVALID] routed:binomial: Connection to lifeline [[1664,0],0] lost
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[1664,1],1]
Exit code: 1
--------------------------------------------------------------------------
solver script exited with status 1.

Error running the coupled calculation.

Either Code_Saturne or SYRTHES may have failed.

Check Code_Saturne log (listing) and SYRTHES log (syrthes.log)
for details, as well as error* files.


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Saving calculation results
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Error in calculation stage.