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#1 2011-07-08 10:38:04

frotscher
Member
From: Aachen, Germany
Registered: 2010-11-17
Posts: 124
Website

[SOLVED]Compilation problem hdf5 in parallel C_A version

Hi,

I'm trying to make the new C_A version run parallelly with MPI. The system is a fresh CAELinux2010 + the newest C_A version without updates (11.0.10-2). I edited the config.txt file as good as I can and already solved some compilation problems. The following compilation problems concerning hdf5 I am not able to solve:

<INFO> Compilation from .../bibc/hdf directory
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfopg.c                        [FAILED]
Exit code : 256
/opt/aster11/PAR11.0/bibc/hdf/hdfopg.c: In function ‘hdfopg_’:
/opt/aster11/PAR11.0/bibc/hdf/hdfopg.c:58: error: too few arguments to function ‘H5Gopen2’


<E>_COMPIL_ERROR   error during compiling /opt/aster11/PAR11.0/bibc/hdf/hdfopg.c (see /opt/aster11/PAR11.0/mpi/obj/asterd/hdf.msg)

compiling /opt/aster11/PAR11.0/bibc/hdf/hdfcrg.c                        [FAILED]
Exit code : 256
/opt/aster11/PAR11.0/bibc/hdf/hdfcrg.c: In function ‘hdfcrg_’:
/opt/aster11/PAR11.0/bibc/hdf/hdfcrg.c:65: error: too few arguments to function ‘H5Gcreate2’


<E>_COMPIL_ERROR   error during compiling /opt/aster11/PAR11.0/bibc/hdf/hdfcrg.c (see /opt/aster11/PAR11.0/mpi/obj/asterd/hdf.msg)

compiling /opt/aster11/PAR11.0/bibc/hdf/hdfcld.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfrsv.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdftyp.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfcrf.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdftsd.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfrat.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfnbo.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfnom.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfclf.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfopf.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfwat.c                        [FAILED]
Exit code : 256
/opt/aster11/PAR11.0/bibc/hdf/hdfwat.c: In function ‘hdfwat_’:
/opt/aster11/PAR11.0/bibc/hdf/hdfwat.c:62: error: too few arguments to function ‘H5Acreate2’


<E>_COMPIL_ERROR   error during compiling /opt/aster11/PAR11.0/bibc/hdf/hdfwat.c (see /opt/aster11/PAR11.0/mpi/obj/asterd/hdf.msg)

compiling /opt/aster11/PAR11.0/bibc/hdf/hdfopd.c                        [FAILED]
Exit code : 256
/opt/aster11/PAR11.0/bibc/hdf/hdfopd.c: In function ‘hdfopd_’:
/opt/aster11/PAR11.0/bibc/hdf/hdfopd.c:65: error: too few arguments to function ‘H5Dopen2’


<E>_COMPIL_ERROR   error during compiling /opt/aster11/PAR11.0/bibc/hdf/hdfopd.c (see /opt/aster11/PAR11.0/mpi/obj/asterd/hdf.msg)

compiling /opt/aster11/PAR11.0/bibc/hdf/hdfclg.c                        [  OK  ]
compiling /opt/aster11/PAR11.0/bibc/hdf/hdfwsv.c                        [FAILED]
Exit code : 256
/opt/aster11/PAR11.0/bibc/hdf/hdfwsv.c: In function ‘hdfwsv_’:
/opt/aster11/PAR11.0/bibc/hdf/hdfwsv.c:117: error: too few arguments to function ‘H5Dcreate2’


<E>_COMPIL_ERROR   error during compiling /opt/aster11/PAR11.0/bibc/hdf/hdfwsv.c (see /opt/aster11/PAR11.0/mpi/obj/asterd/hdf.msg)

<INFO>   16 files compiled from /opt/aster11/PAR11.0/bibc/hdf

<INFO> Compilation from .../bibc/include directory
<INFO> no source file in /opt/aster11/PAR11.0/bibc/include

Do you know what causes these compilation problems?

Thanks a lot in advance,

Ralf

PS: Please find attached my config file.

Last edited by frotscher (2011-08-20 13:50:13)


Attachments:
config.txt, Size: 7.93 KiB, Downloads: 770

Ubuntu 64bit, SALOME 7.2, Code_Aster 12.1 (sequential and parallel), ASTK 1.13.1

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#2 2011-07-08 21:58:24

mathieu.courtois
Administrator
From: France
Registered: 2007-11-21
Posts: 1,178

Re: [SOLVED]Compilation problem hdf5 in parallel C_A version

Hi,

Try to add H5_USE_16_API on the DEFS line (will be passed as "-D...." during compilation).
and rebuild :

cd /opt/aster11/PAR11.0
../bin/as_run --make --clean bibc/hdf
../bin/as_run --make

MC


Code_Aster release : last unstable on Ubuntu 16.04 64 bits - GNU Compilers

Please do not forget to tag your first post as *SOLVED* when it is!

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#3 2011-07-09 08:44:32

frotscher
Member
From: Aachen, Germany
Registered: 2010-11-17
Posts: 124
Website

Re: [SOLVED]Compilation problem hdf5 in parallel C_A version

Thank you, that worked. Now I get another error that I'm not able to interpret:

 Build Code_Aster executable

extracting 'python.o' from libasterd.a...                               [  OK  ]
creating .../PAR11.0/asterd_mpi...                                      [  OK  ]
testing executable /opt/aster11/PAR11.0/asterd_mpi...                   [FAILED]
Exit code : 256
Fin interpreteur Python
*** An error occurred in MPI_comm_size
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
[uniklinik1:21879] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
Content after execution of /tmp/root-uniklinik1-build.15872.proc.0 :
ls: cannot access REPE_OUT: No such file or directory
.:
total 24
drwx------  2 root root 4096 2011-07-09 09:21 .
drwxrwxrwt 21 root root 4096 2011-07-09 09:21 ..
-rwxr-xr-x  1 root root 1390 2011-07-09 09:21 mpi_script.sh
-rw-r--r--  1 root root 8976 2011-07-09 09:21 python.o


<F>_BUILD_FAILED   test of executables failed

Could you please help me again to figure out the solution?

Merci beaucoup,

Ralf


Ubuntu 64bit, SALOME 7.2, Code_Aster 12.1 (sequential and parallel), ASTK 1.13.1

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#4 2011-07-15 10:33:25

jcugnoni
Member
Registered: 2007-12-05
Posts: 65

Re: [SOLVED]Compilation problem hdf5 in parallel C_A version

If I remember well, I had the same issue last year when compiling the parallel Aster version for CAELinux... I think I solved it by removing libmpiseq from the config file.

Libmpiseq is provided with the sequential version of mumps to provide a dummy mpi implementation.. as a results it confilts with the true mpi library if you keep it for the parallel version.

Let us know if it works and if possible publish your final config.txt. It will be really usefull to have for others (like me ;-)

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#5 2011-08-20 11:08:35

frotscher
Member
From: Aachen, Germany
Registered: 2010-11-17
Posts: 124
Website

Re: [SOLVED]Compilation problem hdf5 in parallel C_A version

Hi,

after approximately one month I got the time to test the parallel Code_Aster version and now it works. Please find attached my config-file. If I remember well the main things I had to change in this file were:

1. change all compilers to the mpi equivalents
2. add H5_USE_16_API in the DEFS line (as suggested by courtois)
3. remove libmpiseq from the config file (as suggested by jcugnoni)

As the result one of my .mess-file shows:

 Version parallèle de Code_aster compilée avec MPI
 Exécution sur le processeur de nom uniklinik1 de rang 0
 Nombre de processeurs utilisés 2
==========================================
==========================================
[...]

                                        -- CODE_ASTER -- VERSION DE DEVELOPPEMENT 11.00.10 --

                                                  VERSION PARALLELE COMPILEE AVEC MPI

                                                    COPYRIGHT  EDF-R&D 1991 - 2011

                                               EXECUTION DU : SA-20-AOUT-2011 11:52:54

                                                    PLATE-FORME : UNIKLINIK1      

                                                 NB MAX PROC OpenMP:   1             

                                                      SYSTEME : LINUX           

                                                        CPU : X86_64

I hope that the file will be helpful in a way and thanks for the help I got here. Now I also try to use the parallel MUMPS solver smile

Best regards,

Ralf


Attachments:
config.txt, Size: 8.91 KiB, Downloads: 736

Ubuntu 64bit, SALOME 7.2, Code_Aster 12.1 (sequential and parallel), ASTK 1.13.1

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#6 2011-10-13 02:36:53

JMB365
Member
Registered: 2008-01-19
Posts: 781

Re: [SOLVED]Compilation problem hdf5 in parallel C_A version

frotscher wrote:

I hope that the file will be helpful in a way and thanks for the help I got here.

Hello,  Was a great help to me in getting over some final hurdles!  Thank you!  Regards, JMB


SalomeMeca 2021
Ubuntu 20.04, 22.04

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