[MOAB-dev] building MOAB with CGNS support

Wed Sep 3 08:09:39 CDT 2014

Can you send config.log and your configure.log?
________________________________________
From: Kanaev A.A. [kanaev at ibrae.ac.ru]
Sent: Wednesday, September 03, 2014 7:51 AM
To: Grindeanu, Iulian R.
Subject: RE: [MOAB-dev] building MOAB with CGNS support

export FATHOM_DIR=/home/anton/FATHOM_DIR
export MPI2_PREFIX=/usr/lib/mpich2

export SZIP_VERSION_NUMBER=2.1
export SZIP_VERSION=szip-${SZIP_VERSION_NUMBER}
export SZIP_PREFIX=${FATHOM_DIR}/szip/${SZIP_VERSION}/gcc

export ZLIB_VERSION=zlib-1.2.8
export ZLIB_PREFIX=${FATHOM_DIR}/zlib/${ZLIB_VERSION}/gcc

export HDF5_VERSION=hdf5-1.8.11
export HDF5_PREFIX=${FATHOM_DIR}/hdf5/${HDF5_VERSION}/gcc

export zoltan_VERSION_NUMBER=3.6
export zoltan_PREFIX=${FATHOM_DIR}/zoltan/Zoltan_v${zoltan_VERSION_NUMBER}/gcc
export parmetis_PREFIX=${FATHOM_DIR}/parmetis/ParMETIS3_1

export CC=mpicc
export CXX=mpicxx
export F77=mpif77
export FC=mpif90
export F90=mpif90

./configure --prefix=${FATHOM_DIR}/moab/build --with-mpi=${MPI2_PREFIX} --without-netcdf --with-hdf5=${HDF5_PREFIX} --with-zlib=${ZLIB_PREFIX} --with-szlib=${SZIP_PREFIX} --with-zoltan=${zoltan_PREFIX} --with-parmetis=${parmetis_PREFIX} --with-cgns=/usr/local/lib --enable-igeom  --enable-docs --with-doxygen=/home/anton/doxygen/bin --enable-static 2>&1 | tee configure.log

CGNS was configured with the same HDF5 lib
________________________________________
From: Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Wednesday, September 03, 2014 4:41 PM
To: Kanaev A.A.
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] building MOAB with CGNS support

how did you configure moab?
you should not mix ccmio and cgns
so if you configure with cgns, do not configure with ccmio
this is your file converted to h5m

I don't see any cavity :)

Iulian
________________________________________
From: Kanaev A.A. [kanaev at ibrae.ac.ru]
Sent: Tuesday, September 02, 2014 4:58 PM
To: Grindeanu, Iulian R.
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] building MOAB with CGNS support

3.1.4 works right
next problem is when i do mbconvert Cavity.cgns Cavity.h5m i got an error message:

number of nodes = 5202
number of elems = 2500
number of parts = 3
Read "Cavity.cgns"
Writer with name MOAB for file Cavity.h5m using extension h5m was unsuccessful
Using default writer WriteHDF5Parallel for file Cavity.h5m
Failed to write "Cavity.h5m".
Error code: MB_FAILURE (16)
Error message: Invalid Quad4 element connectivity. Write Aborted

Cavity.cgns is attached, the file was created by Salome's export mesh to CGNS file
________________________________________
From: Grindeanu, Iulian R. [iulian at mcs.anl.gov]
Sent: Tuesday, September 02, 2014 5:05 AM
To: Vijay S. Mahadevan; Kanaev A.A.
Cc: moab-dev at mcs.anl.gov
Subject: RE: [MOAB-dev] building MOAB with CGNS support

I did not test version 3.2.1.
 3.1.4 should be fine
how did you build cgns?
cgns should be built with the same version of hdf5 that you use for moab, to avoid conflicts (especially if you build shared)

Iulian

________________________________________
From: moab-dev-bounces at mcs.anl.gov [moab-dev-bounces at mcs.anl.gov] on behalf of Vijay S. Mahadevan [vijay.m at gmail.com]
Sent: Monday, September 01, 2014 5:09 PM
To: Kanaev A.A.
Cc: moab-dev at mcs.anl.gov
Subject: Re: [MOAB-dev] building MOAB with CGNS support

Anton, send us your config.log. If your configuration for CGNS was
valid, mbconvert should list the format.

Vijay

On Mon, Sep 1, 2014 at 4:36 PM, Kanaev A.A. <kanaev at ibrae.ac.ru> wrote:
> Hello Vijay,
> After building with --with-cgns=/usr/local/lib mbconvert - l shows same list of formats and there's no CGNS in it
> When i do mbconvert Mesh_1.cgns Mesh_1.h5m i got the message:
> HDF5-DIAG: Error detected in HDF5 (1.8.11) MPI-process 0:
>   #000: H5G.c line 463 in H5Gopen2(): unable to open group
>     major: Symbol table
>     minor: Can't open object
>   #001: H5Gint.c line 320 in H5G__open_name(): group not found
>     major: Symbol table
>     minor: Object not found
>   #002: H5Gloc.c line 430 in H5G_loc_find(): can't find object
>     major: Symbol table
>     minor: Object not found
>   #003: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
>     major: Symbol table
>     minor: Object not found
>   #004: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
>     major: Symbol table
>     minor: Callback failed
>   #005: H5Gloc.c line 385 in H5G_loc_find_cb(): object 'tstt' doesn't exist
>     major: Symbol table
>     minor: Object not found
> Failed to load "Mesh_1.cgns".
> Error code: MB_INDEX_OUT_OF_RANGE (1)
> Error message: Mesh_1.cgns: Trouble reading vertices
>
> Thanks,
> Anton
> ________________________________________
> From: Vijay S. Mahadevan [vijay.m at gmail.com]
> Sent: Tuesday, September 02, 2014 12:24 AM
> To: Kanaev A.A.
> Cc: moab-dev at mcs.anl.gov
> Subject: Re: [MOAB-dev] building MOAB with CGNS support
>
> Make sure the LD_LIBRARY_PATH contains the cgns installation library
> path (/usr/local/lib ?). To verify, you can run "ldd mbconvert" and
> see if any of the dynamic libraries are not resolved.
>
> Vijay
>
> On Mon, Sep 1, 2014 at 2:06 PM, Kanaev A.A. <kanaev at ibrae.ac.ru> wrote:
>> Hello MOAB-dev,
>>
>> Here's how i configure Makefile:
>> ...
>> ./configure --prefix=${FATHOM_DIR}/moab/build --with-mpi=${MPI2_PREFIX} --without-netcdf --with-hdf5=${HDF5_PREFIX} --with-zlib=${ZLIB_PREFIX} --with-szlib=${SZIP_PREFIX} --with-zoltan=${zoltan_PREFIX} --with-parmetis=${parmetis_PREFIX} --with-cgns=${FATHOM_DIR}/cgnslib_3.2.1/src --enable-igeom  --enable-docs --with-doxygen=/home/anton/doxygen/bin --enable-static 2>&1 | tee configure.log
>>
>> configure goes ok:
>> ...
>> checking if CGNS support is enabled... yes
>> checking cgnslib.h usability... yes
>> checking cgnslib.h presence... yes
>> checking for cgnslib.h... yes
>> checking for cg_open in -lcgns... no
>> checking for cg_open in -lcgns... yes
>> ...
>>
>>
>> After build is done when i run mbconvert i got the following message:
>>
>> mbconvert: error while loading shared libraries: libcgns.so.3.2: cannot open shared object file: No such file or directory
>>
>> ${FATHOM_DIR}/cgnslib_3.2.1/src contains libcgns.so.3.2, it is also installed to /usr/local/lib
>>
>> What can be wrong?
>>
>> Thanks,
>> Anton