[Trilinos-Users] hdf5

[Eligiusz Postek]

Thank you,  HDF5 passed,
but I still have a problem with netcdf

[ 35%] Building Fortran object
packages/seacas/applications/gjoin/CMakeFiles/gjoin.dir/gj_zmfixd.f.o
[ 35%] Building Fortran object
packages/seacas/libraries/plt/CMakeFiles/plt.dir/pltrsd.f.o
/opt/cray/netcdf-hdf5parallel/4.4.0/GNU/5.1/lib/libnetcdf_parallel.a(libnetcdf4_la-nc4file.o):
In function `sync_netcdf4_file':
/b/ulib/netcdf-support/rpm/BUILD/cray-netcdf-4.4.0-gcc2/netcdf-4.4.0/libsrc4/nc4file.c:3006:
undefined reference to `H5Fflush'
/opt/cray/netcdf-hdf5parallel/4.4.0/GNU/5.1/lib/libnetcdf_parallel.a(libnetcdf4_la-nc4file.o):
In function `close_netcdf4_file':
/b/ulib/netcdf-support/rpm/BUILD/cray-netcdf-4.4.0-gcc2/netcdf-4.4.0/libsrc4/nc4file.c:3090:
undefined reference to `H5Fclose'
/b/ulib/netcdf-support/rpm/BUILD/cray-netcdf-4.4.0-gcc2/netcdf-4.4.0/libsrc4/nc4file.c:3094:
undefined reference to `H5Fget_obj

and ......


I use
 -D TPL_ENABLE_Netcdf:BOOL=ON
-D
Netcdf_LIBRARY_DIRS:FILEPATH="/opt/cray/netcdf-hdf5parallel/4.4.0/GNU/5.1/lib"
\
-D
Netcdf_INCLUDE_DIRS::FILEPATH="/opt/cray/netcdf-hdf5parallel/4.4.0/GNU/5.1/include"
\
-D Netcdf_LIBRARY_NAMES:STRING="netcdf_parallel" \

Could you still help ?

Best regards,
Elek






On Fri, Nov 10, 2017 at 4:13 PM, Eric Bavier <bavier at cray.com> wrote:

> Hello Elek,
>
> The 'H5Tget_tag' symbol is defined in libhdf5.a, so you'll need to make
> sure that the HDF5 TPL includes that library when configuring.  FWIW when I
> build Trilinos with cray-hdf5, I usually set:
>
>   -D TPL_ENABLE_HDF5:BOOL=ON \
>   -D TPL_HDF5_INCLUDE_DIRS:FILEPATH=${HDF5_DIR}/include \
>   -D HDF5_LIBRARY_DIRS:FILEPATH=${HDF5_DIR}/lib \
>   -D HDF5_LIBRARY_NAMES:STRING="hdf5_hl_parallel;hdf5_parallel;z;dl"
>
> Hope that helps,
>
> Eric Bavier, Scientific Libraries, Cray Inc.
>
> ________________________________________
> From: Trilinos-Users <trilinos-users-bounces at trilinos.org> on behalf of
> Eligiusz Postek <ewpostek at googlemail.com>
> Sent: Thursday, November 9, 2017 18:35
> To: trilinos-users at trilinos.org
> Subject: [Trilinos-Users] hdf5
>
> Hello,
> Could it mean that the cray libs (hdf5) are incomplete ?
> Is there any other error ?
> best regards, Elek
>
>
> [ 34%] Building CXX object packages/teuchos/parameterlist/src/CMakeFiles/
> teuchosparameterlist.dir/Teuchos_StringInputStream.cpp.o
> /opt/cray/hdf5/1.8.16/GNU/5.1/lib/libhdf5.a(H5PL.o): In function
> `H5PL_load':
> H5PL.c:(.text+0x634): warning: Using 'dlopen' in statically linked
> applications requires at runtime the shared libraries from the glibc
> version used for linking
> /opt/cray/hdf5/1.8.16/GNU/5.1/lib/libhdf5_hl.a(H5LT.o): In function
> `H5LT_dtype_to_text':
> H5LT.c:(.text+0x2871): undefined reference to `H5Tget_tag'
> /opt/cray/hdf5/1.8.16/GNU/5.1/lib/libhdf5_hl.a(H5LTparse.o): In function
> `H5LTyyparse':
> H5LTparse.c:(.text+0x108d): undefined reference to `H5Tset_tag'
> collect2: error: ld returned 1 exit status
> make[2]: *** [packages/seacas/applications/nem_slice/nem_slice] Error 1
>
>
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