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[netCDF #JVR-483042]: Netcdf-Fortran Configure Error

Hello,

While unrelated to current error, I will first mention that netCDF-Fortran has 
a newer version, 4.5.3.  I would suggest trying to compile that, and see if the 
error persists.  If the problem is resolved, great! If not, please read on.

When searching for information on the symbol lookup error in the config.log 
file you provided, I found the following:

https://software.intel.com/en-us/forums/intel-fortran-compiler/topic/606293

While not precisely the same error, it does provide information about a similar 
error related to a conflict(?) between the libm system library, and the libm 
provided by the Intel compiler.  My guess is that the C library (libnetcdf) was 
compiled with one library whereas you are compiling the Fortran library with 
the other.  Can you provide the config.log and/or libnetcdf.settings file 
generated when you configured and compiled the netCDF library?

Thank you very much,

-Ward



> Dear all,
> I was trying to compile the netcdf with parallel support using intel
> compiler. My installation sequence is zlib_1.2.8 -- szip_2.1 -- hdf5_1.8.13
> -- pnetcdf_1.12.1 --- netcdf-c_4.7.3 -- netcdf-fortran_4.5.2. I installed
> the former five components with no problem (with shared libraries). But I
> encountered an error when I was trying to configure the netcdf-fortran. I
> configured the netcdf-fortran with command below:
> *CPPFLAGS="-I/usr/local/netcdf-intel-mpi/szip/include *
> *-I/usr/local/netcdf-intel-mpi/zlib/include *
> *-I/usr/local/netcdf-intel-mpi/hdf5/include *
> *-I/usr/local/netcdf-intel-mpi/pnetcdf/include *
> *-I/usr/local/netcdf-intel-mpi/netcdf/include" *
> *LDFLAGS="-L/usr/local/netcdf-intel-mpi/szip/lib *
> *-L/usr/local/netcdf-intel-mpi/zlib/lib *
> *-L/usr/local/netcdf-intel-mpi/hdf5/lib -lhdf5_hl -lhdf5 -lz -lm *
> *-L/usr/local/netcdf-intel-mpi/pnetcdf/lib *
> *-lpnetcdf -L/usr/local/netcdf-intel-mpi/netcdf/lib" *
> *./configure --prefix=/usr/local/netcdf-intel-mpi/netcdf *
> *--enable-shared --enable-parallel-tests --disable-static"*
> 
> After trying this command I got the error message:
> *checking size of off_t... configure: error: in
> `/usr/local/netcdf-intel-mpi/tar.used/netcdf-fortran-4.5.2':*
> *configure: error: cannot compute sizeof (off_t)*
> *See `config.log' for more details*
> 
> I was trying to locate the error info in the config.log and I found (I
> uploaded this config.log as attachment)
> 
> 
> *./conftest: symbol lookup error:
> /usr/local/netcdf-intel-mpi/netcdf/lib/libnetcdf.so.15: undefined symbol:
> __libm_exp_table_128configure:23932: $? = 127configure: program exited with
> status 127*
> 
> And I think the above few lines might be the reason which causes this
> error.  I already set up the netcdf library path in LD_LIBRARY_PATH. I
> searched a lot but there are almost no posts online related to my problem.


> Another thing I can't really understand is I installed the same version
> (all six components) on another server successfully, and this error never
> shows up. (while the intel compiler version is older than the one I used
> here).
> 
> I am so confused and I really hope you could offer me some suggestions. Any
> advice might be helpful.
> 
> Thank you so much. I Hope you have a great day.
> 
> Best regards,
> Wang Xiong
> 
> 
> Dear all,
> I was trying to compile the netcdf with parallel support using intel
> compiler. My installation sequence is zlib_1.2.8 -- szip_2.1 -- hdf5_1.8.13
> -- pnetcdf_1.12.1 --- netcdf-c_4.7.3 -- netcdf-fortran_4.5.2. I installed
> the former five components with no problem (with shared libraries). But I
> encountered an error when I was trying to configure the netcdf-fortran. I
> configured the netcdf-fortran with command below:
> *CPPFLAGS="-I/usr/local/netcdf-intel-mpi/szip/include *
> *-I/usr/local/netcdf-intel-mpi/zlib/include *
> *-I/usr/local/netcdf-intel-mpi/hdf5/include *
> *-I/usr/local/netcdf-intel-mpi/pnetcdf/include *
> *-I/usr/local/netcdf-intel-mpi/netcdf/include" *
> *LDFLAGS="-L/usr/local/netcdf-intel-mpi/szip/lib *
> *-L/usr/local/netcdf-intel-mpi/zlib/lib *
> *-L/usr/local/netcdf-intel-mpi/hdf5/lib -lhdf5_hl -lhdf5 -lz -lm *
> *-L/usr/local/netcdf-intel-mpi/pnetcdf/lib *
> *-lpnetcdf -L/usr/local/netcdf-intel-mpi/netcdf/lib" *
> *./configure --prefix=/usr/local/netcdf-intel-mpi/netcdf *
> *--enable-shared --enable-parallel-tests --disable-static"*
> 
> After trying this command I got the error message:
> *checking size of off_t... configure: error: in
> `/usr/local/netcdf-intel-mpi/tar.used/netcdf-fortran-4.5.2':*
> *configure: error: cannot compute sizeof (off_t)*
> *See `config.log' for more details*
> 
> I was trying to locate the error info in the config.log and I found (I
> uploaded this config.log as attachment)
> 
> 
> *./conftest: symbol lookup error:
> /usr/local/netcdf-intel-mpi/netcdf/lib/libnetcdf.so.15: undefined symbol:
> __libm_exp_table_128configure:23932: $? = 127configure: program exited with
> status 127*
> 
> And I think the above few lines might be the reason which causes this
> error.  I already set up the netcdf library path in LD_LIBRARY_PATH. I
> searched a lot but there are almost no posts online related to my problem.
> Another thing I can't really understand is I installed the same version
> (all six components) on another server successfully, and this error never
> shows up. (while the intel compiler version is older than the one I used
> here).
> 
> I am so confused and I really hope you could offer me some suggestions. Any
> advice might be helpful.
> 
> Thank you so much. I Hope you have a great day.
> 
> Best regards,
> Wang Xiong
> 
> 


Ticket Details
===================
Ticket ID: JVR-483042
Department: Support netCDF
Priority: Normal
Status: Closed
===================
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