Re: [netcdfgroup] ncdump MPI error

• To: Marston Sheldon Johnston <marston@xxxxxxxxxxx>
• Subject: Re: [netcdfgroup] ncdump MPI error
• From: Ed Hartnett <ed@xxxxxxxxxxxxxxxx>
• Date: Mon, 15 Nov 2010 09:07:44 -0700

Marston Sheldon Johnston <marston@xxxxxxxxxxx> writes:

> Hi,
>
> I'm trying to install netcdf 4.1.1 together with hdf5 1.8.2.
> I keep getting an error when compiling netcdf:
>
> Making all in ncdump
> make[2]: Entering directory `/home/marston/SOFTWARE/netcdf-4.1.1/ncdump'
> ../ncgen/ncgen -c -o ctest0.nc ./../ncgen/c0.cdl > ./ctest.c
> /home/marston/SOFTWARE/netcdf-4.1.1/ncgen/.libs/lt-ncgen: symbol lookup 
> error: /home/marston/SOFTWARE/netcdf-4.1.1/libsrc4/.libs/libnetcdf.so.6: 
> undefined symbol: ompi_mpi_char
> make[2]: *** [ctest.c] Error 127
> make[2]: Leaving directory `/home/marston/SOFTWARE/netcdf-4.1.1/ncdump'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/marston/SOFTWARE/netcdf-4.1.1'
> make: *** [all] Error 2
>
>
> I've updated openMPI but still I get this error. 
>
> Does anyone know what's going on here?
>
> /M
>
> - 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> ~ Marston S. Johnston                                 e-mail: 
> marston@xxxxxxxxxxx  ~
> ~ Doctoral Student                                    Earth and Space 
> Sciences        ~       
> ~ Chalmers University of Technology     http://www.chalmers.se               ~
> ~ Gothenburg                                                  Tel. (46) 31 
> 772 2235                 ~     
> ~ Sweden                                                      Skype ID 
> marston.johnston       ~       
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Howdy Marston!

You need to get the latest HDF5 - version 1.8.5-patch1.

If you are doing parallel I/O, you want to get the netCDF daily
snapshot, which contains many improvements to parallel I/O performance
that are not yet in a released version:

ftp://ftp.unidata.ucar.edu/pub/netcdf/snapshot/netcdf-4-daily.tar.gz.

You also want to be sure you are compiling with the MPI compiler (mpicc,
usually), and that you have built HDF5 with --enable-parallel and
--with-zlib=/somewhere.

If that does work, please let me know.

Thanks,

Ed

-- 
Ed Hartnett  -- ed@xxxxxxxxxxxxxxxx

• References:
  • [netcdfgroup] ncdump MPI error
    • From: Marston Sheldon Johnston