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[netCDF #JTG-138613]: netcdf-fortran-4.5.0 make error with libnetcdff.so

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  • Subject: [netCDF #JTG-138613]: netcdf-fortran-4.5.0 make error with libnetcdff.so
  • Date: Tue, 03 Sep 2019 17:17:24 -0600
Hello,

My guess would be that there is a different libnetcdf available on the system, 
perhaps compiled with a different compiler? Or perhaps an older version of 
libnetcdf.  Can you find the library you are linking against and run the 
following?

    $ nm [library name] | grep nc_get_chunk_cache_ints

What does this return?

-Ward

> Hi,
> 
> I am trying to install netcdf-fortran-4.5.0 and am getting the following 
> error during "make check":
> 
> 
> /usr/bin/ld: warning: libgfortran.so.3, needed by 
> /central/software/OpenMPI/4.0.1//lib/libmpi_usempi.so.40, may conflict with 
> libgfortran.so.4
> 
> ../fortran/.libs/libnetcdff.so: undefined reference to 
> `nc_get_chunk_cache_ints'
> 
> ../fortran/.libs/libnetcdff.so: undefined reference to 
> `nc_set_var_chunk_cache_ints'
> 
> ../fortran/.libs/libnetcdff.so: undefined reference to 
> `nc_def_var_chunking_ints'
> 
> ../fortran/.libs/libnetcdff.so: undefined reference to 
> `nc_set_chunk_cache_ints'
> 
> ../fortran/.libs/libnetcdff.so: undefined reference to 
> `nc_get_var_chunk_cache_ints'
> 
> ../fortran/.libs/libnetcdff.so: undefined reference to 
> `nc_inq_var_chunking_ints'
> 
> collect2: error: ld returned 1 exit status
> 
> I've successfully installed netcdf-c-4.7.1. I'm using gcc 7.3.0 and OpenMPI 
> 4.0.1, and get the same error when using mvapich2 2.3rc1 and mpich 3.3.1.
> 
> I tried setting LIBS="-lnetcdf" as shown in this post 
> (https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg13784.html),
>  but it had no effect. I then checked my libnetcdff.so file according to this 
> post 
> (https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg10194.html),
>  and this was the output:
> 
> 
> 304: 0000000000010b60   183 FUNC    GLOBAL DEFAULT   11 nf_open_
> 
> 465: 000000000001d970   202 FUNC    GLOBAL DEFAULT   11 nf_open_par_
> 
> 641: 0000000000010dc0   190 FUNC    GLOBAL DEFAULT   11 nf_open_mem_
> 
> 387: 0000000000010b60   183 FUNC    GLOBAL DEFAULT   11 nf_open_
> 
> 548: 000000000001d970   202 FUNC    GLOBAL DEFAULT   11 nf_open_par_
> 
> 724: 0000000000010dc0   190 FUNC    GLOBAL DEFAULT   11 nf_open_mem_
> 
> I've attached config.log for both the netcdf-c and netcdf-fortran builds. I 
> also attached libnetcdff.so.7. I appreciate your help and please let me know 
> what else I can try.
> 
> Please ignore my email from a few days ago; I fixed that error.
> 
> Thank you,
> Elyse
> 
> 


Ticket Details
===================
Ticket ID: JTG-138613
Department: Support netCDF
Priority: Normal
Status: Closed
===================
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