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[netCDF #FSI-652508]: netcdf-4 with hdf5 and zlib not compiling

Hi Jonathan,

Sorry it's taken so long to respond to your question.
> So I am attempting to compile netcdf-4.1.1 with hdf5-1.8.5 and zlib 1.2.3.  
> For the hdf5 library I was originally using version 1.8.2 but I updated as 
> you suggested in the previous e-mail.
> I get the following error when trying to compile:  config.status: error: 
> cannot find input file: 'netcdf.pc.in'

If you are using netCDF-4.1.1, the file netcdf.pc.in is in the top-level
directory after you unpack the distribution from 


I've just checked by downloading and unpacking that distribution:

  /tmp$ ls -l netcdf-4.1.1/netcdf.pc.in
  -rw-r--r--   1 russ     ustaff       311 Nov 11  2009 

I don't know why the file is missing, but perhaps you could try downloading 
and starting with a clean tarball.  If you still have problems, please send us
the information requested here:


and we'll try to diagnose the problem further.


> I am compiling in root. But trying to use netcdf-4.1.1 to open a file with 
> ncdump -h in my home directory /home/jwsmith however I am still unable to 
> open the file.
> What to do?
> I currently have nco-4.0.2 installed. I eventually want to use nco on the 
> file I am trying to open. Will I need to re-compile in lieu of the new netcdf?
> Jonathan
> Jonathan Wynn Smith
> Student Trainee, WRF-Chem Modeling and Long-range transport
> address@hidden
> NASA/Goddard Space Flight Center
> Code 613.3/Atmospheric Chemistry and Dynamics Branch
> Greenbelt, MD
> 301-614-5956
> Doctoral Candidate
> address@hidden
> Howard University Program in Atmospheric Sciences
> Washington, DC
> -----Original Message-----
> From: Unidata netCDF Support [mailto:address@hidden
> Sent: Tuesday, August 31, 2010 4:29 PM
> Cc: address@hidden
> Subject: [netCDF #FSI-652508]: netcdf-4 with hdf5 and zlib not compiling
> Ed wrote:
> > Are you both sure that you tried with netCDF built with --enable-netcdf-4 
> > and --with-hdf5=/somewhere?
> Bingo, that was my problem.  With 4.1.1 and later releases, you only need to 
> use
> --with-hdf5=/somewhere, but for earliere releases such as 4.0 or 4.0.1, you 
> had to
> also explicitly specify --enable-netcdf-4.
> I built with both 4.0 and 4.0.1  --with-hdf5=/share/stdinstall/local/buddy 
> and all
> the tests passed, so I assumed it used HDF5.  But looking at the resulting 
> ncdump
> executables with "ldd" shows the hdf5 library wasn't actually used:
> $ ldd /foo/russ/installs/nc401/bin/ncdump
> libm.so.2 =>   /lib/libm.so.2
> libc.so.1 =>   /lib/libc.so.1
> whereas if it had been built with libhdf5, it would show a much longer list
> of libraries:
> $ ldd /usr/local/bin/ncdump
> libhdf5_hl.so.6 =>     /upc/share/stdinstall/local/buddy/lib/libhdf5_hl.so.6
> libhdf5.so.6 =>        /upc/share/stdinstall/local/buddy/lib/libhdf5.so.6
> libm.so.2 =>   /lib/libm.so.2
> libz.so =>     /upc/share/stdinstall/local/buddy/lib/libz.so
> ...
> So I think you could try ldd or the equivalent on your system, and it would 
> show
> the ncdump you're using is not built with netCDF-4 support and use of libhdf5
> that's needed to provide the ability to open netCDF-4 files, such as you
> are trying to open.
> --Russ
> Russ Rew                                         UCAR Unidata Program
> address@hidden                      http://www.unidata.ucar.edu
> Ticket Details
> ===================
> Ticket ID: FSI-652508
> Department: Support netCDF
> Priority: Normal
> Status: Closed

Russ Rew                                         UCAR Unidata Program
address@hidden                      http://www.unidata.ucar.edu

Ticket Details
Ticket ID: FSI-652508
Department: Support netCDF
Priority: Critical
Status: Closed

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