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cdo configure error not finding nc_open

Added by Benjamin Müller over 9 years ago

Hi,
I'm trying to install cdo 1.6.7 within cygwin.

I get an error on nc_open that reads:

[...]
checking for netcdf.h... yes
checking for library containing nc_open... no
configure: error: Could not link to netcdf library

I tried both installing netcdf 4.3.2 manually per default to /usr/local as well as netcdf 3.6.3 with libs4cdo 0.0.10. Both ending in the same error.

I attached both config.log files.

This is how far I got after getting rid of 20 other errors while installing (including the hdf from cygwin-setup problem) and trying different cygwin versions and this is how far I could get.
Can anybody point to the error I made and how to get rid of it?

Thank you in advance

Ben

Download all files
config.log_wlibs (69.6 KB) config.log_wlibs With libs4cdo
config.log_wolibs (69.4 KB) config.log_wolibs Without libs4cdo

Replies (7)

RE: cdo configure error not finding nc_open - Added by Ralf Mueller over 9 years ago

Under cygwin, you do not need to use libs4cdo. netcdf/hdf5/proj4 are available as system packages. Use setup.exe to install then and build cdo with

./configure --with-netcdf --with-hdf5 --with-proj CLFAGS='-g -fopenmp -02'

RE: cdo configure error not finding nc_open - Added by Benjamin Müller over 9 years ago

Hi,

I tried your advice and reinstalled cygwin to get the libraries and configuring works well, but 'make' stops with an error that recipe for target 'cdo.exe' fails.

The rerun make-log is attached.

Am I still missing anything?

make.log (9.87 KB) make.log

RE: cdo configure error not finding nc_open - Added by Ralf Mueller over 9 years ago

have your run 

make clean
before? Or a fresh extraction of the tar-ball?

RE: cdo configure error not finding nc_open - Added by Benjamin Müller over 9 years ago

I tried both ways and it still ends with the same error. (See logfile)

By now, I'm trying to get cdo to run for 2 straight months ;)

make.log (107 KB) make.log

RE: cdo configure error not finding nc_open - Added by David Gampe over 9 years ago

Hi everyone!

I am stuck at the very same point, getting the same error over and over again. Meanwhile I am pretty sure, it is not a cdo problem, but a Cygwin or Win7 related. Perhaps someone had the same issue and found a solution? A 'workarround' is the win32 version of cdo, however the 2GB limit is existent). I would also be glad for any suggestions and help! :)

Thank you in advance!

David

RE: cdo configure error not finding nc_open - Added by Ralf Mueller over 9 years ago

Benjamin Müller wrote:

I tried both ways and it still ends with the same error. (See logfile)

By now, I'm trying to get cdo to run for 2 straight months ;)

The error is different now. Add 

LIBS=-lm
to your configure call

RE: cdo configure error not finding nc_open - Added by Benjamin Müller over 9 years ago

Hi Ralf,

I finally solved the problem:

"sqrtl" isn't coded in gcc-4.9.2 on cygwin anymore!

Thanks to this link here (look at the first answer):
http://stackoverflow.com/questions/11315761/how-to-install-cufflinks-on-cygwin

leading to this manual:
http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/dyer/software/cufflinksforwindows/

I tried to add the lines

#define logl(X) log(X)
#define sqrtl(X) sqrt(X)

to common.h as stated in the manual, but this didn't work either.

The traceback of the cdo make error lead to the file .../clipping/intersection.c.

I added the lines after the include section and voila, everything worked great.

Maybe you can add these lines (I think the second one would be enough) or change the respective lines in intersection.c.

All the best and thanks for the support.

Ben

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