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CDO installation error

Added by Lyndon Mark Olaguera over 5 years ago

Dear All,

I encountered a problem when using CDO. Below is the following error:

cdo selyear: Open failed on >precip.mon.mean.nc<
                         Unsupported file type (library support not compiled in)
                         To create a CDO application with NetCDF4 support use: ./configure --with-netcdf=&lt;NetCDF4 root directory&gt; ...

Details:
1. I installed CDO via miniconda (i.e., conda install cdo).

2. cdo -V

Climate Data Operators version 1.9.5 (http://mpimet.mpg.de/cdo)
System: x86_64-apple-darwin16.7.0
CXX Compiler: clang++ -std=gnu++11 -mmacosx-version-min=10.9 -stdlib=libc++ -m64 -fPIC -D_THREAD_SAFE -pthread
CXX version : Apple LLVM version 9.0.0 (clang-900.0.37)
C Compiler: clang -mmacosx-version-min=10.9 -m64 -fPIC -D_THREAD_SAFE -pthread -D_THREAD_SAFE -D_THREAD_SAFE -pthread
C version : Apple LLVM version 9.0.0 (clang-900.0.37)
F77 Compiler: gfortran -g -O2
F77 version : GNU Fortran (GCC) 4.8.5
Features: 8GB 4threads C++11 Fortran DATA PTHREADS SSE3
Libraries:
Filetypes: srv ext ieg grb1
CDI library version : 1.9.5
CGRIBEX library version : 1.9.1
EXSE library version : 1.4.0
FILE library version : 1.8.3

I am not sure why this is happening. It seems that netcdf4 is not properly included in the cdo installation?
Any suggestions on how to install this correctly?

I'll appreciate any help.

Lyndz


Replies (3)

RE: CDO installation error - Added by Karin Meier-Fleischer over 5 years ago

Hi Lyndon,
you are working on a Mac and the easiest way to install the new version of CDO is to use MacPorts https://www.macports.org.

sudo port install cdo

-Karin

RE: CDO installation error - Added by Lyndon Mark Olaguera over 5 years ago

Hi Karin,

I tried your suggestion from this link:

I tried installing CDO using the following commands but there's an error at the end of the installation:

port install cdo +grib_api +magicspp +szip

Error: Install port:fftw-3 gcc7
Error: Failed to configure libemos: port:fftw-3 +gcc7 not installed
Error: See
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_science_libemos/libemos/main.log for details.
Error: Follow https://guide.macports.org/#project.tickets to report a bug.
Error: Processing of port cdo failed
---> Some of the ports you installed have notes:
hdf5 has the following notes:
Mac users may need to set the environment variable "HDF5_USE_FILE_LOCKING"
to the five-character string "FALSE" when accessing network mounted files.
This is an application run-time setting, not a configure or build setting.
Otherwise errors such as "unable to open file" or "HDF5 error" may be
encountered.
libidn has the following notes:
Please be aware that GNU libidn2 is the successor of GNU libidn. It comes
with IDNA 2008
and TR46 implementations and also provides a compatibility layer for GNU
libidn.
libpsl has the following notes:
libpsl API documentation is provided by the port 'libpsl-docs'.
netcdf has the following notes:
As of version 4.2 c+ and fortran interfaces are separate ports, netcdf-cxx
and netcdf-fortran, respectively.
python27 has the following notes:
To make this the default Python or Python 2 (i.e., the version run by the
'python' or 'python2' commands), run one or both of:
sudo port select --set python python27
sudo port select --set python2 python27

I also tried instaling it the normal way and it worked.
port install cdo

I wonder what's causing the above error.

Sincerely,
Lyndz

RE: CDO installation error - Added by Karin Meier-Fleischer over 5 years ago

The problem comes with libemos at the cdo installation. But I used eccodes instead of grib_api and maybe this is the cause why it is working on may Mac (macOS Mojave 10.14). 

sudo port install cdo +eccodes +szip +magicspp
-Karin

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