Configuring CDO on WSL with netCDF4 and HDF5
Added by Lucas Do over 5 years ago
Hello,
I'm attempting to use CDO for the first time and set up an Ubuntu 18.04.3 LTS subsystem on Windows 10 using WSL. After setting up the WSL environment I ran sudo apt update and sudo apt upgrade, and then
sudo apt-get install libnetcdf-dev libhdf5-dev
I downloaded and unpacked cdo-1.9.7.1 into /opt/cdo-install and then ran
sudo ./configure --enable-netcdf4 --enable-zlib --with-netcdf=/usr/ --with-hdf5=/usr/
to configure because I know I'll need to work with .nc4 files. I got the response in the attached text file, ending with the error:
configure: error: Cannot link to hdf5!
Any help in resolving this would be appreciated.
| hdf5error.txt (8 KB) hdf5error.txt |
Replies (8)
RE: Configuring CDO on WSL with netCDF4 and HDF5 - Added by Ralf Mueller over 5 years ago
hi Lucas!
there is a debian-package called cdo - this might fit your needs without manual installation
cheers
ralf
RE: Configuring CDO on WSL with netCDF4 and HDF5 - Added by Ralf Mueller over 5 years ago
could you uploads the config.log file?
RE: Configuring CDO on WSL with netCDF4 and HDF5 - Added by Lucas Do over 5 years ago
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by cdo configure 1.9.7.1, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --enable-netcdf4 --enable-zlib --with-netcdf=/usr/ --with-hdf5=/usr/- --------- ##
- Platform. ##
- --------- ##
hostname = DESKTOP-VQ1E2QL
uname -m = x86_64
uname -r = 4.4.0-18362-Microsoft
uname -s = Linux
uname -v = #1-Microsoft Mon Mar 18 12:02:00 PST 2019
/usr/bin/uname -p = unknown
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = unknown
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/local/sbin
PATH: /usr/local/bin
PATH: /usr/sbin
PATH: /usr/bin
PATH: /sbin
PATH: /bin
PATH: /snap/bin
config.log
RE: Configuring CDO on WSL with netCDF4 and HDF5 - Added by Ralf Mueller over 5 years ago
I meant: upload it as file attachemnt
RE: Configuring CDO on WSL with netCDF4 and HDF5 - Added by Lucas Do over 5 years ago
Thank you for the help Ralf!
Then would simply running:
sudo apt install cdo
install it with netCDF4 supported? Or would I need to run anything else? thanks again
-Lucas
RE: Configuring CDO on WSL with netCDF4 and HDF5 - Added by Ralf Mueller over 5 years ago
netcdf4 should be included - just give it a try.
RE: Configuring CDO on WSL with netCDF4 and HDF5 - Added by Lucas Do over 5 years ago
Ralf,
I ran it and it seems to be working, cdo -V gives
Climate Data Operators version 1.9.3 (http://mpimet.mpg.de/cdo)
CXX Compiler: g++ -g -O2 -fdebug-prefix-map=/build/cdo-g3Qjnd/cdo-1.9.3+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp
CXX version : g++ (Ubuntu 7.3.0-1ubuntu1) 7.3.0
C Compiler: gcc -g -O2 -fdebug-prefix-map=/build/cdo-g3Qjnd/cdo-1.9.3+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -fPIC -fopenmp
C version : gcc (Ubuntu 7.3.0-1ubuntu1) 7.3.0
F77 Compiler: f77 -g -O2 -fdebug-prefix-map=/build/cdo-g3Qjnd/cdo-1.9.3+dfsg.1=. -fstack-protector-strong
F77 version : unknown
Features: 7GB C++14 Fortran DATA PTHREADS OpenMP45 HDF5 NC4/HDF5/threadsafe OPeNDAP SZ UDUNITS2 PROJ.4 MAGICS CURL FFTW3 SSE2
Libraries: HDF5/1.10.0 proj/4.93 curl/7.58.0
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.3
GRIB_API library version : 2.6.0
NetCDF library version : 4.6.0 of Feb 9 2018 19:21:24 $
HDF5 library version : library undefined
EXSE library version : 1.4.0
FILE library version : 1.8.3
Also, sorry about that, the config.log is now attached. Thanks again for the quick help.
-Lucas
| config.log (58.3 KB) config.log |
RE: Configuring CDO on WSL with netCDF4 and HDF5 - Added by Ralf Mueller over 5 years ago
yeah, look good. netcdf4-upport is there.
just for the record: the debian packages are correct IMO, So I am not sure, why the configure fails. but problem seems to solved anyway, so ... ;-)