CDO

hi Ludovica!

1. if only a single test fails out of 384, it's not that bad
2. the test, which is failing is know to fail on system with a non-threadsafe installation of hdf5. when you use the cdo binary, make sure that you prepend

   -L

   to the operators
3. hence, your cdo build was a success, just type make install

you can check the binary manually after running make you can start it with ./src/cdo . Please upload the output of

./src/cdo -V

hth
ralf

I dont know, what kind of system you are using, but there might be an easier way of getting CDO running than compiling it yourself. In case you are interested, have a closer look into this

cheers
ralf

Hi Ralf,

Thank you - I'll delete my recent post which is answered by this.

Cheers

Harry

Hi Ralf,
Thanks for your reply.
I agree that one test failing out of 384 is not bad, but still, when I try to use remapbil or just look for other available operators I get "cdo: command not found" (this happens also if I prepend -L as you suggest).
The output of ./src/cdo -V is:

Climate Data Operators version 1.9.5rc1 (http://mpimet.mpg.de/cdo)
System: x86_64-apple-darwin15.6.0
CXX Compiler: g++ -std=gnu++11 -g -O2 -D_THREAD_SAFE -pthread
CXX version : Apple LLVM version 8.0.0 (clang-800.0.42.1)
C Compiler: gcc -fPIC -D_THREAD_SAFE -pthread -D_THREAD_SAFE -D_THREAD_SAFE -pthread
C version : Apple LLVM version 8.0.0 (clang-800.0.42.1)
F77 Compiler:
Features: 8GB C++11 DATA PTHREADS HDF5 NC4/HDF5 OPeNDAP PROJ.4 SSE3
Libraries: HDF5/1.8.12 proj/5.01
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.5rc1
CGRIBEX library version : 1.9.1
GRIB_API library version : 1.14.4
NetCDF library version : 4.6.1 of May 22 2018 17:21:48 $
HDF5 library version : 1.8.12
EXSE library version : 1.4.0
FILE library version : 1.8.3

Thank you!
Ludovica

Ludovica Beltrame wrote:

Hi Ralf,
Thanks for your reply.
I agree that one test failing out of 384 is not bad, but still, when I try to use remapbil or just look for other available operators I get "cdo: command not found" (this happens also if I prepend -L as you suggest).

not finding the CDO binary is another issue. can you upload the config.log created during the build-process of CDO? or the output of

make install

The output of ./src/cdo -V is:

Climate Data Operators version 1.9.5rc1 (http://mpimet.mpg.de/cdo)
System: x86_64-apple-darwin15.6.0
CXX Compiler: g++ -std=gnu++11 -g -O2 -D_THREAD_SAFE -pthread
CXX version : Apple LLVM version 8.0.0 (clang-800.0.42.1)
C Compiler: gcc -fPIC -D_THREAD_SAFE -pthread -D_THREAD_SAFE -D_THREAD_SAFE -pthread
C version : Apple LLVM version 8.0.0 (clang-800.0.42.1)
F77 Compiler:
Features: 8GB C++11 DATA PTHREADS HDF5 NC4/HDF5 OPeNDAP PROJ.4 SSE3
Libraries: HDF5/1.8.12 proj/5.01
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5
CDI library version : 1.9.5rc1
CGRIBEX library version : 1.9.1
GRIB_API library version : 1.14.4
NetCDF library version : 4.6.1 of May 22 2018 17:21:48 $
HDF5 library version : 1.8.12
EXSE library version : 1.4.0
FILE library version : 1.8.3

looks good, IMO

the output of make install is:

Making install in libcdi
Making install in src
/Library/Developer/CommandLineTools/usr/bin/make install-exec-hook
rmdir: /Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz/lib: Directory not empty
make⁴: [install-exec-hook] Error 1 (ignored)
/Library/Developer/CommandLineTools/usr/bin/make install-data-hook
rmdir: /Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz/include: Directory not empty
make⁴: [install-data-hook] Error 1 (ignored)
Making install in interfaces
make³: Nothing to be done for `install-data-am'.
Making install in app
make<sup>3</sup>: Nothing to be done for `install-data-am'.
Making install in examples
make³: Nothing to be done for `install-exec-am'.
make<sup>3</sup>: Nothing to be done for `install-data-am'.
Making install in examples/pio
make³: Nothing to be done for `install-exec-am'.
make<sup>3</sup>: Nothing to be done for `install-data-am'.
Making install in tests
make³: Nothing to be done for `install-exec-am'.
make<sup>3</sup>: Nothing to be done for `install-data-am'.
make³: Nothing to be done for `install-exec-am'.
make<sup>3</sup>: Nothing to be done for `install-data-am'.
Making install in src/lib/ncl
make²: Nothing to be done for `install-exec-am'.
make<sup>2</sup>: Nothing to be done for `install-data-am'.
Making install in src/lib/yac
make²: Nothing to be done for `install-exec-am'.
make<sup>2</sup>: Nothing to be done for `install-data-am'.
Making install in src
../config/install-sh -c -d '/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz/bin'
/bin/sh ../libtool --mode=install /usr/bin/install -c cdo '/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz/bin'
libtool: install: /usr/bin/install -c cdo /Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz/bin/cdo
make²: Nothing to be done for `install-data-am'.
Making install in contrib
make<sup>2</sup>: Nothing to be done for `install-exec-am'.
make²: Nothing to be done for `install-data-am'.
Making install in test/data
make<sup>2</sup>: Nothing to be done for `install-exec-am'.
make²: Nothing to be done for `install-data-am'.
Making install in test
make<sup>2</sup>: Nothing to be done for `install-exec-am'.
make²: Nothing to be done for `install-data-am'.
make<sup>2</sup>: Nothing to be done for `install-exec-am'.
make²: Nothing to be done for `install-data-am'.

Thanks for your help!

your cdo binary is installed into

/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz/bin/cdo

when your run configure to build cdo, you should use the option --prefix=/usr/local or --prefix=/opt/local - depending what's already in your PATH variable. you can check it with

echo $PATH

so, just rerun configure with one of the additions above, run

make install

On MacOS you just use 'sudo', same as any *nix.

Harry

there is no directory "cdo" in /Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz/bin.
when I ran configure to build cdo I did use prefix, but maybe I did something wrong there, as I chose /Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz as location. Was this part wrong then?
(Then I had added the path to this directory for using cdo operators but that didn't seem to help).
Thanks!!!

then upload the config.log located in the directory where you ran configure ........

here it is. Thank you!

This

./configure -prefix=/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz \
         CFLAGS=-fPIC \
         -with-netcdf=/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz \
         -with-jasper=/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz \
         -with-hdf5=/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz \
         -with-grib_api=/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz \
         -with-proj=/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz

all the options you used, must be used with two '-', like --prefix and --with-netcdf

did you installed anything (like netcdf) into the directory /Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz? if you can use sudo, I'd recommend to install things into /usr/local. If you do not have root-access to your system, I usually use $HOME/local and append $HOME/local/bin to my PATH variable.

Which shell do you use? run

echo $SHELL

Yes, I had chosen to install everything in that directory. I will try again fixing the -- issue.
I can't use sudo, that's why I had chosen this directory to install things in.
If I run echo $SHELL I get /bin/bash
Sorry for this and thanks again.

using this dir is technically no problem,

1. rerun the configure with two '-' in the options
2. make && make install
3. open a shell and run

   export PATH=/Users/edoardobeltrame/Desktop/paper3/cdoStuff/cartellaPerConfiguraz/bin:$PATH

4. check installation with

   cdo -V

thanks ralf. you were right. the problem was due to the -- typo. all sorted for now. sorry about that and super thanks for your help again!

Climate Data Operators (CDO) installation
Cannot Setup CDO! Some .dll missing files appear

I downloaded cdo-1.9.10-cygwin64-Win10 file. But when I opened it and tried to start the cdo application to setup, some system errors came out as follows:
cygwin1.dll was not found
cyghdf5-101.dll was not found
cygnetcdf-13.dll was not found
cygproj-13.dll was not found
Please help me to get these system files or show me the way to solve this problem and install the program.
My aim is to extract and regrid a specific region from daily CMIP6 data sets.
Thank you

Hi Feyissa,

I guess cygwin is not installed. Did you follow the installation instructions https://code.mpimet.mpg.de/projects/cdo/wiki/Win32?
Note: There are two different ways to use CDO on a Windows computer, one using cygwin and one with WSL.

I have installed Cygwin and it displays like this

Didn't know the problem with it

I'm not a Windows 10 user but I would guess that you have to add the C:\cygwin\bin path to your system path.

Hello! I wanted to install cdo with spack as recommended in the geos chem wiki. I assumed I should specify the same compiler (gcc 9.3.0)

Hi Feyissa!

I think you installed the binary from the out webpage here, but this is not needed anymore. CDO is not an official cygwin package. you can download the latest setup.exe from cygwin.com and install cdo as a normal package. you will have the latest release version of CDO with that installation.

cheers
ralf

I'm not a Windows 10 user but I would guess that you have to add the C:\cygwin\bin path to your system path.

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