CDO

Hi!

I guess you make use of https://code.mpimet.mpg.de/attachments/download/14759/cdo-1.8.2-cygwin64.zip.

Just put the file in /usr/bin within the cygwin installation. Or you can change the PATH variable to include windows/system32 which is /cygdrive/c/windows/system32 AFAIK.

hth
ralf

I am receiving this error...sigh

Joseph Renken wrote:

I am receiving this error after placing it into the /cygwin/usr/bin folder...sigh

install the udunits2 library - you can check what the binary is linked to with

ldd ./cdo.exe

This was the result of ldd ./cdo.exe

I went ahead and downloaded the latest libs4cdo and placed it in my cdo folder. Upon attempting to make libs4cdo it states command not found??

Joseph Renken wrote:

This was the result of ldd ./cdo.exe

What happens, when you run

./cdo.exe

Joseph Renken wrote:

I went ahead and downloaded the latest libs4cdo and placed it in my cdo folder. Upon attempting to make libs4cdo it states command not found??

libs4cdo is a source code package, where all libraries for cdo are included. so you have to build it all yourself. As a results what you tried cannot work, sorry.

hth
ralf

This is such a headache...I attempted to run ./cdo.exe and this was the same result.

Ok, lets face it ...

• I took my win10 box, updated the cygwin installation (download and rerun latest https://cygwin.com/setup-x86_64.exe)
• downloaded and unpack https://code.mpimet.mpg.de/attachments/download/14759/cdo-1.8.2-cygwin64.zip in the home directory (within cygwin terminal)
• I ran

  ./cdo.exe

  and got your failiure regarding libudunits (cygudunit) - so I reran setup-x86_64.exe and installed all libudunits packages
• I ran ./cdo.exe again and got the missing libproj.dll (cygproj) error - so I reran setup-x86_64.exe and installed all libproj packages
• I ran ./cdo.exe, and it worked ;-)
• I copied cdo.exe to /usr/bin to use it from everywhere withing the cygwin system

My list of installed cygwin packages: https://code.mpimet.mpg.de/attachments/download/15112/installed-packages.txt

hth
ralf

Hello!

The time came for me to upgrade from cdo 1.6.9 and I am hitting an issue in getting the 64 bit windows cdo.exe to run. When I run ./cdo.exe there is simply no output at all - no errors are reported, but no output either.

I have followed Ralf's post above (in my case it's on a Windows 7 64 bit system).

I reinstalled Cygwin, and have used cygcheck -c to verify that I have all the packages installed that are listed in your file above.
I have then tried cdo version 1.8.2 (as per your post above) as well as version 1.9.3. I have tried cdo.exe in the home directory, and in /usr/local/bin with the same result.

When I try ldd ./cdo.exe I get the output as shown in the attached. What I notice is that the linked cygwin paths are all in /usr/bin/, but in my cygwin install there is no such directory. Instead my cygwin installation has all the linked dlls in /bin. Could this be an issue?

regards
David

PS: After writing this, I tried installing Cygwin on a different Windows 7 64 bit machine, and followed Ralf's post above to install libudunits and libproj packages - this time cdo works fine! So the path to the linked dlls shown by ldd doesn't seem to be the issue.

Hi David!

I will check thw binary again on my windows box. could be that thw cygwin installation on the huilding machine needs an update. in general it dosnt matter where the dll are, but not getting any output is weird.

Since you have installed all dependencies you could build cdo on you own.

cheers
Ralf

I updated the cygwin installation on the building machine and rebuild cdo (cdo.exe uploaded). the ldd output looks like this

mpimet@cdo4windows-cyg ~/ralf/builds/remote/gcc/develop/src
$ ldd cdo.exe 
    ntdll.dll => /cygdrive/c/Windows/SYSTEM32/ntdll.dll (0x77590000)
    kernel32.dll => /cygdrive/c/Windows/system32/kernel32.dll (0x77370000)
    KERNELBASE.dll => /cygdrive/c/Windows/system32/KERNELBASE.dll (0x7fefd500000)
    cyggcc_s-seh-1.dll => /usr/bin/cyggcc_s-seh-1.dll (0x50caa0000)
    cygwin1.dll => /usr/bin/cygwin1.dll (0x180040000)
    cyggomp-1.dll => /usr/bin/cyggomp-1.dll (0x5f6ec0000)
    cygstdc++-6.dll => /usr/bin/cygstdc++-6.dll (0x57b190000)
    cygcurl-4.dll => /usr/bin/cygcurl-4.dll (0x482aa0000)
    cygcrypto-1.0.0.dll => /usr/bin/cygcrypto-1.0.0.dll (0x4e76b0000)
    cygz.dll => /usr/bin/cygz.dll (0x597fd0000)
    cyggssapi_krb5-2.dll => /usr/bin/cyggssapi_krb5-2.dll (0x5f6cf0000)
    cygk5crypto-3.dll => /usr/bin/cygk5crypto-3.dll (0x41bf60000)
    cygkrb5support-0.dll => /usr/bin/cygkrb5support-0.dll (0x433a90000)
    cygintl-8.dll => /usr/bin/cygintl-8.dll (0x5ee2d0000)
    cygiconv-2.dll => /usr/bin/cygiconv-2.dll (0x3ffa50000)
    cygkrb5-3.dll => /usr/bin/cygkrb5-3.dll (0x4cc8c0000)
    cygcom_err-2.dll => /usr/bin/cygcom_err-2.dll (0x3fff60000)
    cygidn2-0.dll => /usr/bin/cygidn2-0.dll (0x484880000)
    cygunistring-2.dll => /usr/bin/cygunistring-2.dll (0x5f5a70000)
    cyglber-2-4-2.dll => /usr/bin/cyglber-2-4-2.dll (0x54fba0000)
    cygldap-2-4-2.dll => /usr/bin/cygldap-2-4-2.dll (0x54fb00000)
    cygsasl2-3.dll => /usr/bin/cygsasl2-3.dll (0x49c4f0000)
    cygssl-1.0.0.dll => /usr/bin/cygssl-1.0.0.dll (0x4c4da0000)
    cygnghttp2-14.dll => /usr/bin/cygnghttp2-14.dll (0x5ba920000)
    cygpsl-5.dll => /usr/bin/cygpsl-5.dll (0x5d5880000)
    cygssh2-1.dll => /usr/bin/cygssh2-1.dll (0x54e8e0000)
    cygproj-13.dll => /usr/bin/cygproj-13.dll (0x4fc8f0000)
    cygudunits2-0.dll => /usr/bin/cygudunits2-0.dll (0x49e260000)
    cygexpat-1.dll => /usr/bin/cygexpat-1.dll (0x5d5bf0000)

on my system /lib and /usr/lib hold the same files. Could you re-run the cdo binary I attached here?

hth
ralf

forgot the upload - a classic ...

some report from that binary for comparison

mpimet@cdo4windows-cyg ~/ralf/builds/remote/gcc/develop
$ ./src/cdo -V
Climate Data Operators version 1.9.4rc1 (http://mpimet.mpg.de/cdo)
System: x86_64-unknown-cygwin
CXX Compiler: g++ -g -O2 -fopenmp 
CXX version : g++ (GCC) 6.4.0
C Compiler: gcc -g -Wall -O2 -DPIC -pie -mwindows -fopenmp 
C version : gcc (GCC) 6.4.0
F77 Compiler: gfortran -g -O2
F77 version : GNU Fortran (GCC) 6.4.0
Features: 3GB C++14 Fortran DATA PTHREADS OpenMP45 HDF5 NC4/HDF5/threadsafe OPeNDAP UDUNITS2 PROJ.4 SSE2
Libraries: HDF5/1.8.17 proj/5
Filetypes: srv ext ieg grb1 grb2 nc1 nc4 nc4c nc5 
     CDI library version : 1.9.3 of Mar 13 2018 15:54:29
 CGRIBEX library version : 1.9.0 of Jan 22 2018 09:24:03
GRIB_API library version : 1.16.0
  NetCDF library version : 4.4.0 of Jun 21 2016 15:28:18 $
    HDF5 library version : 1.8.17 threadsafe
    EXSE library version : 1.4.0 of Mar 13 2018 15:54:15
    FILE library version : 1.8.3 of Mar 13 2018 15:54:45

Hi Ralf,

Many thanks for your quick response. Yes, I tried your new binary and it works just fine and produces the same output as above - that has solved the problem! It runs OK both in my home directory run as ./cdo.exe, and when I copy it to /usr/local/bin.

On my Cygwin install I have a /lib but no /usr/lib (and no /usr/bin). There is also a /usr/local/lib but that is an empty folder.

Thanks again for resolving this issue. I am now starting to play with cdo.py, and look forward to seeing what it will do.

Regards
David

Hello!

I'm having the same issue with installing CDO 1.9.4 (current latest) on Cygwin. The version Ralf attached above works fine (1.9.4r1) but the new one doesn't. It additionally requires 'cyguuid-1.dll' (the old one didn't) but won't start even if I add that library manually. Seems like there's something else missing but I can't figure it out Any help will be highly appreciated.

Hi Alexander!

After installing you have to open a new terminal to get the changes activated in your system. did you try it?

And why don't you take the uploaded one from this thread? if it works, it works.

cheers
ralf

Hi, Ralf!

Yes, it works but the thing that it's not a stable release is bugging me a little bit I performed a simple test: copied the 'CDO.exe' you've posted several messages above to a folder with all the libraries you've mentioned - it ran and worked fine. Then I copied an executable I'd downloaded from the official website to the same folder. Tried to run it, got an exception saying that 'cyguuid-1.dll' was missing. Copied that dll over and... nothing happened, the executable wouldn't run. No messages, nothing. It feels like it needs some more libraries. Also, the size difference between 1.9.4r1 and 1.9.4 says that there must be something else.

Cheers!
Alexander

Meanwhile I did some x-checks with our building system regarding cygwin and could re-produce this behavior. If I do a manual build, these are the dependencies:

$ ldd cdo.exe 
    ntdll.dll => /cygdrive/c/Windows/SYSTEM32/ntdll.dll (0x77500000)
    kernel32.dll => /cygdrive/c/Windows/system32/kernel32.dll (0x773e0000)
    KERNELBASE.dll => /cygdrive/c/Windows/system32/KERNELBASE.dll (0x7fefd220000)
    cyggcc_s-seh-1.dll => /usr/bin/cyggcc_s-seh-1.dll (0x50caa0000)
    cygwin1.dll => /usr/bin/cygwin1.dll (0x180040000)
    cyggomp-1.dll => /usr/bin/cyggomp-1.dll (0x3f54a0000)
    cygstdc++-6.dll => /usr/bin/cygstdc++-6.dll (0x3ea020000)
    cygcurl-4.dll => /usr/bin/cygcurl-4.dll (0x3f68b0000)
    cygcrypto-1.0.0.dll => /usr/bin/cygcrypto-1.0.0.dll (0x4e76b0000)
    cygz.dll => /usr/bin/cygz.dll (0x597fd0000)
    cyggssapi_krb5-2.dll => /usr/bin/cyggssapi_krb5-2.dll (0x5f6cf0000)
    cygk5crypto-3.dll => /usr/bin/cygk5crypto-3.dll (0x41bf60000)
    cygkrb5support-0.dll => /usr/bin/cygkrb5support-0.dll (0x433a90000)
    cygintl-8.dll => /usr/bin/cygintl-8.dll (0x5ee2d0000)
    cygiconv-2.dll => /usr/bin/cygiconv-2.dll (0x3ffa50000)
    cygkrb5-3.dll => /usr/bin/cygkrb5-3.dll (0x4cc8c0000)
    cygcom_err-2.dll => /usr/bin/cygcom_err-2.dll (0x3fff60000)
    cygidn2-0.dll => /usr/bin/cygidn2-0.dll (0x3ec4d0000)
    cygunistring-2.dll => /usr/bin/cygunistring-2.dll (0x3e9850000)
    cyglber-2-4-2.dll => /usr/bin/cyglber-2-4-2.dll (0x3ebee0000)
    cygldap-2-4-2.dll => /usr/bin/cygldap-2-4-2.dll (0x3ebe30000)
    cygsasl2-3.dll => /usr/bin/cygsasl2-3.dll (0x3ea550000)
    cygssl-1.0.0.dll => /usr/bin/cygssl-1.0.0.dll (0x3ea200000)
    cygnghttp2-14.dll => /usr/bin/cygnghttp2-14.dll (0x3eb700000)
    cygpsl-5.dll => /usr/bin/cygpsl-5.dll (0x3ea910000)
    cygssh2-1.dll => /usr/bin/cygssh2-1.dll (0x3ea270000)
    cygproj-13.dll => /usr/bin/cygproj-13.dll (0x3ea9c0000)
    cygudunits2-0.dll => /usr/bin/cygudunits2-0.dll (0x3e99f0000)
    cygexpat-1.dll => /usr/bin/cygexpat-1.dll (0x3f6420000)
    cyguuid-1.dll => /usr/bin/cyguuid-1.dll (0x3e9820000)

things should not be copied, but installed with the setup.exe program: libuuid-devel, libnetcdf-devel, libproj-devel, ...

I could not run this binary on another system, though.

cheers
ralf

my dependencies list looks exactly the same. I did install all the required packages (including devs) via Cygwin's setup. But the latest stable version still won't run It's weird that there are no errors. It simply won't start at all.

Alexander Smirnov wrote:

my dependencies list looks exactly the same. I did install all the required packages (including devs) via Cygwin's setup. But the latest stable version still won't run It's weird that there are no errors. It simply won't start at all.

its the same with the windows7-based cygwin box I use - god, how I love Windows .....

could you try a manual installation? with all libs installed, it should work with

1. download and extract https://code.mpimet.mpg.de/attachments/download/17374/cdo-1.9.4.tar.gz
2. configure with

   ./configure --prefix=/usr/local --with-netcdf=/usr/local --with-hdf5=/usr/local --with-grib_api=/usr/local \
       --with-udunits2=/usr --with-proj=/usr --enable-all-static CC=gcc CFLAGS='-g -Wall -O2 -DPIC -pie -mwindows' CXX=g++ \
       CXXFLAGS='-g -Wall -O2 -DPIC -pie -mwindows' LDFLAGS=-L/usr/local/lib LIBS='-lpthread -lm -lcurl -lhdf5_hl -lhdf5 -lz  -lsz -laec -ldl'

3. build

   make

4. install

   make install

hth
ralf

could you try this gziped binary? https://code.mpimet.mpg.de/attachments/download/18106/cdo.exe.gz that's the one I build on my win7 box ....

Hi, Ralf! Sorry for replying late. I spent last night trying to compile the source code but didn't succeed. The binary you've posted right above won't start in my system, as well as the stable one.