free(): invalid pointer error on CDO installed from Ubuntu package

Added by Daniel Victoria almost 3 years ago

I'm running Ubuntu 20.04 and I installed CDO from the ubuntu package repository with the command sudo apt install cdo

When I run any CDO command, even without an argument, I get the usual usage explanation and then it ends with following error:

$ cdo

No operator given!

usage : cdo [Options] Operator1 [-Operator2 [-OperatorN]]

(... clipped...)

CDO version 1.9.9rc1, Copyright (C) 2003-2019 Uwe Schulzweida
This is free software and comes with ABSOLUTELY NO WARRANTY
Report bugs to <https://mpimet.mpg.de/cdo>

free(): invalid pointer
Aborted (core dumped)

This has been reported in Ubuntu launchpad (https://bugs.launchpad.net/ubuntu/+source/cdo/+bug/1946727). Any idea what is going on or how to debug this?

Thanks
Daniel

Replies (9)

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Ralf Mueller almost 3 years ago

hi!

as a workaround you can use CDO via conda. it's a bit hard to comment on non-release versions to be honest. I think this a problem to be solved by the devian/ubuntu maintainers. maybe they can provide a 1.9.10 version.

cheers
ralf

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Daniel Victoria almost 3 years ago

Thanks,

I'm suspecting it's something that is installed on my system. A colleague of my has a similar setup and all works just fine.

Will try to investigate further and any news, I'll get back

Cheers

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Daniel Victoria almost 3 years ago

I looks as though some libs from UbuntuGIS PPA [1] are messing with CDO installation. Removing this PPA from may package sources and reinstalling CDO fixed the problem. However, I need some software from UbuntuGIS. So off to try the Conda instalation

Cheers

[1] - https://launchpad.net/~ubuntugis/+archive/ubuntu/ppa?field.series_filter=focal

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Ralf Mueller almost 3 years ago

thx for the feedback, Daniel. I agree - another package manager like conda might be helpful. But using multiple at the same time can always lead to inconsistencies.

Keep the conda stuff as simple as possible, at best you only install CDO.

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Miles Sowden about 2 years ago

error still persisting
cdo -v gave the following errors

CDO version 1.9.9rc1, Copyright (C) 2003-2019 Uwe Schulzweida
  This is free software and comes with ABSOLUTELY NO WARRANTY
  Report bugs to &lt;https://mpimet.mpg.de/cdo&gt;
free(): invalid pointer
Aborted (core dumped)

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Ralf Mueller about 2 years ago

we dont manage the ubuntu packages, sorry. In that case you have to get in contact with the debian package manager

you can use this link for more information https://packages.debian.org/de/sid/cdo

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Daniel Victoria about 2 years ago

I've contacted Angelos Tzotsos from the the UbuntuGIS. He did try to fix this issue but things haven't evolved. You can check our email exchange here:

https://lists.osgeo.org/pipermail/ubuntu/2022-February/thread.html

https://lists.osgeo.org/pipermail/ubuntu/2022-March/thread.html

Cheers

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Ralf Mueller about 2 years ago

As long as the original ubuntu package is not fixed, you might use conda instead

RE: free(): invalid pointer error on CDO installed from Ubuntu package - Added by Daniel Victoria about 2 years ago

In case it helps, I found an old docker recipe online and I updated it to compile CDO 2.0.6. If anyone is interested, it's on github: https://github.com/dvictori/docker-cdo

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