free(): invalid pointer for every cdo call

Bug #1946727 reported by Jialin Wang
8
This bug affects 1 person
Affects Status Importance Assigned to Milestone
cdo (Ubuntu)
New
Undecided
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Bug Description

Got following
```
free(): invalid pointer
[1] [PID] abort cdo sinfo xxxxx.nc
```
at the end of every output of cdo call, with or without data manipulation.

I'm using cdo (1.9.9~rc1-1) [universe] on Ubuntu 20.04 LTS.

description: updated
Revision history for this message
DanielVictoria (daniel-victoria) wrote :

I'm also seeing something similar. After a `cdo sinfo xxx.nc` I get:

```
...
cdo sinfo: Processed 1 variable over 7152 timesteps [0.06s 55MB].
free(): invalid pointer
Aborted (core dumped)
```

In fact, I get the error even if I just call `cdo` without any parameters

```
$ cdo
(... clipped output ...)
output file <0, 64, 96>; Default is 64

  Operators:
    Use option --operators for a list of all operators.

  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)
```

Revision history for this message
DanielVictoria (daniel-victoria) wrote :

Jialin. Do you have packages installed from the UbuntuGIS repository? I belive some libraries will conflict

Revision history for this message
Jialin Wang (choumingzhao) wrote :

Daniel. Thanks for your help. As far I can recalled, I've installed GDAL related pacakges from UbuntuGIS. But I cannot find which exact package may cause the conflict.

After encountering this, I've tried using `cdo` version 1.9.10 from conda and it works great.

In fact, `cdo` is quite a complicate packages to compile. It requires many additional support to include. For this version I use, it features "50GB 12threads C++11 OpenMP45 Fortran PTHREADS HDF5 NC4/HDF5/threadsafe OPeNDAP SZ UDUNITS2 PROJ XML2 MAGICS CURL FFTW3 SSE3'. I think it work great in my WSL2 machine so far.

So, for anyone who also has the need, I highly recommend you to try this conda version `cdo`.

Revision history for this message
DanielVictoria (daniel-victoria) wrote :

Hi Jialin, I'll try the conda version.

What I just found out is that I had UbuntuGIS in my sources list. And when installing CDO, it brought some libs from that PPA.

Removing the UbuntuGIS PPA and reinstalling CDO worked.
I tryed with both stable and unstable UbuntuGIS PPAs. None worked.

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