[Debichem-devel] Bug#1107330: Bug#1107330: openbabel: autopkgtest uses incredible amount of memory on s390x

[Andrius Merkys]

Hello,

On 2025-06-05 20:41, Paul Gevers wrote:
> I was debugging performance issues on ci.debian.net today, and noticed 
> that s390x was running into memory problems. openbabel quickly became a 
> suspect and indeed it turns out to use an insane amount of it during the 
> test.
> 
> I have spotted at least this (not the worse) in top:
>      PID USER      PR  NI    VIRT    RES    SHR S  %CPU  %MEM     TIME+ 
> COMMAND
>   653405 xxxxx     20   0   90.1g  26.7g   9908 D   6.3  85.0  10:04.02 
> python3
> 
> And the peak I spotted while looping free -h was 72 GB added by the test
> and then I killed the test run.
> 
> I'll add openbabel to the reject_list and will remove it again when this 
> bug report is closed.

Certain modes of operation of openbabel are known to leak memory, for 
example [1][2][3]. I did not investigate further, but running tests 
under valgrind might be the first step to that direction.

Best,
Andrius

[1] https://github.com/openbabel/openbabel/issues/2370
[2] https://github.com/openbabel/openbabel/pull/2772
[3] https://github.com/openbabel/openbabel/pull/2735