codepy NOT working with gcc 11.2.0

[Overcraft90]

Hi there,

I'm struggling to make codepy to work with the following gcc version:

gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Now, I really need it because it is required by a tool that performs scaffolding and leverages both GPU acceleration and PyCUDA. If it is helpful I cna report the error; however, based on what the developer for the tool said codepy for working need gcc vesion not greater than 8.x.x.

On the other hand, I really do not want to remove my gcc version since this might cause issues with XOrg driver (which I experienced before and are rather unpleasant to deal with). I also tried to install gcc 8.5.0 from shell, but unsuccessfully; later, I resorted to install it from the .bin file but even so, there is no way for me to use it in combination with the tool I need.

Thus, I was wondering is there any chance I can make it work with gcc 11.2.0

[inducer]

Your report doesn't nearly have enough information for anyone to help you.

• What did you do? (precisely)
• What happened?
• What did you expect to happen instead?

[Overcraft90]

Sorry, I apologize I will start explaining what I was doing.

I basically tried to scaffold a human genome using a tool (instaGRAAL) which requires both CUDA and PyCUDA to be installed. I did so, and after struggling a bit, I got both my nvidia-smi & nvcc -V commands showing the correct output.

However, after few moments the tool was running I faced the issue reported in this log file, stdout_codepy.log, which based on the developers of the tool is related to an incompatibility between GCC and codepy...
Here, it is also mentioned toolchian.py which I'm not familiar with neither do the developers addressed that particular script.

Coming to what I'm expecting to get, I essentially should have the tool processing my scaffolds (portions of the human genome) so that they can be re-ordered according to the information about their positions generated by the tool in a former step, which didn't call for codepy yet.

Let me know if you need any further details.

[inducer]

I'd say your main problem is

/usr/bin/ld: cannot find -lpython3.10m: No such file or directory

Codepy seems to think that file should be in /usr/lib/x86_64-linux-gnu.

[Overcraft90]

Hi again,

You were right! Sorry but I'm quite new to the field and couldn't figure out the issue myself... However, as per another library, I created a soft-link to the one the tool was pointing at.

Now it works perfectly, thanks a lot! I think we can close this issue.