Docker container is sleeping with -p 0 option

[chrstphdm]

Hello,

I'm using the Docker to run cnvkit with the -p 0 option.

After Splitting step and Indexing bam step, the program is freezed with no error. Nothing seems to be running with 'docker top container_name'.

I've suspected a multithread problem because when I try to stop the program with ctrl-c, the following message is printed :
Traceback (most recent call last): File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap

So I've tried to execute the same command with -p 1; -p 2; etc. -> NO MORE PROBLEM !

I think that there is a problem with the -p 0 option with docker container. I'm sorry not to be more usefull but my expertise stop here. :/
Tell me if you want me to do more tests.

[etal]

Thanks for reporting, this is pretty weird.

I've just updated the container image on docker hub to the latest version 0.8.0. This includes some recent changes to the parallelism code, namely using concurrent.futures instead of multiprocessing directly. Could you try again with the latest?