neherlab/pan-genome-analysis

segfault error

amilesj opened this issue · 2 comments

amilesj commented

Hello,

I would like to try out panx but I am getting a generic segfault error when attempting to run it on the TestSet on my local cluster. I'm not an experienced programmer, so any guidance for how to troubleshoot would be greatly appreciated.

Arianna

rneher commented

could you give us some more detail? At what stage does it crash? What is the last entry in the logs? You might want to change the following line in the run-TestSet.sh
./panX.py -fn ./data/TestSet -sl TestSet -t 64 > TestSet.log

to

./panX.py -fn ./data/TestSet -sl TestSet -t 2 > TestSet.log

if you are running it on your local computer.

amilesj commented

Thanks for the quick response, it's working now! Turns out I just didn't reduce my number of threads quite enough for my computing environment.