HMRF on big dataset about giotto HOT 1 CLOSED

Hi Marco,

CODEX is indeed a large dataset. The error is caused by low stack limit. To increase it:

in bash and before running R:

ulimit -s #check your limit, it may be 8MB.
ulimit -s 100000 #increase stack limit to 100MB

Then run R followed by loading Giotto and doHMRF again.
If trying this did not help it or you run into other issues in the process, still increase the stack limit above, and here are a few more tips:

• Check ~/R/x86_64-pc-linux-gnu-library/3.6/Giotto/python/reader2.py. There is a line that says "sys.setrecursionlimit(50000)". Increase it to a very large number such as 100000000.
• Check ~/R/x86_64-pc-linux-gnu-library/3.6/Giotto/python/reader2.py. There is a line containing "-Xmx32g -Xms32g". Increase each of 32g to a large number such as 64g. if this is a memory issue.

Cheers,

from giotto.