When setting a mem-usage smaller than 10MB, segway will fail to run regardless of input

hoffmangroup / segway

Application for semi-automated genomic annotation.

http://segway.hoffmanlab.org/

GNU General Public License v2.0

13 stars 7 forks source link

When setting a mem-usage smaller than 10MB, segway will fail to run regardless of input #51

Closed EricR86 closed 8 years ago

EricR86 commented 9 years ago

Original report (BitBucket issue) by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

When trying to run segway with a small memory progression, the ulimit running in segway-wrapper.sh is given a negative value and will produce an "invalid argument" error.

This is because in calc_mem_limit inside segway/cluster/common.py, the given memory is subtracted by MEM_GUARD without a bounds check. MEM_GUARD is preset to 10 MB.

EricR86 commented 8 years ago

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

changed state from "new" to "wontfix"

Practically, no one is going to be running segway with less than 10MB of memory