-max-memory ignored

[osowiecki]

In [DSK: Pass 1/1, Step 2: counting kmers ] the memory limit seems to be ignored. Minia went over the ram limit and entered SWAP.

[rchikhi]

by a lot? (thanks for the report anyhow) DSK tries to aim for that memory usage but it's not a hard threshold, it may go higher due to hashing biases

[osowiecki]

Told it to use --max-memory 180000 and it used up 189G/189G (htop) and moved to swap. Can't tell how much swap it used as other applications filled up some swap previously. I assumed GATB is using Megabytes, not Mebibytes for this option.

free --mega total used free shared buff/cache available Mem: 198027 2780 908 0 194338 19378

free --mebi total used free shared buff/cache available Mem: 193386 2716 900 0 189768 189246

[rchikhi]

I see. I'd say it's a bit risky to ask minia (or in fact, any big data program) to use close to the max memory of a system. If you significantly lower max-memory, all's fine?

[osowiecki]

Waiting for new results. Will edit this reply.