Not enough memory

[stra...@protist.eu]

Hi Minh,

I was trying to calculate a tree and although in the log file it says "NOTE: 170943 MB RAM (166 GB) is required!" and I booked a node with >250 GB and also used the -mem option in the command (see below), I got the following error:

ERROR: STACK TRACE FOR DEBUGGING:
ERROR: Not enough memory, allocation of 111316391712 bytes failed (bad_alloc)

Here is the command I used:

Host:    r1.uppmax.uu.se (AVX2, FMA3, 251 GB RAM)
Command: /home/user/software/iqtree-1.6.5-Linux/bin/iqtree -s file.fasta -m LG+C60+G+F -bb 1000 -bnni -wbtl -nt 20 -mem 250G
Seed:    743690 (Using SPRNG - Scalable Parallel Random Number Generator)
Kernel:  AVX+FMA - 20 threads (20 CPU cores detected)

Do you have any idea what caused the crash?

Best, Jurgen

[Minh Bui]

Hi Juergen,

The problem is that currently -bnni option will lead to double the amount of memory required. We’ll fix this but for now, can you switch to another computer with twice RAM the amount reported in "NOTE: 170943 MB RAM (166 GB) is required!”.

Thanks,

Minh

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[stra...@protist.eu]

Hi Minh.

Thanks, this explains why it crashed. Do you have a fixed version already (maybe on GitHub) that can be used? I am asking because I need many trees that would take forever using the resources I have.

Thank you,

Jürgen

[Minh Bui]

Hi Jürgen, 

Not yet, but one thing that could help: use "-mem 120G”. This will restrict the RAM for the tree search phase to this amount and the later -bnni phase as well. So in total IQ-TREE will not exceed 240G. Let me know if that works.

Minh