search

nickjcroucher / gubbins

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
http://nickjcroucher.github.io/gubbins/
GNU General Public License v2.0
175 stars 51 forks source link

Running raxML without -AVX2 options #337

Closed slmiles closed 12 months ago

slmiles commented 2 years ago

Hi,

I keep getting the error below when running gubbins

Illegal instruction (core dumped) Command 'raxmlHPC-PTHREADS-AVX2 -T 4 -safe -m GTRGAMMA -s core.full.aln.snp_sites.aln -n core.full.iteration_1_reconstruction -t /home/ubuntu/slm/gubbins/tmp382_i35u/core.full.iteration_1.tre.rooted -f e -w /home/ubuntu/slm/gubbins/tmp382_i35u' returned non-zero exit status 132.

I understand that it might be because my server doesn't support AVX2. I have installed the standard version of raxML but it is still calling the AVX2 version. Is there a way to change this?

Thank you!

nickjcroucher commented 2 years ago

What version of Gubbins are you using?

slmiles commented 2 years ago

It's version 3.2.0.

nickjcroucher commented 2 years ago

Thanks - what operating system?

slmiles commented 2 years ago

An Ubuntu server. Thank you!

nickjcroucher commented 2 years ago

The function is here: https://github.com/nickjcroucher/gubbins/blob/a9d5dcddc2907c87f695eae86805d12959090f12/python/gubbins/utils.py#L97 Is AVX2 listed in the output of grep flags /proc/cpuinfo?

slmiles commented 2 years ago

AVX2 isn't listed but AVX is.

Thank you for your help.

nickjcroucher commented 2 years ago

Thanks - I see the bug, I'll try to fix ASAP - in the mean time, if you can delete raxmlHPC-PTHREADS-AVX2 and leave raxmlHPC-PTHREADS-AVX, that should work - else IQTREE2 will give similar results.

slmiles commented 2 years ago

Great, thank you!