search

luntergroup / octopus

Bayesian haplotype-based mutation calling
MIT License
299 stars 37 forks source link

Fail to run octopus 0.7.4 on two different HCC installed from anaconda #180

Closed margrzy7 closed 3 years ago

margrzy7 commented 3 years ago

Describe the bug Hi, I have installed octopus (0.7.4) with conda: conda install -c bioconda octopus=0.7.4

on two different HCC (AMD Interlagos (6272 / 6376); Xeon E5-2670) and in both cases after executing octopus I have gotten following error: Illegal instruction

On HCC with Xeon I was able to build octopus from source.

Do you have any suggestion how I can fix this problem?

Best, Marcin

dancooke commented 3 years ago

Hi, the Bioconda package is built to a Haswell architecture - the minimum required for AVX2. I'm not keen to go to an older architecture as performance is substantially worse without AVX2 and I think most HPCs should now support that - I may reconsider if enough people report this problem. For now, your only option is to build from source. If you want to stick with Conda then you can use conda build - you'll need to edit the --architecture option in the build command. Note that if you want to run on both your AMD and Intel compute nodes with the same binary then you'll need to compile to a generic x86 architecture with SSE2. Probably the easier and better option would be to build separate binaries for the two machines - if you just run the build command on the host machine then you can omit the --architecture option as the default is --architecture=native.

brentp commented 2 years ago

Hi, in case anyone else gets here, I also had this problem on multiple installs of octopus on our HPC. When I ran an interactive node with 8G of memory, simply running octopus without any args would result in Illegal instruction . When I ran with 18GB it works fine. (The recent conda build supports sandybridge).

IdoBar commented 1 year ago

Hi @dancooke ,

I'm having the same issue... For some reason, octopus (installed via bioconda) runs well on the login node of our institute's HPC, but fails with the Illegal instruction on the compute nodes. In addition, I noticed that the conda installation is missing the distro and seaborn packages for the profiler.py script to work (and I think the script should be made available as an executable in the conda environment).

Thanks, Ido

ESDeutekom commented 4 months ago

Same issue. Is there a docker image on the docker site? It would work better (easier) with our pipeline integration this way....