Illegal Instruction on on install of qiime2-2022.8

[alexkrohn]

Hi there. I'm getting an illegal instruction error when Qiime2 tries to cache my current deployment. I'm running qiime in a new conda environment on a Ubuntu 20.04 machine. My conda version is 4.14.0

I am following the installation instructions to the letter:

conda update conda
wget https://data.qiime2.org/distro/core/qiime2-2022.8-py38-linux-conda.yml
conda env create -n qiime2-2022.8 --file qiime2-2022.8-py38-linux-conda.yml
conda activate qiime2-2022.8
qiime --help

This yields the error:

QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Illegal instruction (core dumped)

I'm not sure what's going wrong here. I have successfully installed older versions of Qiime on this computer before. For example, this works just fine:

wget https://data.qiime2.org/distro/core/qiime2-2022.2-py38-linux-conda.yml
conda env create -n qiime2-2022.2 --file qiime2-2022.2-py38-linux-conda.yml
conda activate qiime2-2022.2
qiime --help

[lizgehret]

Hi @alexkrohn,

Thanks for reaching out!

This is certainly an interesting error - looks like we've come across this a couple of times before with folks on Ubuntu using virtual machines to run QIIME 2:

Installation error: Illegal instruction (core dumped)

Hi colleagues, I installed Q2 on my ESXi virtual machine (6 CPUs x Intel(R) Xeon(R) W-2133 CPU @ 3.60GHz, Ubuntu 18.04.2) with conda as the official instruction. The installation runs well, but every time when I try to activate the q2 I get the sam error: QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. Illegal instruction (core dumped) I tried to uninstall the qiime2 environment and reinstall it, like …

Error: Illegal instruction (core dumped)

Dear colleagues, We just bought a new computer basically to do a lot of analysis with qiime2 and other bioinformatic software. The processor is an Intel ® Core ™ i9-9820X CPU (20 cores) with 128 GB RAM. I have installed today VIrtual Box v.6.0.8 and the last image of qiime2 (2019.4). This configuration works perfectly in other (older/simpler) PCs. The host operative systems is Windows 10 Pro. We are using the computer as a headless server. The installation of q2 image works apparently very we…

A couple of initial questions for you:

1. Are you doing a native install on Ubuntu, or using a virtual machine?
2. Do you have numpy installed separately in the environment you are attempting to install QIIME 2 within? And if so, what version of numpy is it? You can run conda info to list all of the current packages/versions in your environment.

Cheers

[alexkrohn]

Hi @lizgehret!

I am running it on a native install of Ubuntu, not a virtual machine. My apologies if I missed this error before, but I didn't see any problems with native installs in the forum.

In the new qiime environment where qiime does not work (qiime2-2022.8), the numpy version is 1.23.2. In my base environment, where qiime is not installed, numpy is not installed.

conda activate qiime2-2022.8
conda list | grep numpy
# numpy                     1.23.2           py38h3a7f9d9_0    conda-forge
conda deactivate
conda list | grep numpy
#

[ebolyen (Evan Bolyen)]

Hey @alexkrohn,

Sorry you're running into this, Ubuntu is certainly supported, and a common platform for us. I expect there's something misbehaving between what your processor supports, and what math library is being used (such as openBLAS or MKL, which numpy uses).

I guess to get started, could you tell us more about your processor? Ideally we would like to see the info in /proc/cpuinfo, so if you could run this command and upload the result, that would help out:

cat /proc/cpuinfo > cpuinfo.txt

Next could you provide the result of (in your environment):

conda list blas

and

conda list mkl

(I expect this one to be empty).

Last step, could you run this small script which will load each QIIME 2 plugin and print each import involved? Then if you could upload the result, I expect the last line to be our culprit:

python qiime_more_info.py > more_info.txt  # remember to download the script