Just tried to install the 2026.1 version and got this error:
ERROR conda.core.link:_execute(1033): An error occurred while installing package 'conda-forge::openmpi-4.1.6-hc5af2df_101'.
Rolling back transaction: done
LinkError: post-link script failed for package conda-forge::openmpi-4.1.6-hc5af2df_101
location of failed script: /home/ty/miniforge3/envs/qiime2-amplicon-2026.1/bin/.openmpi-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout:
stderr:
return code: 1
()
The following didn’t work:
conda clean --all
Tried to install version 2025.10, got the same error.
Solution
Check the version of conda and downgrade
#check conda version
conda --version
#if 26.1, then downgrade
conda install conda=25.11
conda clean --all
Install qiime 2026.1 as usual.
This time it was installed, though got a lot of ClobberError and the following warning:
Executing transaction: -
For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
mpiexec --mca opal_cuda_support 1 ...
In addition, the UCX support is also built but disabled by default.
To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
Equivalently, you can set the MCA parameters in the command line:
mpiexec --mca pml ucx --mca osc ucx ...
Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
Please consult UCX's documentation for detail.
@lizgehret Let me know if I need to separate it into a separate topic. Just decided to leave it here if somebody starts searching the same issue.
Hey @timanix, yeah let's split this into a separate topic- I can go ahead and do that! I actually thought I had locked the announcement to prevent any replies, but maybe that doesn't apply to mods
Okay so just to get some more details @timanix, I'm guessing you're using the linux environment file (based on that last warning message)? Is this something you've ever run into with any prior QIIME 2 installs, or just 2026.1? And it looks like you updated (and then subsequently downgraded) your version of conda recently? On your linux machine, can you also run ldd --version and let me know what the output is? Sorry for so many questions, just trying to get more info on where this might be coming from!
Yes, I am using Ubunu 24.04 as main OS (not WSL). So I used the command for Linux/WSL
First encountered it with 2026.1, then right after it with 2025.10 - it is why I decided to downgrade conda, since I already used earlier qiime2 version 2025.10 and it worked. Though, “ClobberError” errors I already had with previous versions.
Yes, that is right.
Output:
ldd (Ubuntu GLIBC 2.39-0ubuntu8.7) 2.39 Copyright (C) 2024 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Written by Roland McGrath and Ulrich Drepper.
Okay so you are running on quite a modern version of ubuntu, it's interesting that downgrading conda had a positive effect...
With regards to the outcome after you downgraded conda, you received those warnings & ClobberError but afterwards you were able to activate/use the environment as expected?
Can you provide the output of qiime info and conda info when that environment is activated?
Thanks for all of this - everything looks as I'd expect, and these are all reasonable virtual package versions & system versions in your conda instance... That being said, since downgrading conda did fix the initial issue, I think we can table this for the time being - but I'll keep a close eye out to see if anyone else runs into the same problem on linux, and please reach back out and let me know if you run into anything else unexpected!
Thank you for keeping an eye on it - probably it is not crucial for 2026.1 release but may pop-up in later releses again.
You probably already saw it somewhere, but with q2 versions 2025.10 and 2026.1 I am getting these warnings with any of q2 commands:
/home/ty/miniforge3/envs/qiime2-amplicon-2025.10/lib/python3.10/site-packages/unifrac/__init__.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
But both versions work as expected, so I just ignore them.
Sadly yes, these pkg_resources deprecation warnings have been the bane of my existence over the last 6 months I have been slowly working through all of the internal (and external) packages that were still calling pkg_resources, and I think these warnings will finally all be gone in the 2026.4 release. We are still seeing them with unifrac because we can't upgrade to a newer version of that package until we upgrade our version of python. Long story short though, you can keep ignoring those warnings and they should be gone in the next release
