q2-2025.7 installation r-base UCX-support

[arwqiime (ARW)]

Hello,
I have received this warning when installing q2-amplicon-2025.7 as a miniconda env under linux. I tested it also with 2025.4 (which I had skipped), but the warning is the same.
Qiime2 seems to be functional, should I follow these recommendation, or can I just ignore it? I assume it has something to do with GPUs, right?

Preparing transaction: done
Verifying transaction: done
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.

In addition, I got this safety message on one of my servers. Could be due to using R also for other tasks. Is there a way to re-install r-base in conda? If yes, should I install exactly this r-base version?

SafetyError: The package for r-base located at /home/<user>/miniconda3/pkgs/r-base-4.3.3-hf0d99cb_1                                                                                         
appears to be corrupted. The path 'lib/R/doc/html/packages.html'                                                                                                                              
has an incorrect size.                                                                                                                                                                        
  reported size: 3423 bytes                                                                                                                                                                   
  actual size: 62958 bytes

Thanks a lot!
Best,

[colinbrislawn (Colin J Brislawn)]

Yes, I think you can ignore both these messages.

The first appears to be about special optimizations for Open MPI using CUDA, which is an API for GPUs, just like you said. Some software included with Qiime2 does use OpenMPI, but I don't think anything uses CUDA. I don't even recognize UCX.

I also got that SafetyError in a new conda install of R. I'm not sure what's wrong with the conda package, but I'm not that worried about a single HTML file.

[arwqiime (ARW)]

Thank you for your comments!
Best,