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,