Hi @Stavrosb,
We've previously seen a similar situation occur. In that case, use of export UNIFRAC_USE_GPU=Y was a viable workaround. We further introduced a bug fix to failover on autodetection in version 1.2.1 to address the discovered issue there, although that version isn't yet part of a QIIME 2 environment.
What's unusual here is the workaround does not work. Could you try adding the following as well? It will tell us a little more about what's going on
$ export UNIFRAC_GPU_INFO=Y
One other possibility, is it feasible to request access to the GPU through your batch system?
Best,
Daniel