Coming back to my own topic ages later, but if anyone in the future ends up on this subject, there is what we found in the end: the problem was from HDF5/Netcdf4 on our new cluster.
It’s still very unclear why, as we don’t have a real solution to the problem, but the parallel HDF5/NetCDF4 version we have on the cluster hangs like crazy when using the parallel I/O in XIOS. Our workaround was to use the multiple_file writing option in XIOS. With that, no more hanging, and everything is fast again.