Dear CCTBX/PHENIX developers, According to PHENIX FAQ: https://www.phenix-online.org/documentation/faqs/index.html#general
In addition to these options, it is also possible to compile phenix.refine and Phaser with the OpenMP library, which automatically parallelizes specific instructions such as the FFT. This requires using the source installer for Phenix, and adding the argument "--openmp" to the install command. Because of threading conflicts, OpenMP is not compatible with the Phenix GUI.
FFT in phenix.refine can be parallelized if OpenMP is enabled. However, it seems incorrect since 2017 due to this change: https://github.com/cctbx/cctbx_project/commit/3e932248e0491847a04ddeee429f8f... The FAQ may need updating, but I am curious to know why it is disabled now. Best regards, Keitaro