Installation
- src files can only be retrieved with phenix login credentials. They are only valid for a month roughly - as a result new credentials need to be requested for academic purpose.
- The build script will therefore expect the un-tared downloaded phenix folder in the BUILD_DIR folder
- the default $PMODULES_TMPDIR is too small for phenix and needs another place. export PMODULES_TMPDIR=/w/y/w/ in the terminal (not in build script, does not work), I used /afs/psi.ch/groups/HPCE/user/assman_g/..
- the installation of Phenix requires the owner of the files in the BUILDBLOCK_DIR to be the same as the owner of the PREFIX DIR. in a nutshell : files need to be owned by adm account in the BUILDBLOCK_DIR . ( which is why AFS is a good place to put this, as I can write as assman_g and assman_g-adm there, and files need to be owned by assman_g-adm for the install )
- phenix needs sourcing of a shell script when loading the module: Problem- when unloading, the variables stay defined. ...TODO: find a way to unset these variables as well.
Installation with Rosetta
As of July 2024, phenix 1.21 exists, and also Rosetta 3.14. These do not work together , as phenix/1.21.1 misses a file called command_line.py , which is existent in phenix 1.20 and is required for Rosetta. Also the compilation of phenix+Rosetta fails on RH7, so def needs to be done on RH8 nodes (Ra) and Rosetta 3.14 fails during compilation. --> check for new phenix releases if the compatabilty with Rosetta latest release was tested etc .
As a result, phenix/1.20 plus Rosetta 3.13 is used. (July 2024)
The installation of Rosetta +phenix requires a fully functional new phenix installation. A phenix command is run after the installation of Rosetta that builds the interface between the two:
- Install Rosetta as usual (see Pmodules MX Rosetta build script)
- copy the site.settings file into the correct folder as described in "NOTE: On linux, if you are using GCC 5.1 or later (Ubuntu 16.04 or later), there is an ABI change that requires an additional flag to allow linking between our CentOS 6 binary build and Rosetta. To apply this flag, copy this site.settings file to ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings before running this final step" "(https://phenix-online.org/documentation/reference/rosetta_install.html)
- the run the command
rosetta.build_phenix_interface nproc=10
- run rosetta.run_tests to test it.
Additional Remarks
the phenix help pages (BB archive) does not work.