Phenix installations at NSC


Directory list:

VersionDescription
1.8.4 PHENIX release 1.8.4

Level of support

Tier 3 NSC will not be able to help you much with this program, either because we lack the in-house experience, or because it is a test installation. In general, these types of installations are untested, and will not be updated unless you send a request to NSC.

Please see the page describing our software support categories for more information.
You can also contact support@nsc.liu.se for further information.

PHENIX is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods.

Developer’s homepage: www.phenix-online.org

The PHENIX installations are generally maintained by Johan Raber or Torben Rasmussen. Please contact NSC Support if you have any questions or problems.

How to run

You can either run the job locally in an interactive allocation or using a batch script that you submit to the queuing system:

  1. Run jobs in an interactive allocation
    • Get an interactive allocation
    • Start the PHENIX GUI
    • Set up the desired job by adding files and choosing relevant options
    • Run the job (Run>Run locally)
  2. Run jobs using a batch script
    • Start the PHENIX GUI
    • Set up the desired job by adding files and choosing relevant options
    • Create a parameter file for the job (Save)
    • Create a batch script for the job
    • Submit the script to the queue using the sbatch command

Please note that the PHENIX GUI currently doesn’t support the queuing system that we use on Triolith, so you cannot submit batch jobs from the PHENIX GUI. Instead you have to use the procedure outlined above.

Getting an interactive allocation

To get an interactive allocation, you need to use the interactive command with options defining how long time you need the allocation and how many processes you want to run. For example:

$ interactive -t 4:00:00 -n 5

This command will set up an interactive allocation for 4 hours, where you can run up to 5 processes in parallel.

To allocate a complete compute node, where you can run up to 16 processes in parallel, you use the following options:

$ interactive -t 4:00:00 -N 1 --exclusive

This command will set up exclusive access to one compute node for 4 hours.

NOTE that it can take quite some time to get a long interactive allocation, so if you need to run a job that requires a long allocation, you should consider running it using a batch script instead!

Starting the PHENIX GUI

When running the PHENIX GUI, NSC recommends using ThinLinc to access Triolith.

For more information on how to use ThinLinc, please see: www.nsc.liu.se/systems/triolith/#accessing_triolith_thinlinc

To start the GUI, you first need to load the desired version of PHENIX and then execute the phenix command:

$ module load phenix/1.8.4
$ phenix

Running jobs using a batch script

Set up the job using the PHENIX GUI and save the parameter file. Open a text editor and create a batch script like the one in the example below. NOTE that you can use any available text editor (e.g. vim/gvim or nedit) to create and edit the batch script.

Example script for runing phenix.autobuild:

#!/bin/bash

#SBATCH --time=1-00:00:00
#SBATCH --ntasks=5
#SBATCH --mail-type=ALL

module load phenix/1.8.4
phenix.autobuild my_parameter_file.eff

This script will allocate 1 day (24 hours) for the job and resources to run 5 processes in parallel. Please note that in order for phenix.autobuild to actually run in parallel, you need to specify the correct parameters in your parameter file. Consult the phenix.autobuild documentation regarding how to do that.

NOTE that you need to change my_parameter_file.eff to whatever you called the parameter file when you saved it.

The script is then submitted to the queue with:

$ sbatch name_of_script

NOTE that you need to change name_of_script to whatever name you gave your script when you saved it.