Welcome to PReSTO

We installed MX software in a HPC environment using Easybuild and called the installation PReSTO. Large HPC clusters, called supercomputers essentially consist of a login node and many compute nodes. At NSC Triolith, login and compute nodes have 16 cores each while at LUNARC Aurora the login node has 40 cores, and the compute nodes 20 cores. Typical HPC workflows involve using the login node to edit sbatch scripts and submit the sbatch script via a scheduling system to one or several compute nodes available. Both Triolith and Aurora use slurm for compute jobs scheduling where the queue is controled by a fairshare algoritm. The algoritm gives queue priority according to how much compute time has been spend for project A in comparison with jobs scheduled for project B etc.

When sharing compute time of a common project the workflow of the individual users have to be adapted not to waste compute time and getting the most out of each session. Questions will arise like:

• what MX software is parallel and able to use several cores of a single compute node?
• what MX software can use multiple compute nodes? and will adding multiple nodes reduce wall-clock time?
• how long wall-clock time will my parallel compute job take?
• how to balance the required resources in cores and compute time to the MX job in question?
• will asking for more nodes, cores and compute time give me a longer wait time in the job queue?
• how to optimize graphics experience?

The correct answer to these set of questions depend on the problem at hand, the software in question and will change due to software upgrades etc. however asking for just right amount of cores and compute time for the compute job at hand is the key to an efficient HPC workflow.

Access to PReSTO installation

Simply join the academic PReSTO project and once a member the thinlinc application from cendio can be downloaded and installed on any Linux/Mac/Windows computer and enable convenient access to Triolith and Aurora. After thinlinc login to Triolith/Aurora you get a linux desktop environment giving you the impression that you just login to your own linux workstation.

Running MX software

Interactive MX graphics software

Many MX graphics softwares are available for interactive work such as coot for macromolecular model building, pymol/ccp4mg/chimera for making publication pictures and presentation movies, or adxv/albula for inspecting diffraction images. Graphics softwares are preferentially launched from the PReSTO menu using accelerated gl mode by default

In some cases you may want to launch coot/pymol from a certain directory and to use the accelerated gl mode from a terminal window one should proceed as:

Open a terminal window, go to the directory of interest and

module load CCP4
coot             - at Aurora
vglrun coot      - at Triolith

where vglrun in front of coot is required at Triolith for open-GL acceleration of graphics, happening automatically at Aurora

To launch pymol in accelerated gl mode from a terminal window

module load PyMOL
pymol             - at Aurora
vglrun pymol      - at Triolith

The interactive softwares should be run at the login node and no compute time is crediting the PReSTO project snic2018-3-251

Interactive MX software that ALWAYS performs parallel computing

Some MX software GUIs are intended to prepare for a parallel compute job by highlighting the relevant input parameters and share output in shape of images instead of ASCII logfiles. There are three softwares of this kind in PReSTO being:

• XDSAPP
  
• XDSGUI
  
• hkl2map

XDSAPP, XDSGUI and hkl2map should always be run at a compute node and by launching the software using the PReSTO menu the software selected will be launched at a compute node using a custom made dialogue box. Another advantage of using the PReSTO menu for XDSAPP, XDSGUI and hkl2map is that once jobs are finished and GUIs terminated the remaining compute time estimated in the dialogue box is saved for later use.

To launch parallel MX software at a compute node (not using PReSTO menu and not recommended)

interactive --nodes=1 --exclusive -t 1:00:00 -A snic2017-1-xxx 
module load XDSAPP
xdsapp

The “interactive” command above reserve a compute node for 1 hour and once finished you must close the XDSAPP window and perform “exit” in the compute node terminal window to save the remaining compute time.

Interactive MX software that can submit jobs to the queue

The Phenix GUI can be run at the login node and submit parallel compute jobs to the HPC job queue via its inherent scheduler. For that reason the PReSTO menu launch Phenix GUI at the login node and whenever a parallel job is required the user can send it to the HPC queue. Examples of parallel phenix routines called wizards are:

phaser
autobuild
rosetta_refine
mr_rosetta

Interactive MX software that CANNOT submit jobs to the queue

The example here is ccp4i and ccp4i2, however we are working to enable slurm scheduling by the "Run on server" option in ccp4i2. Many MX softwares in ccp4 are not parallel such as

refmac5
arpWarp
molrep
chainsaw
etc.

When wanting to run parallel ccp4 software for instance:

phaser
buccaneer

it is recommended to proceed as:

interactive --nodes=1 --exclusive -t 1:00:00 -A snic2017-1-199
module load CCP4
ccp4i2

and set the appropriate keywords in the GUI before pressing “Run”. We are developing a “Run on server” option for slurm scheduling in ccp4i2.

MX software for computing without GUI

Many MX softwares intented for computing do not have a graphical user interface

autoPROC
arcimboldo_lite
buster
crystFEL
pipedream (part of buster)
rhofit (part of buster)
sharp
XDS
XDSME
xia2 --dials
xia2 --3dii

MX software without GUIs are preferentially run using an sbatch script for convenient submission to compute nodes. An sbatch script is the most efficient way of using a HPC system since once jobs are finished the allocation time is terminated.

Members of the protein crystallography community are invited to share your best "tips and tricks" and together we will be able to make the most of the PReSTO installation.

Oskar Aurelius from Stockholm University sharing his first multi-node CrystFEL script.

Welcome to PReSTO!