PReSTO in support of Swedish structural biology

Structural biologists use Macromolecular X-ray crystallography (MX), Nuclear Magnetic Resonance (NMR) and cryo Electron Microscopy (cryo-EM) to determine 3D structures of macromolecules such as proteins, DNA and RNA. To address complex research questions structural biologists is now stretching towards cellular length scales with techniques such as cryo-EM tomography and X-ray imaging while capturing dynamics via correlative microscopy and molecular dynamics (MD) simulations. The multi-purpose and multi-technique approach to characterize how macromolecules and their assemblies interact with virus and other pathogens in space and time is known as integrated structural biology. Today structural biologists experience an increasing amount of experimental raw data being collected by modern photon counting detectors at national and international facilities. Swedish structural biology research groups using the Swedish MAX IV light source for macromolecular X-ray crystallography and the cryo-EM facilities at Science For Life laboratories are generated large amounts of raw data that require supportive and research driven computational and storage solutions.

In november 2015, MAX IV and NSC formally decided to develop a HPC platform for MX in support of Swedish MAX IV users giving the PReSTO project the status of a MAX IV satellite.

Swedish structural biologists can access and use PReSTO by requesting membership in compute project (SNIC 2019/3-326):

  1. Download and install thinlinc client for your computer
  2. Register yourself in SNIC User and Project Repository (SUPR)
  3. Go to SUPR Project page
  4. Search for SNIC 2019/3-326 and Request membership in that project
  5. MX software may require academic online registration (e.g. Phenix), or signing of an academic license agreement on paper (e.g. CCP4). We made a set of links to license pages for MX software available in PReSTO. Once your personal academic registration and licensing is done, please contact LUNARC that will add the newcomer to the PReSTO group for MX software access at LUNARC.
  6. LUNARC Aurora access: General and MAXIV specific instructions
  7. NSC Tetralith access: Accept the user agreement and Request the login account at Tetralith

SMEs can access and use PReSTO via SMILE.

The PReSTO installation has been performed by Easybuild for rapid sharing with other Swedish HPC centers coordinated by SNIC. We have installed the majority of MX software at NSC computer Tetralith, LUNARC computer Aurora and the MAX IV cluster. The installations at NSC and LUNARC is available through SNIC while the MAX IV cluster is accessible when having MX beamtime at MAX IV.

A HPC computer consist of a few login nodes(i.e. computers) and many compute nodes, where the login node is typically used for remote graphics applications and the compute nodes for heavy computing. We develop a Linux Desktop menu for my own Linux computer look and feel that direct the users towards running software either at the login node or at the compute nodes. Easybuild also enable transfer of environment variables to the compute nodes as been shown important to MX software that depend on Perl such as pipedream from GlobalPhasing.

Now in 2020, we have a SNIC storage project (SNIC 2019/35-61) to support the compute project. Storage will be ramped up at NSC Tetralith reaching 20 TB and 10 M files in December 2020, while at LUNARC Aurora we already have 20 TB and 10 M files (no ramping). However if this is too small for your project or if you plan to run molecular dynamics simulations, apply for your own compute time at NSC Triolith or LUNARC Aurora or perhaps at Kebnekaise if interested in Cryo-EM. PReSTO project membership grant access to MX software however having your own compute time allocation is required when combining MX with compute intensive molecular dynamics or Cryo-EM calculations.

Aim of PReSTO tutorial

This homepage contains startup instructions for the Easybuild installation of MX software that we call PReSTO. We attempt to guide HPC beginners in using the PReSTO environment and simply share links to excellent MX software guides and tutorials generated by MX software developers. Many MX softwares can be conveniently launched from the PReSTO menu.

PReSTO and version control

We have placed each individual software package in PReSTO under version control.

  1. Today in April 2020, we have installed version 3.0 at NSC Tetralith, MAX IV and LUNARC Aurora
  2. We can update and test new versions of individual software packages without disturbing the current release of PReSTO version 3.0
  3. When sharing a new release, the default version/module of each individual software package changes
  4. Users can check what Phenix versions are installed using

    module spider Phenix
  5. If required users can load older/newer versions installed but not being the default version by giving full specification of module as

    module load Phenix/1.17.1-3660-Rosetta-3.10-4-PReSTO
  6. Update and test installed software prior to release is the best way to create a stable user experience
  7. Today 2020-02-21, PReSTO version 3.0 is available at MAXIV and Tetralith, and PReSTO version 1.0 at Aurora

Acknowledgements to MX software authors

We are indepted to all MX software authors that kindly share their software for academic use in an HPC environment. We list all MX software currently in PReSTO installation with links to software home page and citations. Specifically we want to mention Gérhard Bricogne and Claus Flensburg from GlobalPhasing supporting the PReSTO project since its very beginning and shared all their MX software for academic HPC use including autoPROC with Staraniso for convenient elliptical scaling of diffraction datasets. We also want to mention the developers behind XDSAPP version 2.99 (Karine Röwer, Uwe Müller and Manfred Weiss) sharing a pre-release that can process Eiger data containers directly and Graeme Winter from the DIALS development team sharing a BioMAX specific software patch for DIALS.

User Area

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Applying for projects and login accounts.

System status

Everything OK!

No reported problems

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