Phaser
From PRAGMAgridWIKI
Contents |
Application Name and Description
MOLECULAR REPLACEMENT - GRID
The most common method in structure deteremination by crystallography is molecular replacement (MR). A method has been devised using a brute force approach to identify candiate models for MR which involves exhaustive MR calculations using representative structures from a database.
It is a project by Dr Ashley M. Buckle with School of Medicine, Nursing and Health Sciences, Department of Biochemistry
Key collaborators:
Professor David Abramson with Faculty of Information Technology at Monash and Michael Kuiper with Victoria Partnership for Advanced Computing
Application driver and contact
Alexe Bojovschi, Victoria Partenership for Advanced Computing & Monash University, abojovschi at vpac.org, etc.
Experiment Status
The experiment is currently running on PRAGMA resources. The experiments will require at least 1000 cpus for testing.
Applicaiton Requirements
PHASER
Hardware requirements
If any. This will help with matching site resources.
CPU architecture (i686, x86_64, ia_64, etc.)
Minimum number of CPUs (per cluster/system)
Memory size (default is per node, unless you specify per CPU)
Storage size (default is online and shared within a cluster. If not, specify.)
Any other requirements (Specify)
Software requirements
If any. Please only specify those software you need the site admins to install. SCMSWeb will be configured to query the availability of these software.
(Name of first software)
Version requirement: (Specify exact version number or range.)
URL and instruction for software download:
URL and/or instruction for the software installation:
Command-line and output for software version query:
For example, if the software is intel fortran compiler:
$ ifort --version
ifort (IFORT) 9.0 20051201
Copyright (C) 1985-2005 Intel Corporation. All rights reserved.
Execution paths: (Specify the executables directory paths relative to the software installation root. The paths will be added into $PATH variable in PRAGMA login script at every site.)
For example, on my cluster, software xyz is installed in /opt/xyz, the executables are in /opt/xyz/bin and /opt/xyz/local/etc, then the executaion paths should be specified as:
PATH: bin, local/etc
Other specifications and comments
(Name of second software)
...
Application run
Please document memos, mile stones, progress reports, issues, results, publication links, etc. and feel free to add other categories.
