BioCluster
A website for the Ashworth Cluster Computing Initiative(s)
Xgrid Cluster
Xgrid is a software suite that allows a controlling computer (the controller node) to send jobs to a series of agent nodes. It runs on Apple computers, and the software is embedded in OSX 10.4.
Joining XGrid | Getting OSX10.4 on your Mac | Submitting jobs to XGrid
Joining Xgrid
In order to speed our Xgrid up, we have now dedicated a G5 Mac as a server: the new xgrid controller/service is called wallace.
If you have previously had your apple cpu serving as an agent on the dorylaimida xgrid, please can you rejoin the wallace xgrid, by
(1) going to System Preferences, and
(2) clicking on "Sharing".
(3) Click on the Xgrid entry in the list of services.
(4) Now click on "Configure",
(5) and under "choose a specific controller" choose "wallace". The Authentication method is "none".
(6) Close the configuration panel by clicking OK,
(7) and then click on "Stop" to stop Xgrid services,
(8) and then on "Start" to restart them with the new settings.
If you havent previously been Xgrid-available, please do consider being so: it means your cpu can be used for big compute jobs when its otherwise idle.
If you have been using the older Xgrid ("dorylaimida"), please contact me to find out the new password for submitting jobs as a client.
Dan Gaffney provided a description of how to join the Ashworth Xgrid, available as a pdf here just swap the "dirofilaria" text for "wallace". This guide also describes briefly the syntax for submission of jobs, and how to use his xgrid_blast.pl script.
Getting OSX 10.4 on your Mac
To get OSX 10.4 installed on your Mac so that you can join/use the Xgrid .... simply email sbscomp@ed.ac.uk to arrange a date/time.
The School of Biological Sciences currently have 300 Mac OS X AMP licenses, where AMP = Apple Maintenance Program, ie instead of the educational price of approx £50 for 10.4 this volume discount works out about £13 per license.
Submitting jobs to Xgrid
Dan Gaffney has written two PERL scripts that format, submit and retrieve BLAST jobs to/from the Ashworth Xgrid cluster.
They are
xgrid_blast.pl for putting together and submitting BLAST jobs for the Xgrid cluster
xgrid_retrieve_blast.pl for getting the results of your BLAST jobs back from the Xgrid controller
cluster name |
what sort of cluster | number of processors and speed | what it is good for | contact for access to cluster |
galaxy |
a static, Linux-based CONDOR cluster | 16 x 2.4 GHz | large volume BLAST jobs, especially those requiring comparisons to large databases such as UniProt or NCBI_nr | Mark Blaxter or Ann Hedley (rm 354) |
hal |
a dynamic, Linux-based CONDOR cluster with variable membership | currently 7 cpus | simulations, large volume BLAST jobs against small databases | Mark Blaxter or Ann Hedley (rm 354) |
taxInspector |
an 8-node (16-process) LINUX-based MPI cluster | 8x dual core 3.4 GHz | MrBayes-type phylogenetic analyses | Martin Jones (rm 354) |
Xgrid |
dynamic Apple Xgrid based cluster | whatever is available; currently ~14 GHz across 5 machines | simulations, large volume BLAST jobs against small databases | Mark Blaxter (rm 355) |
WOOLHOUSE |
SUN Solaris Grid Engine | ? | ? | Mark Woolhouse |
KNOTT |
LINUX-based CONDOR cluster | ? | ? | Sara Knott |