RE: [condor-users] Use of Condor for biological applications

[Ian.McLeod@xxxxxxxx]

We built our CONDOR pool in 2002. We needed access to HTC environment to
support research into spatial optimisation (analysis using methods such
as simulated annealing).  In particular we wanted to run MARXAN analysis
for marine conservation reserve design for an Australian Trawl fishery.
This work was reported to the client in 2003. It would have been
impossible using the pre-CONDOR computer resources to deliver the report
in the given time frame. The CONDOR pool allowed the successful
completion of the project.

MARXAN is software that delivers decision support for reserve system
design. MARXAN finds reasonably efficient solutions to the problem of
selecting a system of spatially cohesive sites that meet a suite of
biodiversity targets. http://www.ecology.uq.edu.au/marxan.htm

Concurrent with the MARXAN work, we had undertaken a contract with the
another client to look at methods of optimising prawn farm locations for
environmental and economic benefits. We had to develop a spatial
optimiser to evaluate environmental and economic consequences of prawn
farm location decisions. I developed a software tool based upon
simulated annealing in a CONDOR environment with an ORACLE database
coordinating and automatically collating results. 

I wrote the tool in VB6 - silly I know - but we had a huge amount of
legacy code that we needed to use and the first attempts at mixed
language programming were problematic. I worked out how to write a
consol app in VB (it is not easy). I hooked in the ORACLE OO4O object
classes and got the app to read to and from ORACLE. This meant I could
spawn as many condor jobs as I wanted and they would each run one
iteration of the simulated annealing, write the results back, check to
see if they needed to continue. It meant we had check pointing in a
windows environment.    

It work far better than expected to the point that we were able to do
sensitivity analysis on the simulated annealing to looking at cooling
rates and grain size. 

I am currently looking at using CONDOR to improve our fisheries reserve
design process.

The original pool consisted of 34 windows machines. We now have 40. The
only major problem I had was getting the oracle client software on each
of the CONDOR machines. Otherwise the rest was all just difficult. 

Ian 

+------------------------------------------------------------+
| Ian McLeod            | Give a man a fish and he will eat  |
| Spatial Analyst       | for a day.  Teach him how to fish  |
| CSIRO Marine Research | and he will sit in a boat & drink  |
| Cleveland Q Australia | beer all day.                      |
|                       |                                    |
| phone  07 3826 7220   | If at first you don't succeed,     |
| fax    07 3826 7222   | skydiving is not for you.          |
| mobile 0407 229 812   |                                    |
+------------------------------------------------------------+
| SPLAT! (a sock full of custard hits wet cement)            |
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