Condor compile of Avida

Fri 11 March 2011 by Dr. Dirk Colbry

Blog post edited by Anonymous - "Migration of unmigrated content due to installation of a new plugin"

Today I figured got a condor_compile version of Avida working on TeraGrid. First, I downloaded Avida to my Teragrid account:

> svn checkout https://avida.devosoft.org/svn/stable

Then I modified the build_avida script as follows:

build_avida

#!/bin/sh
export CC="condor_compile gcc"
mkdir -p cbuild
cd cbuild
cmake "$@" ../
make -j 10
make install

Then I run the build script using the following commands:

> module load cmake
> ./build_avida
> ./run_tests

Once Avida builds and tests successfully I write a condor script

avida.condor

#
# avida.condor
# Example avida condor submission script
#

# Specify your TeraGrid allocation project here.
+TGProject = "YOUR PROJECT NUMBER HERE"

universe = vanilla

#PATH TO CONDOR_COMPILE BUILD OF AVIDA
# The executable to run. Need the full path. ~/ does not work.
executable = /home/ba01/u124/dcolbry/avida_condor/work/avida

#Sets the process id to the avida seed
arguments = -s $(Process)

# false: The executable is already on remote machine.
# true: Copy the executable from the local machine to the remote.
transfer_executable = false

# Filenames for standard output, standard error, and Condor log.
output = output/out.$(Process)
error = output/err.$(Process)
log = output/condor.log

# PATH TO WORK DIRECTORY
initialdir = /home/ba01/u124/dcolbry/avida_condor/work/

# The following line is always required. It is the command to submit the above.
# The number is the number of jobs that you want to run
queue 5

Make an output directory and submit the job to the condor scheduler using the following commands:

> mkdir /home/ba01/u124/dcolbry/avida_condor/work/output
> condor_submit avida.condor

That did it for me.

Dirk

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