See the example tests
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Swift-NAMD work: http://www.ks.uiuc.edu/Research/swift
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Swift-NAMD paper: http://www.mcs.anl.gov/~wozniak/papers/Swift_NAMD_2014.pdf
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Swift/T Guide: http://swift-lang.github.io/swift-t/guide.html
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Swift/T Notes for Titan: http://swift-lang.github.io/swift-t/sites.html#_titan
Normally, we would run namd.sh out of its (git clone) source directory. However, on Titan, we cannot access $HOME from the compute nodes. So we copy namd.sh into the working directory of the workflow using an initialization script (init-titan.sh) and run './namd.sh' . Each workflow run creates its own working directory called TURBINE_OUTPUT . By default, Swift/T create a new directory based on the date under ~/turbine-output and reports it just before the workflow starts. To change the defaults, see here.
I typically make ~/turbine-output a soft link to somewhere writable, on Titan it is currently:
/lustre/atlas/scratch/wozniak/csc242/turbine-output