The following seems to be a problem several people have run into now, so making Pegasus give a real error would be helpful. During planning:

2012.03.18 17:47:17.177 EDT: [FATAL ERROR]
[1] java.lang.NullPointerException: null at edu.isi.pegasus.planner.refiner.InterPoolEngine.incorporateProfiles(InterPoolEngine.java:517)

This comes from missing file system descriptions in the site catalog, and can be hit by either leaving out a file system attribute, or give the wrong staging site. For example, in the condorio mode:

<site handle="local" arch="x86" os="LINUX">
<head-fs>
<scratch>
</scratch>
<storage>
<shared>
<file-server protocol="file" url="file://" mount-point="/home/foo/tmp"/>
<internal-mount-point mount-point="/home/foo/tmp" free-size="100G" total-size="30G"/>
</shared>
</storage>
</head-fs>
<replica-catalog type="LRC" url="rlsn://dummyValue.url.edu"/>
<profile namespace="env" key="PEGASUS_HOME">/apps/share32/pegasus/pegasus-4.0.0</profile>
</site>

Pegasus should give an error describing the problem instead of the NPE. I'm not convinced that just fixing InterPoolEngine.java:517 is enough - there might be other places with the same assumptions on the site catalog. Maybe we should run a check on the site catalog based on the data configuration.