Steven Clark added a comment - Yesterday 2:34 PM
I have noticed a new behavior the the use of distribute. That is in cases where the actual executable (not kickstart) is transfered to the cluster a separate PBS job is run to do a simple chmod. Could the chmod operation be combined with the transfer and avoid an extra PBS submission?
Karan Vahi added a comment - Yesterday 2:49 PM
The property pegasus.transfer.disable.chmod.sites ( https://pegasus.isi.edu/wms/docs/trunk/reference.php#transfer_props ) may do the trick in conjunction with pegasus.gridstart.arguments -X that invokes pegasus-kickstart with -X option that sets the x bit on the executable
Steven Clark added a comment - Yesterday 3:31 PM
Here is what came back:

2015.03.05 18:19:20.522 EST: [WARNING] --output option is deprecated. Replaced by --output-site
2015.03.05 18:19:21.076 EST: [WARNING] unknown profile condor.kill_sig, using anyway
2015.03.05 18:19:21.080 EST: [WARNING] unknown profile condor.kill_sig, using anyway
2015.03.05 18:19:21.084 EST: [WARNING] unknown profile condor.whentotransferoutput, using anyway
2015.03.05 18:19:21.343 EST: [WARNING] unknown profile condor.kill_sig, using anyway
2015.03.05 18:19:21.345 EST: [WARNING] unknown profile condor.kill_sig, using anyway
2015.03.05 18:19:21.345 EST: [WARNING] unknown profile condor.whentotransferoutput, using anyway
2015.03.05 18:19:21.409 EST: [FATAL ERROR]
[1] java.lang.RuntimeException: Job not associated with staging site chmod_00166762_02.sh_FRED_02_0 at edu.isi.pegasus.planner.refiner.createdir.Minimal.addCreateDirectoryNodes(Minimal.java:176)
2015.03.05 18:19:21.669 EST: [WARNING] Non-zero exit-code 1

In my pegasus.rc file I have:

pegasus.gridstart.arguments = -X -B all
pegasus.transfer.disable.chmod.sites = rossmann

where rossmann is the cluster site.