[Swift-user] Setting up Swift at Stanford

[Robert McGibbon]

Hey,

We just heard about the swift project from some colleagues at U Chicago, and we're interested in trying it out with some of our compute resources at Stanford to run parallel molecular dynamics  and x-ray scatting simulations. Currently, I'm most interested in setting up the environment such that I can submit my swift script on a local workstation, with execution on a few different clusters. The head nodes of our local clusters are accessible via ssh, and then job execution is scheduled with pbs.

When I run swift, it can't seem to find qsub on the cluster.

rmcgibbo at Roberts-MacBook-Pro-2 ~/projects/swift
$ swift -sites.file sites.xml hello.swift -tc.file tc.data
Swift 0.94 swift-r6492 cog-r3658

RunID: 20130603-1704-5xii8svc
Progress:  time: Mon, 03 Jun 2013 17:04:10 -0700
2013-06-03 17:04:10.735 java[77051:1f07] Loading Maximizer into bundle: com.apple.javajdk16.cmd
2013-06-03 17:04:11.410 java[77051:1f07] Maximizer: Unsupported window created of class: CocoaAppWindow
Progress:  time: Mon, 03 Jun 2013 17:04:13 -0700  Stage in:1
Execution failed:
	Exception in uname:
   Arguments: [-a]
   Host: vsp-compute
   Directory: hello-20130603-1704-5xii8svc/jobs/y/uname-ydyn5fal
Caused by:
	Cannot submit job: Cannot run program "qsub": error=2, No such file or directory
	uname, hello.swift, line 8

When I switch the execution provider from pbs to ssh, the hob runs successfully, but only on the head node of the vsp-compute cluster. I'd like to run instead using the cluster's pbs queue. Any help would be greatly appreciated.

-Robert
Graduate Student, Pande Lab
Stanford University, Department of Chemistry

p.s.

My sitess.xml file is 
```
<config>
<pool handle="vsp-compute">
 <filesystem provider="ssh" url="vsp-compute-01.stanford.edu"/>
 <execution provider="pbs" jobmanager="ssh:pbs" url="vsp-compute-01.stanford.edu"/>

 <profile namespace="globus" key="maxtime">750</profile>
 <profile namespace="globus" key="jobsPerNode">1</profile>
 <profile namespace="globus" key="queue">default</profile>
 <profile namespace="swift"   key="stagingMethod">file</profile>

 <workdirectory>/scratch/rmcgibbo/swiftwork</workdirectory>  
</pool>

<!-- End -->
</config>
```

My SwiftScript is
```
#hello.swift
type file;

app (file o) uname() {
 uname "-a" stdout=@o;
}
file outfile <"uname.txt">;

outfile = uname();
```
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/swift-user/attachments/20130603/31f5bbf5/attachment.html>