<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hey,<br><br>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.<br><br>When I run swift, it can't seem to find qsub on the cluster.<br><br>rmcgibbo@Roberts-MacBook-Pro-2 ~/projects/swift<br>$ swift -sites.file sites.xml hello.swift -tc.file tc.data<br>Swift 0.94 swift-r6492 cog-r3658<br><br>RunID: 20130603-1704-5xii8svc<br>Progress: time: Mon, 03 Jun 2013 17:04:10 -0700<br>2013-06-03 17:04:10.735 java[77051:1f07] Loading Maximizer into bundle: com.apple.javajdk16.cmd<br>2013-06-03 17:04:11.410 java[77051:1f07] Maximizer: Unsupported window created of class: CocoaAppWindow<br>Progress: time: Mon, 03 Jun 2013 17:04:13 -0700 Stage in:1<br>Execution failed:<br><span class="Apple-tab-span" style="white-space: pre; "> </span>Exception in uname:<br> Arguments: [-a]<br> Host: vsp-compute<br> Directory: hello-20130603-1704-5xii8svc/jobs/y/uname-ydyn5fal<br>Caused by:<br><span class="Apple-tab-span" style="white-space: pre; "> </span>Cannot submit job: Cannot run program "qsub": error=2, No such file or directory<br><span class="Apple-tab-span" style="white-space: pre; "> </span>uname, hello.swift, line 8<br><br>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.<br><br>-Robert<br>Graduate Student, Pande Lab<br>Stanford University, Department of Chemistry<br><br>p.s.<br><br>My sitess.xml file is <br>```<br><config><br><pool handle="vsp-compute"><br> <filesystem provider="ssh" url="<a href="http://vsp-compute-01.stanford.edu/">vsp-compute-01.stanford.edu</a>"/><br> <execution provider="pbs" jobmanager="ssh:pbs" url="<a href="http://vsp-compute-01.stanford.edu/">vsp-compute-01.stanford.edu</a>"/><br><br> <profile namespace="globus" key="maxtime">750</profile><br> <profile namespace="globus" key="jobsPerNode">1</profile><br> <profile namespace="globus" key="queue">default</profile><br> <profile namespace="swift" key="stagingMethod">file</profile><br><br> <workdirectory>/scratch/rmcgibbo/swiftwork</workdirectory> <br></pool><br><br><!-- End --><br></config><br>```<br><br>My SwiftScript is<br>```<br>#hello.swift<br>type file;<br><br>app (file o) uname() {<br> uname "-a" stdout=@o;<br>}<br>file outfile <"uname.txt">;<br><br>outfile = uname();<br>```</body></html>