[Swift-user] Question about swiftR temporary and work directories

[Michael Wilde]

Hi Lorenzo,

Did you want to meet today? If not, I'll go to Argonne as I have a user there that needs some help. But Im happy to come to campus if I can be of help with your user engagements.

Regards,

- Mike

----- Original Message -----
> From: "Lorenzo Pesce" <lpesce at uchicago.edu>
> To: "Michael Wilde" <wilde at mcs.anl.gov>
> Cc: swift-user at ci.uchicago.edu
> Sent: Monday, June 25, 2012 9:58:26 AM
> Subject: Re: [Swift-user] Question about swiftR temporary and work directories
> I was on paternity leave and lost a bit track of things ;-)
> 
> Let me get back to you soon. The last decision was that swiftR was not
> capable of handling this type of problem and that we were most likely
> going to use Swift or Bash + R.
> 
> 
> On Jun 24, 2012, at 9:53 PM, Michael Wilde wrote:
> 
> > Lorenzo, I see now that Tim answered this. Is SwiftR now working for
> > you for this problem?
> >
> > - Mike
> >
> >
> > ----- Original Message -----
> >> From: "Michael Wilde" <wilde at mcs.anl.gov>
> >> To: "Lorenzo Pesce" <lpesce at uchicago.edu>
> >> Cc: swift-user at ci.uchicago.edu
> >> Sent: Sunday, June 24, 2012 9:47:10 PM
> >> Subject: Re: [Swift-user] Question about swiftR temporary and work
> >> directories
> >> The use of /tmp might be set in the R code of the SwiftR package;
> >> will
> >> need to check and get back to you.
> >>
> >> - Mike
> >>
> >> ----- Original Message -----
> >>> From: "Lorenzo Pesce" <lpesce at uchicago.edu>
> >>> To: swift-user at ci.uchicago.edu
> >>> Sent: Wednesday, June 13, 2012 10:51:32 AM
> >>> Subject: [Swift-user] Question about swiftR temporary and work
> >>> directories
> >>> We are using swift R. Since we are working on a machine where the
> >>> compute nodes see only the /lustre file system, we need to be able
> >>> to
> >>> set all the temporary directories there.
> >>> We know how to do that with swift, but swiftR doesn't seem to work
> >>> that way.
> >>>
> >>> This is the command:
> >>>
> >>>> library(Swift)
> >>>> swiftInit(server="custom", tc.file="ROC.tc", cf.file="ROC.cf",
> >>>> sites.file="ROCSites.xml")
> >>> Working in /tmp/lpesce/SwiftR/swift.ZKHU
> >>> Running in /tmp/lpesce/SwiftR/swift.ZKHU (linked to
> >>> /tmp/lpesce/SwiftR/swift.custom)
> >>> Started worker manager with pid 10153
> >>>
> >>> I would like both of those to point to
> >>> /lustre/beagle/`whoami`/<some
> >>> path>
> >>> where I can decide where to send them or at least that the place
> >>> is
> >>> under my /lustre folder.
> >>>
> >>> Any ideas?
> >>>
> >>> We set these variables before running R:
> >>> module load swift
> >>> export SWIFT_HEAP_MAX=1024M
> >>> export USER_HOME=/lustre/beagle/GCNet
> >>> export SWIFT_HOME=/soft/swift/0.93/
> >>>
> >>> # set temporary directory references for R, currdir is
> >>> /lustre/beagle/`whoami`
> >>> export TMP=$currdir/tmp
> >>> export TMPDIR=$TMP
> >>> export TEMP=$TMP
> >>> mkdir -p $TMP
> >>>
> >>>
> >>> This is the sites file:
> >>> less ROCSites.xml
> >>> <config>
> >>> <pool handle="pbs">
> >>> <execution provider="coaster" jobmanager="local:pbs"/>
> >>> <profile namespace="globus" key="project">CI-CCR000070</profile>
> >>>
> >>>
> >>> <profile namespace="globus"
> >>> key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile>
> >>>
> >>> <profile namespace="globus" key="jobsPerNode">24</profile>
> >>> <profile namespace="globus" key="maxTime">1800</profile>
> >>> <profile namespace="globus" key="maxwalltime">0:2:00</profile>
> >>> <profile namespace="globus" key="lowOverallocation">100</profile>
> >>> <profile namespace="globus" key="highOverallocation">100</profile>
> >>>
> >>> <profile namespace="globus" key="slots">1</profile>
> >>> <profile namespace="globus" key="nodeGranularity">1</profile>
> >>> <profile namespace="globus" key="maxNodes">1</profile>
> >>>
> >>> <profile namespace="karajan" key="jobThrottle">.63</profile>
> >>> <profile namespace="karajan" key="initialScore">10000</profile>
> >>>
> >>> <filesystem provider="local"/>
> >>> <workdirectory>/lustre/beagle/lpesce/ROCSwift/swift.workdir</workdirectory>
> >>> </pool>
> >>> </config>
> >>>
> >>>
> >>> _______________________________________________
> >>> Swift-user mailing list
> >>> Swift-user at ci.uchicago.edu
> >>> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
> >>
> >> --
> >> Michael Wilde
> >> Computation Institute, University of Chicago
> >> Mathematics and Computer Science Division
> >> Argonne National Laboratory
> >>
> >> _______________________________________________
> >> Swift-user mailing list
> >> Swift-user at ci.uchicago.edu
> >> https://lists.ci.uchicago.edu/cgi-bin/mailman/listinfo/swift-user
> >
> > --
> > Michael Wilde
> > Computation Institute, University of Chicago
> > Mathematics and Computer Science Division
> > Argonne National Laboratory
> >

-- 
Michael Wilde
Computation Institute, University of Chicago
Mathematics and Computer Science Division
Argonne National Laboratory