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

[Michael Wilde]

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