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

[Lorenzo Pesce]

I set user home wrong there, but it did not seem to be too relevant.

oddly, the tmp files seem to be set correctly

> tempdir()
[1] "/lustre/beagle/lpesce/ROCSwift/tmp/RtmpOzUNxM"
> tempfile()
[1] "/lustre/beagle/lpesce/ROCSwift/tmp/RtmpOzUNxM/file2a984c9ce26"




On Jun 13, 2012, at 10:51 AM, Lorenzo Pesce wrote:

> 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>
> 
> 
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