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

[Lorenzo Pesce]

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>