<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Yes, lustre will of course gel up and then freeze =)</div><div><br></div>You are right. I just wanted a way to change it in case I get a ramdisk explosion. =)<div><br></div><div>In fact I am trying to use ramdisk with some other swift apps I am working on. </div><div><br></div><div>Thanks a lot both for the answer and the advice.</div><div><br><div><div>On Jun 13, 2012, at 11:46 AM, Tim Armstrong wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">There is an environment variable called SWIFTR_TMP that can control this.<br><br>Though... are you sure you want to do this? It should work fine if it's just pointing to /tmp/. It isn't necessary that this temporary directory be visible to nodes in the cluster, since it is just used for temporary storage for the local processes. Many small files are created in the directory, so I have no idea how it will work with lustre.<br>
<br>- Tim<br><br><div class="gmail_quote">On Wed, Jun 13, 2012 at 10:51 AM, Lorenzo Pesce <span dir="ltr"><<a href="mailto:lpesce@uchicago.edu" target="_blank">lpesce@uchicago.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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.<br>
We know how to do that with swift, but swiftR doesn't seem to work that way.<br>
<br>
This is the command:<br>
<br>
> library(Swift)<br>
> swiftInit(server="custom", tc.file="ROC.tc", cf.file="ROC.cf", sites.file="ROCSites.xml")<br>
Working in /tmp/lpesce/SwiftR/swift.ZKHU<br>
Running in /tmp/lpesce/SwiftR/swift.ZKHU (linked to /tmp/lpesce/SwiftR/swift.custom)<br>
Started worker manager with pid 10153<br>
<br>
I would like both of those to point to /lustre/beagle/`whoami`/<some path><br>
where I can decide where to send them or at least that the place is under my /lustre folder.<br>
<br>
Any ideas?<br>
<br>
We set these variables before running R:<br>
module load swift<br>
export SWIFT_HEAP_MAX=1024M<br>
export USER_HOME=/lustre/beagle/GCNet<br>
export SWIFT_HOME=/soft/swift/0.93/<br>
<br>
# set temporary directory references for R, currdir is /lustre/beagle/`whoami`<br>
export TMP=$currdir/tmp<br>
export TMPDIR=$TMP<br>
export TEMP=$TMP<br>
mkdir -p $TMP<br>
<br>
<br>
This is the sites file:<br>
less ROCSites.xml<br>
<config><br>
<pool handle="pbs"><br>
<execution provider="coaster" jobmanager="local:pbs"/><br>
<profile namespace="globus" key="project">CI-CCR000070</profile><br>
<br>
<br>
<profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile><br>
<br>
<profile namespace="globus" key="jobsPerNode">24</profile><br>
<profile namespace="globus" key="maxTime">1800</profile><br>
<profile namespace="globus" key="maxwalltime">0:2:00</profile><br>
<profile namespace="globus" key="lowOverallocation">100</profile><br>
<profile namespace="globus" key="highOverallocation">100</profile><br>
<br>
<profile namespace="globus" key="slots">1</profile><br>
<profile namespace="globus" key="nodeGranularity">1</profile><br>
<profile namespace="globus" key="maxNodes">1</profile><br>
<br>
<profile namespace="karajan" key="jobThrottle">.63</profile><br>
<profile namespace="karajan" key="initialScore">10000</profile><br>
<br>
<filesystem provider="local"/><br>
<workdirectory>/lustre/beagle/lpesce/ROCSwift/swift.workdir</workdirectory><br>
</pool><br>
</config><br>
<br>
<br>
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</blockquote></div><br>
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