[Swift-commit] r4233 - SwiftApps/SwiftR/Swift/exec

[tga at ci.uchicago.edu]

Author: tga
Date: 2011-03-31 17:05:18 -0500 (Thu, 31 Mar 2011)
New Revision: 4233

Modified:
   SwiftApps/SwiftR/Swift/exec/EvalRBatchPersistent.sh
   SwiftApps/SwiftR/Swift/exec/configure-server-crayxt
Log:
Checking in fixes required to get SwiftR running on single node of crayxt:
* Point SwiftR to use tmp directory mounted on lustre file system (node file systems dont work)
* Invoke R directly, rather than using Rscript


Modified: SwiftApps/SwiftR/Swift/exec/EvalRBatchPersistent.sh
===================================================================
--- SwiftApps/SwiftR/Swift/exec/EvalRBatchPersistent.sh	2011-03-31 22:03:37 UTC (rev 4232)
+++ SwiftApps/SwiftR/Swift/exec/EvalRBatchPersistent.sh	2011-03-31 22:05:18 UTC (rev 4233)
@@ -27,7 +27,7 @@
 
 # tmp=/tmp # FIXME: allow this to change eg for sites with main tmp dir elsewhere
 # tmp=/scratch/local # FIXME: allow this to change eg for sites with main tmp dir elsewhere
-tmp=${SWIFTR_TMP:-/tmp}
+tmp=${SWIFTR_TMP:-${TMP:-/tmp}}
 
 RServerScript=$1
 callFile=$2
@@ -140,7 +140,11 @@
   echo LD_LIBRARYPATH= $LD_LIBRARY_PATH
   PATH=.:$PATH
   echo PATH= $PATH
-  $RServerScript $SLOTDIR >> $SLOTDIR/R.log 2>&1 &   # launch R server
+  # Use R instead of Rscript due to Rscript issues on some
+  # platforms (e.g. cray xt)
+  R --slave --no-restore --file=$RServerScript \
+                --args $SLOTDIR >> $SLOTDIR/R.log 2>&1 &   # launch R server
+  #$RServerScript $SLOTDIR >> $SLOTDIR/R.log 2>&1 &   # launch R server
   # idletimer $SLOTDIR </dev/null >/dev/null 2>&1 & # R saves pid in R.pid for idletimer to kill it
   echo "$0: INFO: Launched $RServerScript $SLOTDIR Rscript"
 else

Modified: SwiftApps/SwiftR/Swift/exec/configure-server-crayxt
===================================================================
--- SwiftApps/SwiftR/Swift/exec/configure-server-crayxt	2011-03-31 22:03:37 UTC (rev 4232)
+++ SwiftApps/SwiftR/Swift/exec/configure-server-crayxt	2011-03-31 22:05:18 UTC (rev 4233)
@@ -3,7 +3,6 @@
 # configuration for PBS with manually-started Swift workers (passive coasters)
 
 cores=$1
-
 throttlePBS=$2
 
 cat >tc <<END
@@ -14,6 +13,9 @@
 # FIXME: examine effect of 1-min default maxwalltime above
 # FIXME: determine best value for throttle below
 
+LUSTRE_TMP=/lustre/beagle/$USER/swiftRtmp
+mkdir -p $LUSTRE_TMP
+
 cat >sites.xml <<END
 <config>
 
@@ -32,8 +34,11 @@
     <profile namespace="karajan" key="jobThrottle">$throttlePBS</profile>
     <profile namespace="karajan" key="initialScore">10000</profile>
     <filesystem provider="local" url="none"/>
-    <workdirectory>$(pwd)/swiftwork</workdirectory>
-    <workdirectory>$(pwd)/swiftscratch</workdirectory>
+    <profile namespace="env" key="SWIFTR_TMP">$LUSTRE_TMP</profile>
+    <profile namespace="env" key="TMP">$LUSTRE_TMP</profile>
+    <profile namespace="env" key="LD_LIBRARY_PATH">$LD_LIBRARY_PATH</profile>
+    <workdirectory>$LUSTRE_TMP/swiftwork</workdirectory>
+    <scratch>$LUSTRE_TMP/swiftscratch</scratch>
   </pool>
 
 </config>