[Swift-commit] r4337 - in SwiftApps/SwiftR/Swift: . exec

[tga at ci.uchicago.edu]

Author: tga
Date: 2011-04-12 08:39:36 -0500 (Tue, 12 Apr 2011)
New Revision: 4337

Modified:
   SwiftApps/SwiftR/Swift/DESCRIPTION
   SwiftApps/SwiftR/Swift/exec/configure-server-local
   SwiftApps/SwiftR/Swift/exec/fiforead
   SwiftApps/SwiftR/Swift/exec/passive-coaster-swift
   SwiftApps/SwiftR/Swift/exec/start-swift
Log:
Compatibility changes working towards getting SwiftR working on Mac:
removed dependence on linux-specific version of seq, mktmp, etc.


Modified: SwiftApps/SwiftR/Swift/DESCRIPTION
===================================================================
--- SwiftApps/SwiftR/Swift/DESCRIPTION	2011-04-12 03:46:39 UTC (rev 4336)
+++ SwiftApps/SwiftR/Swift/DESCRIPTION	2011-04-12 13:39:36 UTC (rev 4337)
@@ -1,12 +1,12 @@
 Package: Swift
 Type: Package
 Title: R interface to Swift parallel scripting languaage
-Version: 0.1.7
-Date: 2011-04-29
+Version: 0.1.8
+Date: 2011-04-12
 Author: Michael Wilde
 Maintainer: Michael Wilde <wilde at mcs.anl.gov>
 Description: Routines to invoke R functions on remote resources through Swift.
 License: Apache License
 LazyLoad: yes
-Packaged: 2011-04-29; Tim Armstrong
+Packaged: 2011-04-12; Tim Armstrong
 

Modified: SwiftApps/SwiftR/Swift/exec/configure-server-local
===================================================================
--- SwiftApps/SwiftR/Swift/exec/configure-server-local	2011-04-12 03:46:39 UTC (rev 4336)
+++ SwiftApps/SwiftR/Swift/exec/configure-server-local	2011-04-12 13:39:36 UTC (rev 4337)
@@ -29,7 +29,7 @@
   </pool>
 END
 
-for i in `seq -w 0 $((cores-1))`; do
+for i in `$SEQ 0 $((cores-1))`; do
 
 # FIXME: how to get the right PATH for R in here?
 # use /bin/sh and count on users PATH?

Modified: SwiftApps/SwiftR/Swift/exec/fiforead
===================================================================
--- SwiftApps/SwiftR/Swift/exec/fiforead	2011-04-12 03:46:39 UTC (rev 4336)
+++ SwiftApps/SwiftR/Swift/exec/fiforead	2011-04-12 13:39:36 UTC (rev 4337)
@@ -24,7 +24,7 @@
             echo "Invalid option: $OPTARG" ;;
     esac
 done
-outfile=`mktemp`
+outfile=`mktemp -t swiftR.XXXXXX`
 
 function cleanup {
     if [ "$tout_pid" != "" ]; then

Modified: SwiftApps/SwiftR/Swift/exec/passive-coaster-swift
===================================================================
--- SwiftApps/SwiftR/Swift/exec/passive-coaster-swift	2011-04-12 03:46:39 UTC (rev 4336)
+++ SwiftApps/SwiftR/Swift/exec/passive-coaster-swift	2011-04-12 13:39:36 UTC (rev 4337)
@@ -47,7 +47,7 @@
   exit 1
 fi
 
-out=`mktemp swift.stdouterr.XXXX`
+out=`mktemp -t swift.stdouterr.XXXX`
 touch $out
 sshpidfile=${out/stdouterr/workerpids}
 

Modified: SwiftApps/SwiftR/Swift/exec/start-swift
===================================================================
--- SwiftApps/SwiftR/Swift/exec/start-swift	2011-04-12 03:46:39 UTC (rev 4336)
+++ SwiftApps/SwiftR/Swift/exec/start-swift	2011-04-12 13:39:36 UTC (rev 4337)
@@ -15,7 +15,7 @@
   # Look for:
   # Passive queue processor initialized. Callback URI is http://140.221.8.62:55379
 
-  for try in $(seq 1 20); do
+  for try in $($SEQ 1 20); do
     uriline=$(grep "Passive queue processor initialized. Callback URI is" $out 2> /dev/null)
     if [ "_$uriline" = _ ]; then
       sleep 1
@@ -315,13 +315,13 @@
   # FIXME: set up for capturing batch job id: rm -rf remotepid.* # FIXME: should not be needed if we start in a new dir each time
 
   if [ "${server}" = "cobalt" ] ; then
+      # mktemp only works on some unices - but I don't believe
+      # Cobalt is deployed on too wide a varieties of settings
       SUBMIT_FILE=$(mktemp -p $HOME SwiftR-batch.XXXXXX)
   else
       SUBMIT_FILE=batch.sub
   fi
   make-${server}-submit-file $SUBMIT_FILE
-  #FIXME: doesn't work for SGE on IBI cluster as there is additional text
-  # returned by qsub
   
   if [ "${server}" = "sge" ]
   then
@@ -508,6 +508,7 @@
 done
 
 SWIFTRBIN=$(cd $(dirname $0); pwd)
+source $SWIFTRBIN/compat-setup
 SWIFTBIN=$SWIFTRBIN/../swift/bin  # This depends on ~/SwiftR/Swift/swift being a symlink to swift in RLibrary/Swift
 
 rundir=$tmp/$USER/SwiftR/swift.$server  # rundir prefix # FIXME: handle multiple concurent independent swift servers per user
@@ -581,8 +582,7 @@
     cores=$defaultLocalCores
   fi
   echo project=$project cores=$cores nodes=$nodes queue=$queue server=$server throttle=$throttle
-
-
+ 
   source $SWIFTRBIN/configure-server-local $cores
   function onexit {
     stdcleanup_start