[Swift-commit] r7241 - in SwiftApps/Swift-MapRed/mapred_combiner_V4: . examples/blast

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2013-10-28 16:23:56 -0500 (Mon, 28 Oct 2013)
New Revision: 7241

Added:
   SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/reduce_blast.sh
Modified:
   SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift
   SwiftApps/Swift-MapRed/mapred_combiner_V4/sites.midway.xml
Log:
 

Modified: SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift
===================================================================
--- SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift	2013-10-28 20:55:41 UTC (rev 7240)
+++ SwiftApps/Swift-MapRed/mapred_combiner_V4/blastreduce.swift	2013-10-28 21:23:56 UTC (rev 7241)
@@ -83,5 +83,5 @@
 // Final global reduce
 file final_out <"final_result">;
 file final_err <"final_errors">;
-(final_out, final_err) = reduce_local (red_wrapper, red_func, "naive", redsite_out);
+(final_out, final_err) = reduce_local (red_wrapper, red_func, "local", redsite_out);
 

Added: SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/reduce_blast.sh
===================================================================
--- SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/reduce_blast.sh	                        (rev 0)
+++ SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/reduce_blast.sh	2013-10-28 21:23:56 UTC (rev 7241)
@@ -0,0 +1,12 @@
+#!/bin/bash
+
+#for f in $*
+#do
+#    sort -n $f -o $f
+#done
+#sort -n -m $*
+#rm $*
+
+/home/maheshwari/parallelblast_2.0.9/blastmerge tmp.out $* >/dev/null
+cat tmp.out
+rm $* tmp.out >/dev/null


Property changes on: SwiftApps/Swift-MapRed/mapred_combiner_V4/examples/blast/reduce_blast.sh
___________________________________________________________________
Added: svn:executable
   + *

Modified: SwiftApps/Swift-MapRed/mapred_combiner_V4/sites.midway.xml
===================================================================
--- SwiftApps/Swift-MapRed/mapred_combiner_V4/sites.midway.xml	2013-10-28 20:55:41 UTC (rev 7240)
+++ SwiftApps/Swift-MapRed/mapred_combiner_V4/sites.midway.xml	2013-10-28 21:23:56 UTC (rev 7241)
@@ -6,13 +6,13 @@
     <!-- <profile namespace="globus" key="queue">sandyb</profile> -->
     <!-- <profile namespace="globus" key="queue">amd</profile> -->
     <profile namespace="globus" key="jobsPerNode">8</profile>
-    <profile namespace="globus" key="maxtime">1200</profile>
-    <profile namespace="globus" key="maxWalltime">00:10:00</profile>
+    <profile namespace="globus" key="maxtime">2400</profile>
+    <profile namespace="globus" key="maxWalltime">00:20:00</profile>
     <profile namespace="globus" key="highOverAllocation">100</profile>
     <profile namespace="globus" key="lowOverAllocation">100</profile>
     <profile namespace="globus" key="slots">1</profile>
-    <profile namespace="globus" key="maxNodes">1</profile>
-    <profile namespace="globus" key="nodeGranularity">1</profile>
+    <profile namespace="globus" key="maxNodes">2</profile>
+    <profile namespace="globus" key="nodeGranularity">2</profile>
     <profile namespace="karajan" key="jobThrottle">.1</profile>
     <profile namespace="karajan" key="initialScore">10000</profile>
     <workdirectory>/tmp/maheshwari/swift.work</workdirectory>