[Swift-commit] r7246 - SwiftApps/Swift-MapRed/blast

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2013-10-29 15:45:53 -0500 (Tue, 29 Oct 2013)
New Revision: 7246

Modified:
   SwiftApps/Swift-MapRed/blast/apps
   SwiftApps/Swift-MapRed/blast/cf
   SwiftApps/Swift-MapRed/blast/sites.midway.xml
Log:
 

Modified: SwiftApps/Swift-MapRed/blast/apps
===================================================================
--- SwiftApps/Swift-MapRed/blast/apps	2013-10-29 20:45:32 UTC (rev 7245)
+++ SwiftApps/Swift-MapRed/blast/apps	2013-10-29 20:45:53 UTC (rev 7246)
@@ -1,10 +1,11 @@
-midway blastp /home/maheshwari/ncbi-blast-2.2.28+/bin/blastp
-midway fastasplitn /home/maheshwari/parallelblast_2.0.9/fastasplitn
+midway bash /bin/bash
+midway mid_bash /bin/bash
+midway loc_bash /bin/bash
+beagle bgl_bash /bin/bash
+local  loc_bash /bin/bash
+local  cat /bin/cat
 midway blastmerge /home/maheshwari/parallelblast_2.0.9/blastmerge
 midway blastall /home/maheshwari/blast-2.2.26/bin/blastall
-midway formatdb /home/maheshwari/blast-2.2.26/bin/formatdb
-localhost blastp /home/maheshwari/ncbi-blast-2.2.28+/bin/blastp
 localhost fastasplitn /home/maheshwari/parallelblast_2.0.9/fastasplitn
-localhost blastmerge /home/maheshwari/parallelblast_2.0.9/blastmerge
-localhost blastall /home/maheshwari/blast-2.2.26/bin/blastall
 localhost formatdb /home/maheshwari/blast-2.2.26/bin/formatdb
+

Modified: SwiftApps/Swift-MapRed/blast/cf
===================================================================
--- SwiftApps/Swift-MapRed/blast/cf	2013-10-29 20:45:32 UTC (rev 7245)
+++ SwiftApps/Swift-MapRed/blast/cf	2013-10-29 20:45:53 UTC (rev 7246)
@@ -1,9 +1,9 @@
-wrapperlog.always.transfer=false
-sitedir.keep=true
-file.gc.enabled=false
-status.mode=provider
-execution.retries=0
-lazy.errors=true
 use.provider.staging=true
-provider.staging.pin.swiftfiles=true
 use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+#tcp.port.range=50000,51000
+Dtcp.channel.log.io.performance=true
\ No newline at end of file

Modified: SwiftApps/Swift-MapRed/blast/sites.midway.xml
===================================================================
--- SwiftApps/Swift-MapRed/blast/sites.midway.xml	2013-10-29 20:45:32 UTC (rev 7245)
+++ SwiftApps/Swift-MapRed/blast/sites.midway.xml	2013-10-29 20:45:53 UTC (rev 7246)
@@ -1,18 +1,28 @@
-<?xml version="1.0" encoding="UTF-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
- <pool handle="midway">
-   <execution provider="coaster" jobmanager="local:slurm"/>
-   <profile namespace="globus" key="queue">sandyb</profile>
-   <profile namespace="globus" key="jobsPerNode">16</profile>
-   <profile namespace="globus" key="maxWalltime">01:00:00</profile>
-   <profile namespace="globus" key="maxTime">8000</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="karajan" key="jobThrottle">2.0</profile>
-   <profile namespace="karajan" key="initialScore">10000</profile>
-   <workdirectory>/tmp/swift.workdir</workdirectory>
+  <pool handle="midway">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+    <profile namespace="globus" key="queue">westmere</profile>
+    <!-- <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">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">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>
   </pool>
+   <pool handle="localhost">
+     <execution provider="local" />
+     <profile namespace="karajan" key="jobThrottle">0</profile>
+     <profile namespace="karajan" key="initialScore">10000</profile>
+     <filesystem provider="local"/>
+     <workdirectory>/tmp/swift.work</workdirectory>
+     <profile namespace="swift" key="stagingMethod">local</profile>
+   </pool>
 </config>