[Swift-commit] r8462 - SwiftTutorials/OHBM_2013-06-16
wozniak at ci.uchicago.edu
wozniak at ci.uchicago.edu
Thu May 28 20:01:56 CDT 2015
Author: wozniak
Date: 2015-05-28 20:01:56 -0500 (Thu, 28 May 2015)
New Revision: 8462
Added:
SwiftTutorials/OHBM_2013-06-16/apps.ec2
SwiftTutorials/OHBM_2013-06-16/catsn.swift
SwiftTutorials/OHBM_2013-06-16/cf
SwiftTutorials/OHBM_2013-06-16/coaster-service.conf
SwiftTutorials/OHBM_2013-06-16/hi.swift
SwiftTutorials/OHBM_2013-06-16/sites-localhost.xml
SwiftTutorials/OHBM_2013-06-16/sites-pc.xml
Log:
Add files
Added: SwiftTutorials/OHBM_2013-06-16/apps.ec2
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps.ec2 (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/apps.ec2 2015-05-29 01:01:56 UTC (rev 8462)
@@ -0,0 +1,8 @@
+persistent-coasters sh /bin/sh
+persistent-coasters alignlinear /root/AIR5.3.0/bin/alignlinear
+persistent-coasters align_warp /root/AIR5.3.0/bin/align_warp
+persistent-coasters reslice /root/AIR5.3.0/bin/reslice
+
+localhost softmean /home/wilde/software/AIR5.3.0/bin/softmean
+localhost slicer /project/wilde/software/fsl-5.0.4/fsl/bin/slicer null null env::FSLOUTPUTTYPE=NIFTI
+localhost convert convert
Added: SwiftTutorials/OHBM_2013-06-16/catsn.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/catsn.swift (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/catsn.swift 2015-05-29 01:01:56 UTC (rev 8462)
@@ -0,0 +1,26 @@
+type file;
+
+// app declaration
+app (file o) cat (file i){
+ cat @i stdout=@o;
+}
+
+// input data
+file data<"data.txt">;
+
+/*
+* output data mapped to files with
+* prefix f and suffix .out in the outdir
+* directory
+*/
+
+file out[]<simple_mapper; location="outdir", prefix="f.",suffix=".out">;
+
+/*
+* @arg means n could be specified as commandline argument
+* foreach loop executes 1 to n calls of cat in parallel
+*/
+foreach j in [1:@toInt(@arg("n","1"))] {
+ out[j] = cat(data);
+}
+
Added: SwiftTutorials/OHBM_2013-06-16/cf
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/cf (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/cf 2015-05-29 01:01:56 UTC (rev 8462)
@@ -0,0 +1,6 @@
+use.provider.staging=true
+wrapperlog.always.transfer=false
+execution.retries=10
+provider.staging.pin.swiftfiles=false
+sitedir.keep=false
+use.wrapper.staging=false
Added: SwiftTutorials/OHBM_2013-06-16/coaster-service.conf
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/coaster-service.conf (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/coaster-service.conf 2015-05-29 01:01:56 UTC (rev 8462)
@@ -0,0 +1,41 @@
+#Location of SWIFT. If empty, PATH is referenced
+export SWIFT=
+
+# Where to place/launch worker.pl on the remote machine for sites.xml
+export WORKER_LOCATION=/root
+
+# How to launch workers: local, ssh, or cobalt
+export WORKER_MODE=ssh
+
+# Worker logging setting passed to worker.pl for sites.xml
+export WORKER_LOGGING_LEVEL=DEBUG
+
+export SSH_TUNNELING=yes
+
+# User name to use for all systems
+export WORKER_USERNAME=root
+
+# Worker host names for ssh
+# export WORKER_HOSTS="crush thwomp"
+
+# Directory to keep log files,
+#relative to working directory when launching start-coaster-service
+export LOG_DIR=logs
+export WORKER_LOG_DIR=/root
+
+# Manually define ports. If not specified, ports will be automatically generated
+export LOCAL_PORT=50100
+export SERVICE_PORT=50200
+
+# Set shared filesystem to no since work will be done in local /sandbox directory
+export SHARED_FILESYSTEM=no
+
+# Below are various settings to give information about how to create sites.xml
+export WORK=/tmp/swift.work
+export JOBSPERNODE=4
+HOST_COUNT=$( echo $WORKER_HOSTS |wc -w )
+export JOBTHROTTLE=$( echo " scale = 5; ($JOBSPERNODE * $HOST_COUNT)/100 - 0.00001;" | bc )
+
+# Swift applications
+#app cat=/bin/cat
+#app bash=/bin/bash
Added: SwiftTutorials/OHBM_2013-06-16/hi.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/hi.swift (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/hi.swift 2015-05-29 01:01:56 UTC (rev 8462)
@@ -0,0 +1,2 @@
+app echo (string i) { echo i; }
+echo("hi");
Added: SwiftTutorials/OHBM_2013-06-16/sites-localhost.xml
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/sites-localhost.xml (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/sites-localhost.xml 2015-05-29 01:01:56 UTC (rev 8462)
@@ -0,0 +1,8 @@
+ <pool handle="localhost">
+ <execution provider="local"/>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ <profile namespace="swift" key="stagingMethod">file</profile>
+ <profile namespace="karajan" key="jobThrottle">.03</profile> <!-- eg .11 -> 12 -->
+ </pool>
Added: SwiftTutorials/OHBM_2013-06-16/sites-pc.xml
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/sites-pc.xml (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/sites-pc.xml 2015-05-29 01:01:56 UTC (rev 8462)
@@ -0,0 +1,22 @@
+<config>
+ <pool handle="localhost">
+ <execution provider="local"/>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ <profile namespace="swift" key="stagingMethod">file</profile>
+ <profile namespace="karajan" key="jobThrottle">.03</profile> <!-- eg .11 -> 12 -->
+ </pool>
+
+ <pool handle="persistent-coasters">
+ <execution provider="coaster-persistent"
+ url="http://localhost:50200"
+ jobmanager="local:local"/>
+ <profile namespace="globus" key="workerManager">passive</profile>
+ <profile namespace="globus" key="jobsPerNode">4</profile>
+ <profile key="jobThrottle" namespace="karajan">.15999</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <filesystem provider="local" url="none" />
+ <workdirectory>/tmp/swift.work</workdirectory>
+ </pool>
+</config>
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