From ketan at ci.uchicago.edu  Mon Jun  3 00:38:55 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Mon,  3 Jun 2013 00:38:55 -0500 (CDT)
Subject: [Swift-commit] r6528 - trunk/docs/designs
Message-ID: <20130603053855.6CD0F9CC8F@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-03 00:38:54 -0500 (Mon, 03 Jun 2013)
New Revision: 6528

Modified:
   trunk/docs/designs/swiftrun.txt
Log:
 

Modified: trunk/docs/designs/swiftrun.txt
===================================================================
--- trunk/docs/designs/swiftrun.txt	2013-05-31 16:19:44 UTC (rev 6527)
+++ trunk/docs/designs/swiftrun.txt	2013-06-03 05:38:54 UTC (rev 6528)
@@ -208,7 +208,7 @@
 app.beagle.* = * 
 -----
 
-NOTE: If the form of line in tc is so generic, it could also be considered a default/generate on the fly. Eg. pick site name from swift commandline and generate a tc internally on-the-fly.
+NOTE: If the form of line in tc is so generic, it could also be considered a default/generate on the fly. Eg. pick site name from swift commandline and generate a tc internally on-the-fly. In other words, only if user has a special need to define specific path for a specific app, tc should appear otherwise, it should be auto-generated internally. --Ketan.
 
 Sites
 -----
@@ -220,7 +220,7 @@
 $ swift -site midway hello.swift
 -----
 
-NOTE: Is the -site switch needed? Could we say "swift -local hello.swift" or "swift -midway,beagle hello.swift"
+NOTE: Is the -site switch needed? Could we say "swift -local hello.swift" or "swift -midway,beagle hello.swift" --Ketan.
 
 To run on multiple sites, separate site names by a comma.
 
@@ -278,6 +278,8 @@
   </pool>
 -----
 
+NOTE: This came up in one or more past discussions: sites file should be less cluttered. Some suggestions: 1) Default values for some attributes be used and should be only visible if a user explicitly wants a new value for them. eg. lowOverAllocation, highOverAllocation, initialscore. 2) One of the walltime and maxwalltime could be done away with. Ditto with depth/ppn and jobspernode. --Ketan
+
 By default in this template, jobsPerNode is set to 24. However, for
 our application we would like to set this to 12. To do this, we add
 this line to the Swift configuration file we are using:
@@ -313,10 +315,12 @@
 Run directories and logs
 ------------------------
 
-Every time Swift runs, it should create a directory called called
+Every time Swift runs, it should create a directory called
 $PWD/.swift/runNNN, where NNN is a numeric value that gets incremented
 with every run.
 
+NOTE: I think the runNNN directory should be created in a visible directory, not a hidden one. It could be simply named runs. --Ketan.
+
 These run directories contain:
 
 * kml and swiftx files



From ketan at ci.uchicago.edu  Mon Jun  3 23:22:05 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Mon,  3 Jun 2013 23:22:05 -0500 (CDT)
Subject: [Swift-commit] r6529 - branches/release-0.94/docs/userguide
Message-ID: <20130604042205.17B3B9CCBD@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-03 23:22:04 -0500 (Mon, 03 Jun 2013)
New Revision: 6529

Modified:
   branches/release-0.94/docs/userguide/coasters
   branches/release-0.94/docs/userguide/log-processing
Log:
fixes for bug 1008

Modified: branches/release-0.94/docs/userguide/coasters
===================================================================
--- branches/release-0.94/docs/userguide/coasters	2013-06-03 05:38:54 UTC (rev 6528)
+++ branches/release-0.94/docs/userguide/coasters	2013-06-04 04:22:04 UTC (rev 6529)
@@ -90,3 +90,16 @@
 |remoteMonitorEnabled|If true, show a graphical display of the status of
 the coaster service
 |==================
+
+Submitting to a specific job queue
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+In order to submit to a specific job scheduler queue, the +queue+ parameter of
+coasters sites file should be used. For example, submitting to the +normal+
+queue of a PBS scheduler, one would use the following sites line:
+
+----
+<profile namespace="globus" key="queue">normal</profile>
+----
+
+

Modified: branches/release-0.94/docs/userguide/log-processing
===================================================================
--- branches/release-0.94/docs/userguide/log-processing	2013-06-03 05:38:54 UTC (rev 6528)
+++ branches/release-0.94/docs/userguide/log-processing	2013-06-04 04:22:04 UTC (rev 6529)
@@ -112,18 +112,22 @@
 the "-resume" option. The .rlog file is only for Swift's internal purpose and
 not to be interpreted by the user.
 
-Each line in the log file is typically made up of three parts. The first part
+Each line in the log file typically consists of three parts. The first part
 is the timestamp, the second is the type of log message and the third is the
 message itself. The types of log messages follows the java log4j standard types
-of TRACE, DEBUG, INFO, WARN, ERROR and FATAL. This section lists the various
-Swift log messages and explains the meaning and likely interpretation of those
-messages. Please note that the list is not comprehensive at this time. Also
-note that we will ignore the timestamps here.
+of TRACE, DEBUG, INFO, WARN, ERROR and FATAL.
 
+////
+This section lists the various Swift log messages and explains the meaning and
+likely interpretation of those messages. Note that the list is not
+comprehensive at this time. Also note that we will ignore the timestamps here.
+
 . _DEBUG Loader arguments: [-sites.file, sites.xml, -config, cf, -tc.file, tc, postproc-gridftp.swift]_
+    Swift commandline arguments
 . _DEBUG Loader Max heap: 5592449024_
+    The java runtime heap size
 . _DEBUG textfiles BEGIN_
-. _DEBUG Loader kmlversion is_
+    A dump of config and source files associated with this run
 . _DEBUG VDL2ExecutionContext Stack dump_
 . _INFO  SetFieldValue Set_
 . _INFO  get__site STARTCOMPOUND thread=0-8 name=get__site_
@@ -142,7 +146,9 @@
 . _INFO  ThrottleManager mem=113.54 MB, heap=482.88 MB, maxHeap=5.21 GB_
 . _INFO  ThrottleManager I maxBuffers=512, crtBuffers=0, allowedTransfers=256, active=0, suspended=0_
 . _INFO  PerformanceDiagnosticInputStream [MEM] Heap total: 482.88 MB, Heap used: 118.58 MB_
+Heap sizes for performance
 . _INFO  vdl:execute END_SUCCESS thread=0-8-0 tr=getsite_
+The job ended successfully
 . _INFO  WeightedHostScoreScheduler CONTACT_SELECTED host=localhost, score=99.854_
 . _
-
+////



From ketan at ci.uchicago.edu  Mon Jun  3 23:22:38 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Mon,  3 Jun 2013 23:22:38 -0500 (CDT)
Subject: [Swift-commit] r6530 - trunk/docs/userguide
Message-ID: <20130604042238.4D2D59CCBD@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-03 23:22:38 -0500 (Mon, 03 Jun 2013)
New Revision: 6530

Modified:
   trunk/docs/userguide/coasters
   trunk/docs/userguide/log-processing
Log:
fixes for bug 1008

Modified: trunk/docs/userguide/coasters
===================================================================
--- trunk/docs/userguide/coasters	2013-06-04 04:22:04 UTC (rev 6529)
+++ trunk/docs/userguide/coasters	2013-06-04 04:22:38 UTC (rev 6530)
@@ -91,21 +91,16 @@
 the coaster service
 |==================
 
+////
 Submitting to a specific job queue
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-In order to submit to a specific job schedular queue, the +queue+ parameter of coasters sites file should be used. For example, submitting to the +normal+ queue of a PBS schedular, one would use the following sites line:
+In order to submit to a specific job scheduler queue, the +queue+ parameter of
+coasters sites file should be used. For example, submitting to the +normal+
+queue of a PBS scheduler, one would use the following sites line:
 
 ----
 <profile namespace="globus" key="queue">normal</profile>
 ----
+////
 
-Jobs and Coasters Parameters Equation
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-The parameters provided in the coasters specification affect jobs submitted by Swift to the scheduling system.
-
-----
-Jobs Submitted = slots X jobsPerNode X nodeGranularity X maxNodes
-----
-

Modified: trunk/docs/userguide/log-processing
===================================================================
--- trunk/docs/userguide/log-processing	2013-06-04 04:22:04 UTC (rev 6529)
+++ trunk/docs/userguide/log-processing	2013-06-04 04:22:38 UTC (rev 6530)
@@ -115,11 +115,13 @@
 Each line in the log file typically consists of three parts. The first part
 is the timestamp, the second is the type of log message and the third is the
 message itself. The types of log messages follows the java log4j standard types
-of TRACE, DEBUG, INFO, WARN, ERROR and FATAL. This section lists the various
-Swift log messages and explains the meaning and likely interpretation of those
-messages. Note that the list is not comprehensive at this time. Also
-note that we will ignore the timestamps here.
+of TRACE, DEBUG, INFO, WARN, ERROR and FATAL.
 
+////
+This section lists the various Swift log messages and explains the meaning and
+likely interpretation of those messages. Note that the list is not
+comprehensive at this time. Also note that we will ignore the timestamps here.
+
 . _DEBUG Loader arguments: [-sites.file, sites.xml, -config, cf, -tc.file, tc, postproc-gridftp.swift]_
     Swift commandline arguments
 . _DEBUG Loader Max heap: 5592449024_
@@ -149,4 +151,4 @@
 The job ended successfully
 . _INFO  WeightedHostScoreScheduler CONTACT_SELECTED host=localhost, score=99.854_
 . _
-
+////



From ketan at ci.uchicago.edu  Fri Jun  7 18:15:10 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Fri,  7 Jun 2013 18:15:10 -0500 (CDT)
Subject: [Swift-commit] r6531 - branches/release-0.94/docs/userguide
Message-ID: <20130607231510.88F2C9CCA5@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-07 18:15:10 -0500 (Fri, 07 Jun 2013)
New Revision: 6531

Modified:
   branches/release-0.94/docs/userguide/coasters
Log:
remove queue selection section from coasters

Modified: branches/release-0.94/docs/userguide/coasters
===================================================================
--- branches/release-0.94/docs/userguide/coasters	2013-06-04 04:22:38 UTC (rev 6530)
+++ branches/release-0.94/docs/userguide/coasters	2013-06-07 23:15:10 UTC (rev 6531)
@@ -91,15 +91,3 @@
 the coaster service
 |==================
 
-Submitting to a specific job queue
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-In order to submit to a specific job scheduler queue, the +queue+ parameter of
-coasters sites file should be used. For example, submitting to the +normal+
-queue of a PBS scheduler, one would use the following sites line:
-
-----
-<profile namespace="globus" key="queue">normal</profile>
-----
-
-



From ketan at ci.uchicago.edu  Fri Jun  7 19:15:43 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Fri,  7 Jun 2013 19:15:43 -0500 (CDT)
Subject: [Swift-commit] r6532 - branches/release-0.94/docs/userguide
Message-ID: <20130608001544.0075C9CCA5@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-07 19:15:43 -0500 (Fri, 07 Jun 2013)
New Revision: 6532

Modified:
   branches/release-0.94/docs/userguide/coasters
Log:
update coaster parameters and jobs relationship

Modified: branches/release-0.94/docs/userguide/coasters
===================================================================
--- branches/release-0.94/docs/userguide/coasters	2013-06-07 23:15:10 UTC (rev 6531)
+++ branches/release-0.94/docs/userguide/coasters	2013-06-08 00:15:43 UTC (rev 6532)
@@ -91,3 +91,35 @@
 the coaster service
 |==================
 
+Coaster config parameters and Job Quantities
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This section presents information on coaster configuration parameters and their effect on application and scheduler jobs submitted by Swift. In order to achieve optimal performance, the number of application tasks must correspond to the total number of coaster workers. Coaster configuration parameters influence both application tasks and the LRM (Local Resource Manager) jobs that are submitted by Swift. Specifically, the following quantities are influenced by coasters configuration parameters:
+
+* Number of application tasks Swift will pack in one "wave" to be executed in parallel depends on the +foreach.max.threads+ and the +throttle+ parameters. Furthermore, the number of +foreach+ loops in a Swift script influences the aggregate +foreach.max.threads+. The relation between application tasks and the above mentioned quantities could be explained as follows:
+----
+app_tasks = min{nforeach X foreach.max.threads), (throttle X 100 +1)}
+----
+
+Where +nforeach+ is the number of independent foreach loops appearing in a Swift script.
+
+* Number of jobs Swift will submit via the LRM interface is determined by the +slots+ configuration parameter in sites file.
+
+----
+LRM jobs = slots
+----
+
+* Size of each LRM job in terms of number of compute nodes per job is determined by the +maxnodes+ and +nodegranularity+ parameters. LRM jobs submitted by Swift will be of size spread between +nodegranularity+ and +maxnodes+ values.
+
+----
+nodegranularity <= LRM job size <= maxnodes
+----
+
+* Number of coaster workers to be run per LRM job on a target cluster is determined by the +jobspernode+ parameter.
+
+Considering the above factors, the following paramter expressions must match in order for a Swift run to be optimal:
+
+----
+min{nforeach X foreach.max.threads), (throttle X 100 +1)} ~= 
+            slots X avg(nodegranularity,maxnodes) X jobspernode
+----



From davidk at ci.uchicago.edu  Tue Jun 11 06:56:22 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 11 Jun 2013 06:56:22 -0500 (CDT)
Subject: [Swift-commit] r6533 - branches/release-0.94/docs/siteguide
Message-ID: <20130611115622.D8F819CCB6@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-11 06:56:21 -0500 (Tue, 11 Jun 2013)
New Revision: 6533

Added:
   branches/release-0.94/docs/siteguide/ssh
Modified:
   branches/release-0.94/docs/siteguide/siteguide.txt
Log:
SSH example


Modified: branches/release-0.94/docs/siteguide/siteguide.txt
===================================================================
--- branches/release-0.94/docs/siteguide/siteguide.txt	2013-06-08 00:15:43 UTC (rev 6532)
+++ branches/release-0.94/docs/siteguide/siteguide.txt	2013-06-11 11:56:21 UTC (rev 6533)
@@ -26,6 +26,8 @@
 
 include::midway[]
 
+include::ssh[]
+
 include::stampede[]
 
 include::uc3[]

Added: branches/release-0.94/docs/siteguide/ssh
===================================================================
--- branches/release-0.94/docs/siteguide/ssh	                        (rev 0)
+++ branches/release-0.94/docs/siteguide/ssh	2013-06-11 11:56:21 UTC (rev 6533)
@@ -0,0 +1,91 @@
+SSH
+---
+This section describes how to use the SSH provider to connect to remote sites
+and to handle data transfer.
+
+Generate a unique SSH key
+~~~~~~~~~~~~~~~~~~~~~~~~~
+It is recommended that you create a new SSH key exclusively for this purpose.
+In order to avoid being prompted for passwords/passphrases, your SSH passphrase
+will be stored in a read protected file. Instead of using your real SSH key and
+passphrase for this purpose, create a new one. Run this command on the machine
+where you will be running Swift:
+
+-----
+ssh-keygen -t dsa -f $HOME/.ssh/id_dsa-swift
+-----
+
+You will be prompted to create a passphrase. This will create two files: 
+$HOME/.ssh/id_dsa-swift and $HOME/.ssh/id_dsa-swift.pub. 
+
+Add your public key to the remote host
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+On the remote host where you will be running, edit or create the file 
+$HOME/.ssh/authorized_keys. Paste in the contents of the newly created 
+$HOME/.ssh/id_dsa-swift.pub from the previous step to the end of the file.
+
+Verify your new key works
+~~~~~~~~~~~~~~~~~~~~~~~~~
+From the host where you will be running Swift, run the following 
+command to verify your keys are working:
+
+-----
+ssh -i $HOME/.ssh/id_dsa-swift user at login.remotehost.edu
+-----
+
+You should be able to connect without being asked for a password or passphrase.
+
+Create auth.defaults
+~~~~~~~~~~~~~~~~~~~~
+Once you verify your keys are working, create a file called 
+$HOME/.ssh/auth.defaults by running the following commands
+
+-----
+touch $HOME/.ssh/auth.defaults
+chmod 600 $HOME/.ssh/auth.defaults
+-----
+
+Next, edit $HOME/.ssh/auth.defaults and add the following lines:
+------
+login.remotehost.edu.type=key
+login.remotehost.edu.username=your_remote_username
+login.remotehost.edu.key=/your/home/.ssh/id_dsa-swift
+login.remotehost.edu.passphrase=your_passphrase
+-----
+
+Replace the values for "your_remote_username", "your_passphrase", and the path 
+to the private key you generated.
+
+Create a sites.xml file
+~~~~~~~~~~~~~~~~~~~~~~~
+Here is an example sites.xml file that will allow you to connect and transfer
+data to a remote host:
+
+-----
+<config>
+   <pool handle="remotehost">
+      <execution provider="coaster" jobmanager="ssh:local" url="login.remotehost.edu"/> 
+      <filesystem provider="ssh" url="login.remotehost.edu"/>
+      <profile namespace="karajan" key="jobThrottle">0</profile>
+      <profile namespace="karajan" key="initialScore">10000</profile>
+      <workdirectory>/path/to/remote/workdirectory</workdirectory>
+   </pool>
+</config>
+-----
+
+NOTE: This example will run work directly on login.remotehost.edu. In most 
+cases you will not want to do this. You'll like want to modify your sites.xml
+to use a remote scheduler, by setting jobmanager to ssh:pbs or ssh:slurm, for
+example. This usually requires also setting things like queues and walltimes.
+This example is provided for simplicity and testing.
+
+Setting your properties
+~~~~~~~~~~~~~~~~~~~~~~~
+Since you want to data transfer via ssh, you'll want to verify that you're not
+using any other file transfer mechanisms. Make sure you have the following 
+swift properties defined in your configuration file:
+
+-----
+use.provider.staging=false
+use.wrapper.staging=false
+-----



From davidk at ci.uchicago.edu  Tue Jun 11 07:27:37 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 11 Jun 2013 07:27:37 -0500 (CDT)
Subject: [Swift-commit] r6534 - branches/release-0.94/docs/siteguide
Message-ID: <20130611122737.CF3D09CCB6@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-11 07:27:37 -0500 (Tue, 11 Jun 2013)
New Revision: 6534

Modified:
   branches/release-0.94/docs/siteguide/ssh
Log:
Some minor updates for formatting


Modified: branches/release-0.94/docs/siteguide/ssh
===================================================================
--- branches/release-0.94/docs/siteguide/ssh	2013-06-11 11:56:21 UTC (rev 6533)
+++ branches/release-0.94/docs/siteguide/ssh	2013-06-11 12:27:37 UTC (rev 6534)
@@ -7,8 +7,7 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~
 It is recommended that you create a new SSH key exclusively for this purpose.
 In order to avoid being prompted for passwords/passphrases, your SSH passphrase
-will be stored in a read protected file. Instead of using your real SSH key and
-passphrase for this purpose, create a new one. Run this command on the machine
+will be stored in a read protected file. Run this command on the machine
 where you will be running Swift:
 
 -----
@@ -37,12 +36,12 @@
 
 Create auth.defaults
 ~~~~~~~~~~~~~~~~~~~~
-Once you verify your keys are working, create a file called 
-$HOME/.ssh/auth.defaults by running the following commands
+Create a file called $HOME/.ssh/auth.defaults on the host where you are running Swift.
+Use the following commands to create this file:
 
 -----
-touch $HOME/.ssh/auth.defaults
-chmod 600 $HOME/.ssh/auth.defaults
+$ touch $HOME/.ssh/auth.defaults
+$ chmod 600 $HOME/.ssh/auth.defaults
 -----
 
 Next, edit $HOME/.ssh/auth.defaults and add the following lines:
@@ -53,8 +52,9 @@
 login.remotehost.edu.passphrase=your_passphrase
 -----
 
-Replace the values for "your_remote_username", "your_passphrase", and the path 
-to the private key you generated.
+Replace login.remotehost.edu with the hostname you want to use, replace the
+values for "your_remote_username", "your_passphrase", and set the correct path 
+of private key you generated.
 
 Create a sites.xml file
 ~~~~~~~~~~~~~~~~~~~~~~~
@@ -73,7 +73,7 @@
 </config>
 -----
 
-NOTE: This example will run work directly on login.remotehost.edu. In most 
+NOTE: This example will run work directly on login.remotehost.edu. In many 
 cases you will not want to do this. You'll like want to modify your sites.xml
 to use a remote scheduler, by setting jobmanager to ssh:pbs or ssh:slurm, for
 example. This usually requires also setting things like queues and walltimes.



From swift at ci.uchicago.edu  Tue Jun 11 15:20:03 2013
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Tue, 11 Jun 2013 15:20:03 -0500 (CDT)
Subject: [Swift-commit] cog r3671
Message-ID: <20130611202003.B0A2E8D00087@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3671 | davidkelly999 | 2013-06-11 15:17:32 -0500 (Tue, 11 Jun 2013) | 2 lines

Condor leave in queue fix for trunk

------------------------------------------------------------------------
Index: modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java
===================================================================
--- modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java	(revision 3670)
+++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java	(working copy)
@@ -150,7 +150,7 @@
 	    }
 	    
 		wr.write("notification = Never\n");
-		wr.write("leave_in_queue = TRUE\n");
+		wr.write("leave_in_queue = FALSE\n");
 		wr.write("queue\n");
 		wr.close();
 	}


From wilde at ci.uchicago.edu  Tue Jun 11 15:25:17 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Tue, 11 Jun 2013 15:25:17 -0500 (CDT)
Subject: [Swift-commit] r6535 - SwiftTutorials
Message-ID: <20130611202517.750D49CCC0@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-11 15:25:17 -0500 (Tue, 11 Jun 2013)
New Revision: 6535

Added:
   SwiftTutorials/OHBM_2013-06-16/
Log:
Initial dir for new tutorial.



From davidk at ci.uchicago.edu  Tue Jun 11 15:56:11 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 11 Jun 2013 15:56:11 -0500 (CDT)
Subject: [Swift-commit] r6536 - branches/release-0.94/docs/quickstart
Message-ID: <20130611205611.5A4619CCB6@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-11 15:56:11 -0500 (Tue, 11 Jun 2013)
New Revision: 6536

Modified:
   branches/release-0.94/docs/quickstart/quickstart.txt
Log:
Updates to checkout procedure


Modified: branches/release-0.94/docs/quickstart/quickstart.txt
===================================================================
--- branches/release-0.94/docs/quickstart/quickstart.txt	2013-06-11 20:25:17 UTC (rev 6535)
+++ branches/release-0.94/docs/quickstart/quickstart.txt	2013-06-11 20:56:11 UTC (rev 6536)
@@ -46,13 +46,13 @@
 and http://www.oracle.com/technetwork/java/javase/downloads/index.html[Java JDK]. Once
 built, the dist/swift-svn directory will contain your build.
 
-To download and build Swift 0.93, follow these instructions:
+To download and build Swift 0.94, follow these instructions:
 -----
-$ mkdir swift-0.93 
-$ cd swift-0.93 
-$ svn co https://cogkit.svn.sourceforge.net/svnroot/cogkit/branches/4.1.9/src/cog 
+$ mkdir swift-0.94
+$ cd swift-0.94
+$ svn co https://svn.code.sf.net/p/cogkit/svn/branches/4.1.10/src/cog
 $ cd cog/modules 
-$ svn co https://svn.ci.uchicago.edu/svn/vdl2/branches/release-0.93 swift 
+$ svn co https://svn.ci.uchicago.edu/svn/vdl2/branches/release-0.94 swift
 $ cd swift 
 $ ant redist
 -----
@@ -62,9 +62,9 @@
 Once Swift is installed, it is useful to add the swift binary to your PATH
 environment variable. To do this, first determine where the Swift bin
 directory is located. If you installed Swift from a binary release, it will
-be in the swift-0.93/bin directory where you installed it. If you followed
+be in the swift-0.94/bin directory where you installed it. If you followed
 the instructions above for installing Swift from a source repository, it
-will be located in swift-0.93/cog/modules/swift/dist/swift-svn/bin.
+will be located in swift-0.94/cog/modules/swift/dist/swift-svn/bin.
 
 Add the following line to the bottom of ~/.bashrc:
 
@@ -98,4 +98,4 @@
 Swift script!
 
 More documentation on how to run Swift can be found at 
-http://www.ci.uchicago.edu/swift/docs/index.php,
+http://www.ci.uchicago.edu/swift/docs/index.php.



From wilde at ci.uchicago.edu  Tue Jun 11 17:23:37 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Tue, 11 Jun 2013 17:23:37 -0500 (CDT)
Subject: [Swift-commit] r6537 - in SwiftTutorials/OHBM_2013-06-16: . data
	original
Message-ID: <20130611222337.550F59CCB6@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-11 17:23:37 -0500 (Tue, 11 Jun 2013)
New Revision: 6537

Added:
   SwiftTutorials/OHBM_2013-06-16/README
   SwiftTutorials/OHBM_2013-06-16/align.sh
   SwiftTutorials/OHBM_2013-06-16/apps
   SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere
   SwiftTutorials/OHBM_2013-06-16/clean.sh
   SwiftTutorials/OHBM_2013-06-16/data/
   SwiftTutorials/OHBM_2013-06-16/data/anatomy1.hdr
   SwiftTutorials/OHBM_2013-06-16/data/anatomy1.img
   SwiftTutorials/OHBM_2013-06-16/data/anatomy2.hdr
   SwiftTutorials/OHBM_2013-06-16/data/anatomy2.img
   SwiftTutorials/OHBM_2013-06-16/data/anatomy3.hdr
   SwiftTutorials/OHBM_2013-06-16/data/anatomy3.img
   SwiftTutorials/OHBM_2013-06-16/data/anatomy4.hdr
   SwiftTutorials/OHBM_2013-06-16/data/anatomy4.img
   SwiftTutorials/OHBM_2013-06-16/data/reference.hdr
   SwiftTutorials/OHBM_2013-06-16/data/reference.img
   SwiftTutorials/OHBM_2013-06-16/genatlas.swift
   SwiftTutorials/OHBM_2013-06-16/original/
   SwiftTutorials/OHBM_2013-06-16/original/workflow.sh
   SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh
   SwiftTutorials/OHBM_2013-06-16/output/
   SwiftTutorials/OHBM_2013-06-16/sites.xml
   SwiftTutorials/OHBM_2013-06-16/swift.properties
   SwiftTutorials/OHBM_2013-06-16/volmapper
   SwiftTutorials/OHBM_2013-06-16/work/
Log:
Initial revision.

Added: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,24 @@
+
+fMRI Data Processing demo for OHBM 2013
+
+Setup
+
+  # Get the scripts from svn
+
+  svn co https://svn.ci.uchicago.edu/svn/vdl2/SwiftTutorials/OHBM_2013-06-16 
+  cd OHBM_2013-06-16
+
+  # Set default swift.properties in $HOME/.swift.  Points to "." for apps (tc) and sites.xml
+
+  mkdir -p ~/.swift
+  cp ~/.swift/swift.properties ~/.swift/save.swift.properties # If needed, as needed.
+  cp swift.properties ~/.swift
+
+  # Get swift
+
+  module load swift
+
+To run:
+
+ swift genatlas.swift
+

Added: SwiftTutorials/OHBM_2013-06-16/align.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/align.sh	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/align.sh	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,52 @@
+#!/bin/sh
+
+AIR5=/home/wilde/software/AIR5.3.0
+fsl=/project/wilde/software/fsl-5.0.4/fsl
+
+# Arguments: referenceImage (in) anatomicalImage (in) reslicedImage (out)
+
+ref=$1
+anat=$2
+resliced=$3
+
+time $AIR5/bin/alignlinear $ref $anat init.warp \
+  -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 
+time $AIR5/bin/align_warp  $ref $anat refined.warp \
+  -m 1 12 -b1 .1 .1 .1  -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01
+time $AIR5/bin/reslice refined.warp $resliced -a $anat
+
+exit
+
+
+
+
+
+
+
+clean=y
+
+if [ $clean = y ]; then
+  rm *warp atlas* resliced*
+fi
+
+
+
+if true; then
+
+  warp 1
+  warp 2
+  warp 3
+  warp 4
+
+  time  $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img
+fi
+
+export FSLOUTPUTTYPE=NIFTI
+
+time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm
+time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm
+time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm
+
+time convert atlas-x.pgm atlas-x.gif
+time convert atlas-y.pgm atlas-y.gif
+time convert atlas-z.pgm atlas-z.gif


Property changes on: SwiftTutorials/OHBM_2013-06-16/align.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/OHBM_2013-06-16/apps
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/apps	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,4 @@
+localhost sh       /bin/sh
+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/apps.midway-westmere
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,4 @@
+westmere  sh       /bin/sh
+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/clean.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/clean.sh	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/clean.sh	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,4 @@
+#! /bin/sh
+
+rm -rf _concurrent work/* output/* *.log *.rlog *.d *.kml *.swiftx 
+


Property changes on: SwiftTutorials/OHBM_2013-06-16/clean.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy1.hdr
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy1.hdr
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy1.img
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy1.img
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy2.hdr
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy2.hdr
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy2.img
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy2.img
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy3.hdr
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy3.hdr
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy3.img
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy3.img
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy4.hdr
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy4.hdr
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/anatomy4.img
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/anatomy4.img
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/reference.hdr
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/reference.hdr
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/data/reference.img
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/data/reference.img
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/OHBM_2013-06-16/genatlas.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/genatlas.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,77 @@
+type file;
+
+type Volume {
+  file header;
+  file image;
+};
+
+app (Volume alignedVol) align (file alignScript, Volume reference, Volume input)
+{
+  sh @alignScript @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
+}
+
+app (Volume atlas) softmean (Volume v[])
+{
+  softmean @filename(atlas.header) "y" "null" imageNames(v);
+}
+
+app (Volume atlas) softmeanORIG (Volume v[])
+{
+  softmean @filename(atlas.header) "y" "null" @filenames(v);
+}
+
+app (file pgm) slicer (Volume v, string axis)
+{
+  slicer @filename(v.header) @strcat("-",axis) .5 @filename(pgm);
+}
+
+app (file o) convert (file i)
+{
+  convert @i @o;
+}
+
+Volume referenceVolume<ext; exec="volmapper",name="data/reference">;
+Volume inputVolumes []<ext; exec="volmapper",prefix="data/anatomy">;
+Volume outputVolumes[];
+
+file alignScript<"align.sh">;
+
+foreach v, i in inputVolumes {
+  Volume aligned<ext; exec="volmapper",name=@strcat("work/aligned",i)>;
+  aligned = align(alignScript,referenceVolume, v);
+  outputVolumes[i] = aligned;
+}
+
+Volume atlasVolume<ext; exec="volmapper",name="output/atlas">;
+atlasVolume = softmean(outputVolumes);
+
+file xSlice<"output/atlas-x.png">;
+file ySlice<"output/atlas-y.png">;
+file zSlice<"output/atlas-z.png">;
+
+xSlice = convert(slicer(atlasVolume,"x"));
+ySlice = convert(slicer(atlasVolume,"y"));
+zSlice = convert(slicer(atlasVolume,"z"));
+
+
+
+
+
+
+string testNames[] = imageNames(outputVolumes);
+foreach n, i in testNames {
+  tracef("testNames[%i] = %s\n", i, n);
+}
+
+
+(string onames[]) imageNames (Volume v[])
+{
+  string names[] = @filenames(v);
+  foreach n, i in names {
+    if ( i %% 2 == 0) {
+      // tracef("n[%i] = %s\n", i, n);
+      onames[i] = n;
+    }
+  }
+}
+

Added: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/original/workflow.sh	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/original/workflow.sh	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,30 @@
+#!/bin/sh
+
+AIR5=$HOME/software/AIR5.3.0
+fsl=/project/wilde/software/fsl-5.0.4/fsl
+
+if true; then
+
+#time  $AIR5/bin/align_warp anatomy1.img reference.img warp1.warp -m 1 12 -s 1024 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  -h 10000 -v -j # -q
+
+time  $AIR5/bin/align_warp reference.img anatomy1.img warp1.warp -m 1 12  -b1 .1 .1 .1  -b2 .1 .1 .1  -h 10000 -v -s 1024 2 2 -c .01  -f out # -q -s 1024 2 2 -c .01
+
+
+time  $AIR5/bin/align_warp anatomy2.img reference.img warp2.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
+time  $AIR5/bin/align_warp anatomy3.img reference.img warp3.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
+time  $AIR5/bin/align_warp anatomy4.img reference.img warp4.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
+time  $AIR5/bin/reslice warp1.warp resliced1
+time  $AIR5/bin/reslice warp2.warp resliced2
+time  $AIR5/bin/reslice warp3.warp resliced3
+time  $AIR5/bin/reslice warp4.warp resliced4
+time  $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img
+fi
+
+export FSLOUTPUTTYPE=NIFTI
+
+time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm
+time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm
+time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm
+time convert atlas-x.pgm atlas-x.gif
+time convert atlas-y.pgm atlas-y.gif
+time convert atlas-z.pgm atlas-z.gif


Property changes on: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,40 @@
+#!/bin/sh
+
+AIR5=$HOME/software/AIR5.3.0
+
+
+clean=y
+
+if [ $clean = y ]; then
+  rm *warp atlas* resliced*
+fi
+
+warp()
+{
+time $AIR5/bin/alignlinear reference.img anatomy$1.img initwarp$1.warp -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 
+time $AIR5/bin/align_warp reference.img anatomy$1.img warp$1.warp -m 1 12  -b1 .1 .1 .1  -b2 .1 .1 .1  -h 10000 -v -s 1024 2 2 -c .01 -f initwarp$1.warp # -q -s 1024 2 2 -c .01
+}
+
+if true; then
+
+warp 1
+warp 2
+warp 3
+warp 4
+
+time  $AIR5/bin/reslice warp1.warp resliced1 -a anatomy1
+time  $AIR5/bin/reslice warp2.warp resliced2 -a anatomy2
+time  $AIR5/bin/reslice warp3.warp resliced3 -a anatomy3
+time  $AIR5/bin/reslice warp4.warp resliced4 -a anatomy4
+
+time  $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img
+fi
+
+export FSLOUTPUTTYPE=NIFTI
+
+time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm
+time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm
+time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm
+time convert atlas-x.pgm atlas-x.gif
+time convert atlas-y.pgm atlas-y.gif
+time convert atlas-z.pgm atlas-z.gif


Property changes on: SwiftTutorials/OHBM_2013-06-16/original/workflow2.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/OHBM_2013-06-16/sites.xml
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/sites.xml	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/sites.xml	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,41 @@
+<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="karajan" key="jobThrottle">.03</profile> <!-- eg .11 -> 12 -->
+  </pool>
+
+  <pool handle="westmere">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">westmere</profile>
+    <profile namespace="globus" key="ppn">12</profile>
+    <!-- <profile namespace="globus" key="project">pi-wilde</profile> -->
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <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="jobsPerNode">12</profile> <!-- apps per node! -->
+    <profile namespace="karajan" key="jobThrottle">.11</profile> <!-- eg .11 -> 12 -->
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+  </pool>
+
+</config>

Added: SwiftTutorials/OHBM_2013-06-16/swift.properties
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/swift.properties	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/swift.properties	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,14 @@
+
+sites.file=sites.xml
+tc.file=apps
+
+status.mode=provider
+use.provider.staging=false
+use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+file.gc.enabled=false
+#tcp.port.range=50000,51000

Added: SwiftTutorials/OHBM_2013-06-16/volmapper
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/volmapper	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/volmapper	2013-06-11 22:23:37 UTC (rev 6537)
@@ -0,0 +1,29 @@
+#! /bin/sh
+
+case $1 in
+
+  -prefix)
+
+    prefix=$2
+    names=$(echo ${prefix}*.img)
+
+    for n in $names; do
+      name=$(echo $n | sed -e 's,\..*,,')
+      num=$(echo $n | sed -e 's,\..*,,' -e "s,${prefix},,")
+      echo "[$num].header $name.hdr"
+      echo "[$num].image  $name.img"
+    done
+    ;;
+
+  -name)
+
+    echo 'header' $2.hdr
+    echo 'image ' $2.img
+    ;;
+
+  *)
+    echo error in external mapper $0
+    ;;
+esac
+    
+


Property changes on: SwiftTutorials/OHBM_2013-06-16/volmapper
___________________________________________________________________
Added: svn:executable
   + *



From wilde at ci.uchicago.edu  Tue Jun 11 17:25:47 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Tue, 11 Jun 2013 17:25:47 -0500 (CDT)
Subject: [Swift-commit] r6538 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130611222547.ABCB59CCB6@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-11 17:25:47 -0500 (Tue, 11 Jun 2013)
New Revision: 6538

Added:
   SwiftTutorials/OHBM_2013-06-16/apps.midway
Removed:
   SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere
Modified:
   SwiftTutorials/OHBM_2013-06-16/README
Log:
Add instructions and minor tweak for miway execution.

Modified: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	2013-06-11 22:23:37 UTC (rev 6537)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-11 22:25:47 UTC (rev 6538)
@@ -20,5 +20,10 @@
 
 To run:
 
+ # On localhost:
+
  swift genatlas.swift
 
+ # With most parallel work on midway westmere parition:
+
+ swift -tc.file apps.midway genatlas.swift

Copied: SwiftTutorials/OHBM_2013-06-16/apps.midway (from rev 6537, SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere)
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps.midway	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/apps.midway	2013-06-11 22:25:47 UTC (rev 6538)
@@ -0,0 +1,4 @@
+westmere  sh       /bin/sh
+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

Deleted: SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere	2013-06-11 22:23:37 UTC (rev 6537)
+++ SwiftTutorials/OHBM_2013-06-16/apps.midway-westmere	2013-06-11 22:25:47 UTC (rev 6538)
@@ -1,4 +0,0 @@
-westmere  sh       /bin/sh
-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



From wilde at ci.uchicago.edu  Tue Jun 11 17:50:42 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Tue, 11 Jun 2013 17:50:42 -0500 (CDT)
Subject: [Swift-commit] r6539 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130611225042.DED6D9CCC0@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-11 17:50:42 -0500 (Tue, 11 Jun 2013)
New Revision: 6539

Modified:
   SwiftTutorials/OHBM_2013-06-16/README
Log:
Update README

Modified: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	2013-06-11 22:25:47 UTC (rev 6538)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-11 22:50:42 UTC (rev 6539)
@@ -27,3 +27,29 @@
  # With most parallel work on midway westmere parition:
 
  swift -tc.file apps.midway genatlas.swift
+
+The output files of the workflow are placed under output/,
+intermediate files under work/.
+
+The 3 final png output files (a "slice" of the final atlas) should
+look like this:
+
+  http://www.ci.uchicago.edu/~wilde/atlas-x.png
+  http://www.ci.uchicago.edu/~wilde/atlas-y.png
+  http://www.ci.uchicago.edu/~wilde/atlas-z.png
+
+Notes:
+
+  The "aligin" initial stage runs 3 AIR tools under as a single shell
+  script, to reduce staging between these steps.
+
+TODO
+
+  Show the workflow with the 3 AIR tools expanded as separate workflow
+  steps, and as a Swift procedure.
+
+  Run on other sites and Multisite
+
+  Add performance monitoring and plotting
+
+



From wilde at ci.uchicago.edu  Thu Jun 13 08:02:23 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 08:02:23 -0500 (CDT)
Subject: [Swift-commit] r6540 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130613130223.DDAE09CCA7@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-13 08:02:22 -0500 (Thu, 13 Jun 2013)
New Revision: 6540

Added:
   SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx
Log:
Initial revision of OHBM talk.

Added: SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream



From wilde at ci.uchicago.edu  Thu Jun 13 08:43:03 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 08:43:03 -0500 (CDT)
Subject: [Swift-commit] r6541 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130613134303.4466D9CCA7@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-13 08:43:03 -0500 (Thu, 13 Jun 2013)
New Revision: 6541

Modified:
   SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx
Log:
Update title/speaker and fix formats in OHBM talk.

Modified: SwiftTutorials/OHBM_2013-06-16/Swift-OHBM.2013.0616.pptx
===================================================================
(Binary files differ)



From wilde at ci.uchicago.edu  Thu Jun 13 10:13:05 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 10:13:05 -0500 (CDT)
Subject: [Swift-commit] r6542 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130613151305.AA9109CC82@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-13 10:13:05 -0500 (Thu, 13 Jun 2013)
New Revision: 6542

Added:
   SwiftTutorials/OHBM_2013-06-16/TODO
   SwiftTutorials/OHBM_2013-06-16/apps.beagle
   SwiftTutorials/OHBM_2013-06-16/makedata.sh
Modified:
   SwiftTutorials/OHBM_2013-06-16/README
   SwiftTutorials/OHBM_2013-06-16/align.sh
   SwiftTutorials/OHBM_2013-06-16/apps
   SwiftTutorials/OHBM_2013-06-16/genatlas.swift
   SwiftTutorials/OHBM_2013-06-16/sites.xml
   SwiftTutorials/OHBM_2013-06-16/swift.properties
Log:
Misc changes; updated README; add beagle and midway site defs; adjust properties.

Modified: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	2013-06-13 13:43:03 UTC (rev 6541)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-13 15:13:05 UTC (rev 6542)
@@ -18,16 +18,30 @@
 
   module load swift
 
+To generate test data directories:
+
+  ./makedata data_100 100 # create 100 anatomical image volumes in directory data_100
+
 To run:
 
  # On localhost:
 
- swift genatlas.swift
+ swift genatlas.swift             # processes data/ directory by default
+ swift genatlas.swift -d=data_100 # process data_100/ directory
 
  # With most parallel work on midway westmere parition:
 
  swift -tc.file apps.midway genatlas.swift
 
+ # Choices for -tc.file are:
+
+ apps         # default, runs on localhost
+ apps.beagle  # on beagle, 8 nodes
+ apps.midway  # on midway westmere, 1 node
+ apps.amazon  # on Amazon EC2 - needs start-coaster-service, see below
+ apps.UC3     # submits to UC3, needs apps to be sent.
+
+
 The output files of the workflow are placed under output/,
 intermediate files under work/.
 

Added: SwiftTutorials/OHBM_2013-06-16/TODO
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/TODO	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/TODO	2013-06-13 15:13:05 UTC (rev 6542)
@@ -0,0 +1,5 @@
+timeseries:
+
+/scratch/midway/wilde/ds107/ds107/sub001/model/model001
+
+

Modified: SwiftTutorials/OHBM_2013-06-16/align.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/align.sh	2013-06-13 13:43:03 UTC (rev 6541)
+++ SwiftTutorials/OHBM_2013-06-16/align.sh	2013-06-13 15:13:05 UTC (rev 6542)
@@ -1,7 +1,6 @@
 #!/bin/sh
 
-AIR5=/home/wilde/software/AIR5.3.0
-fsl=/project/wilde/software/fsl-5.0.4/fsl
+#AIR5=/home/wilde/software/AIR5.3.0
 
 # Arguments: referenceImage (in) anatomicalImage (in) reslicedImage (out)
 
@@ -23,6 +22,8 @@
 
 
 
+fsl=/project/wilde/software/fsl-5.0.4/fsl
+
 clean=y
 
 if [ $clean = y ]; then

Modified: SwiftTutorials/OHBM_2013-06-16/apps
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps	2013-06-13 13:43:03 UTC (rev 6541)
+++ SwiftTutorials/OHBM_2013-06-16/apps	2013-06-13 15:13:05 UTC (rev 6542)
@@ -1,4 +1,5 @@
-localhost sh       /bin/sh
+localhost sh       /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0
+#localhost sh       /bin/sh
 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/apps.beagle
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps.beagle	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/apps.beagle	2013-06-13 15:13:05 UTC (rev 6542)
@@ -0,0 +1,4 @@
+beagle    sh       /bin/sh null null env::AIR5=/lustre/beagle/wilde/software/AIR5.3.0
+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

Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-13 13:43:03 UTC (rev 6541)
+++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-13 15:13:05 UTC (rev 6542)
@@ -5,18 +5,13 @@
   file image;
 };
 
-app (Volume alignedVol) align (file alignScript, Volume reference, Volume input)
+app (Volume alignedVol) align (file script, Volume reference, Volume input)
 {
-  sh @alignScript @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
+  sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
 }
 
 app (Volume atlas) softmean (Volume v[])
 {
-  softmean @filename(atlas.header) "y" "null" imageNames(v);
-}
-
-app (Volume atlas) softmeanORIG (Volume v[])
-{
   softmean @filename(atlas.header) "y" "null" @filenames(v);
 }
 
@@ -30,12 +25,13 @@
   convert @i @o;
 }
 
+string dataDir = @arg("d","data");
+file   alignScript<"align.sh">;
+
 Volume referenceVolume<ext; exec="volmapper",name="data/reference">;
-Volume inputVolumes []<ext; exec="volmapper",prefix="data/anatomy">;
+Volume inputVolumes []<ext; exec="volmapper",prefix=@strcat(dataDir,"/anatomy")>;
 Volume outputVolumes[];
 
-file alignScript<"align.sh">;
-
 foreach v, i in inputVolumes {
   Volume aligned<ext; exec="volmapper",name=@strcat("work/aligned",i)>;
   aligned = align(alignScript,referenceVolume, v);
@@ -54,16 +50,19 @@
 zSlice = convert(slicer(atlasVolume,"z"));
 
 
+/******* The following code to be removed
 
-
-
-
 string testNames[] = imageNames(outputVolumes);
 foreach n, i in testNames {
   tracef("testNames[%i] = %s\n", i, n);
 }
 
+app (Volume atlas) softmeanALT (Volume v[]) # A better version
+{
+  softmean @filename(atlas.header) "y" "null" imageNames(v); # puts only the .img on command line
+}
 
+
 (string onames[]) imageNames (Volume v[])
 {
   string names[] = @filenames(v);
@@ -75,3 +74,4 @@
   }
 }
 
+*******/
\ No newline at end of file

Added: SwiftTutorials/OHBM_2013-06-16/makedata.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/makedata.sh	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/makedata.sh	2013-06-13 15:13:05 UTC (rev 6542)
@@ -0,0 +1,24 @@
+#! /bin/sh
+
+datadir=${1:-data_10}
+nfiles=${2:-10}
+
+rm -rf $datadir
+mkdir $datadir
+cp data/anatomy1.{hdr,img} $datadir
+
+n=0
+( cd  $datadir
+  mv anatomy1.hdr s.hdr
+  mv anatomy1.img s.img
+  for id in $(seq -w 000 999); do
+      n=$((n+1))
+      if [ $n -gt $nfiles ]; then
+        break;
+      else
+        ln s.img anatomy$id.img
+        ln s.hdr anatomy$id.hdr
+      fi
+  done
+  rm s.{img,hdr}
+)


Property changes on: SwiftTutorials/OHBM_2013-06-16/makedata.sh
___________________________________________________________________
Added: svn:executable
   + *

Modified: SwiftTutorials/OHBM_2013-06-16/sites.xml
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/sites.xml	2013-06-13 13:43:03 UTC (rev 6541)
+++ SwiftTutorials/OHBM_2013-06-16/sites.xml	2013-06-13 15:13:05 UTC (rev 6542)
@@ -5,6 +5,7 @@
     <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>
 
@@ -38,4 +39,24 @@
     <profile namespace="karajan" key="initialScore">10000</profile>
   </pool>
 
+  <pool handle="beagle">
+    <execution provider="coaster" jobmanager="ssh-cl:pbs" url="login.beagle.ci.uchicago.edu"/>
+    <profile namespace="globus" key="jobsPerNode">24</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile>
+    <!-- to use a beage reservation, eg:
+         <profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24;pbs.resource_list=advres=wilde.1768</profile>
+    -->
+    <profile namespace="globus" key="maxtime">3600</profile>
+    <profile namespace="globus" key="maxWalltime">00:05:00</profile>
+    <profile namespace="globus" key="userHomeOverride">/lustre/beagle/{env.USER}/swiftwork</profile>
+    <profile namespace="globus" key="slots">20</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="nodeGranularity">1</profile>
+    <profile namespace="karajan" key="jobThrottle">4.80</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+    <workdirectory>/tmp/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
 </config>

Modified: SwiftTutorials/OHBM_2013-06-16/swift.properties
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/swift.properties	2013-06-13 13:43:03 UTC (rev 6541)
+++ SwiftTutorials/OHBM_2013-06-16/swift.properties	2013-06-13 15:13:05 UTC (rev 6542)
@@ -3,12 +3,12 @@
 tc.file=apps
 
 status.mode=provider
-use.provider.staging=false
+use.provider.staging=true
 use.wrapper.staging=false
 wrapperlog.always.transfer=true
 execution.retries=0
 lazy.errors=false
-provider.staging.pin.swiftfiles=false
+provider.staging.pin.swiftfiles=true
 sitedir.keep=true
 file.gc.enabled=false
 #tcp.port.range=50000,51000



From ketan at ci.uchicago.edu  Thu Jun 13 11:31:22 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 11:31:22 -0500 (CDT)
Subject: [Swift-commit] r6543 - trunk/docs/siteguide
Message-ID: <20130613163122.A2E3C9CCA7@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-13 11:31:22 -0500 (Thu, 13 Jun 2013)
New Revision: 6543

Added:
   trunk/docs/siteguide/ec2
Log:
first cut for running Swift on EC2 resources

Added: trunk/docs/siteguide/ec2
===================================================================
--- trunk/docs/siteguide/ec2	                        (rev 0)
+++ trunk/docs/siteguide/ec2	2013-06-13 16:31:22 UTC (rev 6543)
@@ -0,0 +1,116 @@
+Amazon EC2 Cloud
+----------------
+Amazon EC2 offers virtualized resources on demand from its cloud data centers.
+This section describes how to use Swift to run applications on EC2 resources.
+More information on EC2 can be found link:https://aws.amazon.com/ec2[here].
+
+Getting Access
+~~~~~~~~~~~~~~
+
+==Users with EC2 Allocation
+
+If you already have an EC2 allocation, you can use either the web console or command-line interface to manage resources.
+
+Before using EC2 for Swift you must create a security group in order to allow Swift communicate with EC2 instances via open ports. In order to create a security group, follow instructions link:http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.html#creating-security-group[here]. Preferably, open ports between 50000 and 51000.
+
+Paste your credentials from the EC2 web console into AWS_ACCESS_KEY and AWS_SECRET_KEY and export them in your .bashrc as follows:
+----
+export AWS_ACCESS_KEY=<your access key>
+export AWS_SECRET_KEY=<your secret key>
+----
+
+A public AMI for Swift user is available with id: ami-332e585a.
+
+Create instances from the above AMI as follows:
+
+----
+ec2run -k <keypair_name> -g <sec_group_name> -n <count> ami-332e585a
+----
+
+==Users without EC2 Allocation
+
+Configuring coaster-service.conf
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+To run on EC2, you will need a file called coaster-service.conf.
+This file contains many options to control how things run. Here is
+an example of a working coaster-service.conf for EC2.
+
+-----
+# Where to copy worker.pl on the remote machine for sites.xml
+export WORKER_LOCATION=/tmp
+
+# How to launch workers: local, ssh, cobalt
+export WORKER_MODE=ssh
+
+# Do all the worker nodes you're using have a shared filesystem? (yes/no)
+export SHARED_FILESYSTEM=no
+
+# Username to use on worker nodes
+export WORKER_USERNAME=root
+
+# Enable SSH tunneling? (yes/no)
+export SSH_TUNNELING=yes
+
+# Directory to keep log files, relative to working directory when launching start-coaster-service
+export LOG_DIR=logs
+
+# Swift information for creating sites.xml
+export WORK=/tmp
+
+# Application locations for tc.data
+#app convert=/usr/bin/convert
+-----
+
+Add a list of any applications you want to run in the format "#app myapp=/path/to/app".
+
+Starting the Coaster Service Script
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Now that everything is configured, change to the location of the coaster-service.conf file
+and run this command to start the coaster service:
+
+-----
+$ start-coaster-service
+-----
+
+This command will start the VMs, start the required processes on the worker nodes,
+and generate Swift configuration files for you to use. The configuration files
+will be generated in your current directory. These files are sites.xml, tc.data,
+and cf.
+
+Running Swift
+~~~~~~~~~~~~~
+Now that you have all of your configuration files generated, run the following command:
+
+-----
+$ swift -sites.file sites.xml -tc.file tc.data -config cf <yourscript.swift>
+-----
+
+If you like to create a custom tc and/or cf file for repeated use, rename it to something other
+than tc.data/cf to prevent it from being overwritten. The sites.xml however will need to be
+regenerated every time you start the coaster service. If you need to repeatedly modify some
+sites.xml options, you may edit the template in Swift's etc/sites/persistent-coasters. You
+may also create your own custom tc files with the hostname of persistent-coasters. More
+information about this can be found in the Swift userguide at
+http://www.ci.uchicago.edu/swift/guides/trunk/userguide/userguide.html.
+
+Stopping the Coaster Service Script
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+To stop the coaster service, run the following command:
+-----
+$ stop-coaster-service
+-----
+
+This will kill the coaster service, kill the worker scripts on remote systems.
+
+Terminate the virtual machines that were created for this work as follows:
+
+----
+ec2din|grep running|awk '{print $2}'|xargs ec2kill
+----
+
+More Help
+~~~~~~~~~
+The best place for additional help is the Swift user mailing list. You can subscribe to this list at
+http://mail.ci.uchicago.edu/mailman/listinfo/swift-user. When submitting information, send
+your sites.xml file, your tc.data, and any error messages you run into.
+



From ketan at ci.uchicago.edu  Thu Jun 13 11:37:12 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 11:37:12 -0500 (CDT)
Subject: [Swift-commit] r6544 - trunk/docs/siteguide
Message-ID: <20130613163712.B081F9CCA7@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-13 11:37:12 -0500 (Thu, 13 Jun 2013)
New Revision: 6544

Modified:
   trunk/docs/siteguide/ec2
Log:
updates

Modified: trunk/docs/siteguide/ec2
===================================================================
--- trunk/docs/siteguide/ec2	2013-06-13 16:31:22 UTC (rev 6543)
+++ trunk/docs/siteguide/ec2	2013-06-13 16:37:12 UTC (rev 6544)
@@ -36,31 +36,46 @@
 an example of a working coaster-service.conf for EC2.
 
 -----
-# Where to copy worker.pl on the remote machine for sites.xml
-export WORKER_LOCATION=/tmp
+#Location of SWIFT. If empty, PATH is referenced
+export SWIFT=
 
-# How to launch workers: local, ssh, cobalt
+# 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
 
-# Do all the worker nodes you're using have a shared filesystem? (yes/no)
-export SHARED_FILESYSTEM=no
+# Worker logging setting passed to worker.pl for sites.xml
+export WORKER_LOGGING_LEVEL=DEBUG
 
-# Username to use on worker nodes
+export SSH_TUNNELING=yes
+
+# User name to use for all systems
 export WORKER_USERNAME=root
 
-# Enable SSH tunneling? (yes/no)
-export SSH_TUNNELING=yes
+# Worker host names for ssh
+# export WORKER_HOSTS="crush thwomp stomp crank grind churn trounce thrash vanquish"
 
 # Directory to keep log files, relative to working directory when launching start-coaster-service
 export LOG_DIR=logs
+export WORKER_LOG_DIR=/root
 
-# Swift information for creating sites.xml
-export WORK=/tmp
+# Manually define ports. If not specified, ports will be automatically generated
+export LOCAL_PORT=50100
+export SERVICE_PORT=50200
 
-# Application locations for tc.data
-#app convert=/usr/bin/convert
+# 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
+export JOBTHROTTLE=$( echo "scale=5; ($JOBS_PER_NODE * $( echo $WORKER_HOSTS | wc -w ))/100 - 0.00001"|bc )
+
+# Swift applications
+#app cat=/bin/cat
+#app bash=/bin/bash
 -----
-
 Add a list of any applications you want to run in the format "#app myapp=/path/to/app".
 
 Starting the Coaster Service Script



From ketan at ci.uchicago.edu  Thu Jun 13 12:00:02 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 12:00:02 -0500 (CDT)
Subject: [Swift-commit] r6545 - trunk/docs/siteguide
Message-ID: <20130613170002.9D8CD9CCA7@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-13 12:00:02 -0500 (Thu, 13 Jun 2013)
New Revision: 6545

Modified:
   trunk/docs/siteguide/ec2
Log:
 

Modified: trunk/docs/siteguide/ec2
===================================================================
--- trunk/docs/siteguide/ec2	2013-06-13 16:37:12 UTC (rev 6544)
+++ trunk/docs/siteguide/ec2	2013-06-13 17:00:02 UTC (rev 6545)
@@ -29,6 +29,17 @@
 
 ==Users without EC2 Allocation
 
+Please request access to prepared instances and PKI credentials by mailing: email at mcs.anl.gov.
+
+Log in to the swift.rcc.uchicago.edu and copy the swift_cloud directory to your home:
+
+----
+cp -r ~maheshwari/swift_cloud $HOME/
+----
+
+Replace the hosts.txt by adding the address/DNS of instances.
+
+
 Configuring coaster-service.conf
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 To run on EC2, you will need a file called coaster-service.conf.



From davidk at ci.uchicago.edu  Thu Jun 13 12:07:15 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 12:07:15 -0500 (CDT)
Subject: [Swift-commit] r6546 - branches/release-0.94/docs/siteguide
Message-ID: <20130613170715.EDBA39CCA7@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-13 12:07:15 -0500 (Thu, 13 Jun 2013)
New Revision: 6546

Modified:
   branches/release-0.94/docs/siteguide/ssh
Log:
Fix error in verification step


Modified: branches/release-0.94/docs/siteguide/ssh
===================================================================
--- branches/release-0.94/docs/siteguide/ssh	2013-06-13 17:00:02 UTC (rev 6545)
+++ branches/release-0.94/docs/siteguide/ssh	2013-06-13 17:07:15 UTC (rev 6546)
@@ -29,10 +29,10 @@
 command to verify your keys are working:
 
 -----
-ssh -i $HOME/.ssh/id_dsa-swift user at login.remotehost.edu
+$ ssh -o IdentitiesOnly=true -i $HOME/.ssh/id_dsa-swift user at login.remotehost.edu
 -----
 
-You should be able to connect without being asked for a password or passphrase.
+You should be prompted for your new passphrase and be able to connect.
 
 Create auth.defaults
 ~~~~~~~~~~~~~~~~~~~~



From ketan at ci.uchicago.edu  Thu Jun 13 13:51:24 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 13:51:24 -0500 (CDT)
Subject: [Swift-commit] r6547 - trunk/docs/siteguide
Message-ID: <20130613185124.B6E579CC82@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-13 13:51:24 -0500 (Thu, 13 Jun 2013)
New Revision: 6547

Modified:
   trunk/docs/siteguide/ec2
   trunk/docs/siteguide/siteguide.txt
Log:
refinements

Modified: trunk/docs/siteguide/ec2
===================================================================
--- trunk/docs/siteguide/ec2	2013-06-13 17:07:15 UTC (rev 6546)
+++ trunk/docs/siteguide/ec2	2013-06-13 18:51:24 UTC (rev 6547)
@@ -7,39 +7,40 @@
 Getting Access
 ~~~~~~~~~~~~~~
 
-==Users with EC2 Allocation
+ ==Users with EC2 Allocation
 
 If you already have an EC2 allocation, you can use either the web console or command-line interface to manage resources.
 
 Before using EC2 for Swift you must create a security group in order to allow Swift communicate with EC2 instances via open ports. In order to create a security group, follow instructions link:http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.html#creating-security-group[here]. Preferably, open ports between 50000 and 51000.
 
 Paste your credentials from the EC2 web console into AWS_ACCESS_KEY and AWS_SECRET_KEY and export them in your .bashrc as follows:
+
 ----
 export AWS_ACCESS_KEY=<your access key>
 export AWS_SECRET_KEY=<your secret key>
 ----
 
-A public AMI for Swift user is available with id: ami-332e585a.
+Command-line tools are pre-installed on +swift.rcc.uchicago.edu+. In order to use them add the following lines to your .bashrc:
 
+----
+export EC2_HOME=/home/maheshwari/.ec2
+export PATH=$PATH:$EC2_HOME/bin
+----
+
+A public AMI on EC2 is available to create instance. The id of this AMI is: ami-332e585a.
+
 Create instances from the above AMI as follows:
 
 ----
 ec2run -k <keypair_name> -g <sec_group_name> -n <count> ami-332e585a
 ----
 
-==Users without EC2 Allocation
+ ==Users without EC2 Allocation
 
 Please request access to prepared instances and PKI credentials by mailing: email at mcs.anl.gov.
 
-Log in to the swift.rcc.uchicago.edu and copy the swift_cloud directory to your home:
 
-----
-cp -r ~maheshwari/swift_cloud $HOME/
-----
 
-Replace the hosts.txt by adding the address/DNS of instances.
-
-
 Configuring coaster-service.conf
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 To run on EC2, you will need a file called coaster-service.conf.
@@ -91,24 +92,32 @@
 
 Starting the Coaster Service Script
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-Now that everything is configured, change to the location of the coaster-service.conf file
-and run this command to start the coaster service:
+Now that everything is configured, run this command to start the coaster service:
 
 -----
-$ start-coaster-service
+source setup
 -----
 
-This command will start the VMs, start the required processes on the worker nodes,
-and generate Swift configuration files for you to use. The configuration files
-will be generated in your current directory. These files are sites.xml, tc.data,
-and cf.
+This command will add the instances to coaster configuration, start the
+required processes on the worker nodes, and generate Swift configuration files
+for you to use. The configuration files will be generated in your current
+directory. These files are sites.xml, tc.data, and cf.
 
 Running Swift
 ~~~~~~~~~~~~~
+
+Log in to the +swift.rcc.uchicago.edu+ and copy the swift_cloud directory to your home:
+
+----
+cp -r ~maheshwari/swift_cloud $HOME/
+----
+
+Replace the hosts.txt by adding the address/DNS of instances.
+
 Now that you have all of your configuration files generated, run the following command:
 
 -----
-$ swift -sites.file sites.xml -tc.file tc.data -config cf <yourscript.swift>
+$ swift -sites.file sites.xml -tc.file tc.data -config cf catsn.swift
 -----
 
 If you like to create a custom tc and/or cf file for repeated use, rename it to something other

Modified: trunk/docs/siteguide/siteguide.txt
===================================================================
--- trunk/docs/siteguide/siteguide.txt	2013-06-13 17:07:15 UTC (rev 6546)
+++ trunk/docs/siteguide/siteguide.txt	2013-06-13 18:51:24 UTC (rev 6547)
@@ -28,5 +28,7 @@
 
 include::stampede[]
 
+include::ec2[]
+
 link:http://www.ci.uchicago.edu/swift/docs/index.php[home]
 



From ketan at ci.uchicago.edu  Thu Jun 13 14:01:38 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 14:01:38 -0500 (CDT)
Subject: [Swift-commit] r6548 - trunk/docs/siteguide
Message-ID: <20130613190138.7EECB9CC82@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-13 14:01:38 -0500 (Thu, 13 Jun 2013)
New Revision: 6548

Modified:
   trunk/docs/siteguide/ec2
Log:
cleanup

Modified: trunk/docs/siteguide/ec2
===================================================================
--- trunk/docs/siteguide/ec2	2013-06-13 18:51:24 UTC (rev 6547)
+++ trunk/docs/siteguide/ec2	2013-06-13 19:01:38 UTC (rev 6548)
@@ -11,7 +11,11 @@
 
 If you already have an EC2 allocation, you can use either the web console or command-line interface to manage resources.
 
-Before using EC2 for Swift you must create a security group in order to allow Swift communicate with EC2 instances via open ports. In order to create a security group, follow instructions link:http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.html#creating-security-group[here]. Preferably, open ports between 50000 and 51000.
+Before using EC2 for Swift you must create a security group in order to allow
+Swift communicate with EC2 instances via open ports. In order to create a
+security group, follow instructions
+link:http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/using-network-security.html#creating-security-group[here].
+Preferably, open ports between 50000 and 51000.
 
 Paste your credentials from the EC2 web console into AWS_ACCESS_KEY and AWS_SECRET_KEY and export them in your .bashrc as follows:
 
@@ -66,9 +70,10 @@
 export WORKER_USERNAME=root
 
 # Worker host names for ssh
-# export WORKER_HOSTS="crush thwomp stomp crank grind churn trounce thrash vanquish"
+# export WORKER_HOSTS="crush thwomp" 
 
-# Directory to keep log files, relative to working directory when launching start-coaster-service
+# Directory to keep log files,
+#relative to working directory when launching start-coaster-service
 export LOG_DIR=logs
 export WORKER_LOG_DIR=/root
 
@@ -82,7 +87,7 @@
 # Below are various settings to give information about how to create sites.xml
 export WORK=/tmp/swift.work
 export JOBSPERNODE=4
-export JOBTHROTTLE=$( echo "scale=5; ($JOBS_PER_NODE * $( echo $WORKER_HOSTS | wc -w ))/100 - 0.00001"|bc )
+export JOBTHROTTLE=$( echo "scale=5; ($JOBS_PER_NODE * $( echo $WORKER_HOSTS|wc -w ))/100 - 0.00001"|bc )
 
 # Swift applications
 #app cat=/bin/cat



From ketan at ci.uchicago.edu  Thu Jun 13 17:29:27 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 17:29:27 -0500 (CDT)
Subject: [Swift-commit] r6549 - in trunk/docs: siteguide userguide
Message-ID: <20130613222927.EA58F9CC82@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-13 17:29:27 -0500 (Thu, 13 Jun 2013)
New Revision: 6549

Modified:
   trunk/docs/siteguide/ec2
   trunk/docs/userguide/coasters
Log:
structure of doc

Modified: trunk/docs/siteguide/ec2
===================================================================
--- trunk/docs/siteguide/ec2	2013-06-13 19:01:38 UTC (rev 6548)
+++ trunk/docs/siteguide/ec2	2013-06-13 22:29:27 UTC (rev 6549)
@@ -7,7 +7,8 @@
 Getting Access
 ~~~~~~~~~~~~~~
 
- ==Users with EC2 Allocation
+Users with EC2 Allocation
+^^^^^^^^^^^^^^^^^^^^^^^^^
 
 If you already have an EC2 allocation, you can use either the web console or command-line interface to manage resources.
 
@@ -31,7 +32,8 @@
 export PATH=$PATH:$EC2_HOME/bin
 ----
 
-A public AMI on EC2 is available to create instance. The id of this AMI is: ami-332e585a.
+A public AMI on EC2 is available to create instance. Everything needed to run
+Swift is preinstalled on this image. The id of this AMI is: ami-332e585a.
 
 Create instances from the above AMI as follows:
 
@@ -39,12 +41,12 @@
 ec2run -k <keypair_name> -g <sec_group_name> -n <count> ami-332e585a
 ----
 
- ==Users without EC2 Allocation
+Users without EC2 Allocation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Please request access to prepared instances and PKI credentials by mailing: email at mcs.anl.gov.
 
 
-
 Configuring coaster-service.conf
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 To run on EC2, you will need a file called coaster-service.conf.

Modified: trunk/docs/userguide/coasters
===================================================================
--- trunk/docs/userguide/coasters	2013-06-13 19:01:38 UTC (rev 6548)
+++ trunk/docs/userguide/coasters	2013-06-13 22:29:27 UTC (rev 6549)
@@ -91,16 +91,4 @@
 the coaster service
 |==================
 
-////
-Submitting to a specific job queue
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-In order to submit to a specific job scheduler queue, the +queue+ parameter of
-coasters sites file should be used. For example, submitting to the +normal+
-queue of a PBS scheduler, one would use the following sites line:
-
-----
-<profile namespace="globus" key="queue">normal</profile>
-----
-////
-



From swift at ci.uchicago.edu  Thu Jun 13 18:25:03 2013
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 18:25:03 -0500 (CDT)
Subject: [Swift-commit] cog r3672
Message-ID: <20130613232504.2D4758D00087@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3672 | hategan | 2013-06-13 18:20:18 -0500 (Thu, 13 Jun 2013) | 1 line

fixed heartbeat to 30s; the wrongly set 300s could cause channel timeouts
------------------------------------------------------------------------
Index: modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java
===================================================================
--- modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java	(revision 3671)
+++ modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java	(working copy)
@@ -371,7 +371,7 @@
     protected RemoteConfiguration.Entry getChannelConfiguration(String contact) {
         return new RemoteConfiguration.Entry(
                 contact.replaceAll("\\.", "\\."),
-                "KEEPALIVE, RECONNECT(8), HEARTBEAT(300)");
+                "KEEPALIVE, RECONNECT(8), HEARTBEAT(30)");
     }
 
     public static void main(String[] args) {


From ketan at ci.uchicago.edu  Thu Jun 13 23:07:57 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Thu, 13 Jun 2013 23:07:57 -0500 (CDT)
Subject: [Swift-commit] r6550 - trunk/docs/siteguide
Message-ID: <20130614040757.49FA09CCA7@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-13 23:07:57 -0500 (Thu, 13 Jun 2013)
New Revision: 6550

Modified:
   trunk/docs/siteguide/ec2
Log:
adding ec2 command to obtain instance ips

Modified: trunk/docs/siteguide/ec2
===================================================================
--- trunk/docs/siteguide/ec2	2013-06-13 22:29:27 UTC (rev 6549)
+++ trunk/docs/siteguide/ec2	2013-06-14 04:07:57 UTC (rev 6550)
@@ -99,6 +99,21 @@
 
 Starting the Coaster Service Script
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Log in to the +swift.rcc.uchicago.edu+ and copy the swift_cloud directory to your home:
+
+----
+cp -r ~maheshwari/swift_cloud $HOME/
+----
+
+Replace the hosts.txt found in +swift_cloud+ directory by adding the address/DNS of instances.
+
+With the ec2 commandline, the list of ip addresses of running instances can be obtained and added to hosts.txt as follows:
+
+----
+ec2din | grep running | awk '{print $15}' > hosts.txt
+----
+
 Now that everything is configured, run this command to start the coaster service:
 
 -----
@@ -113,14 +128,8 @@
 Running Swift
 ~~~~~~~~~~~~~
 
-Log in to the +swift.rcc.uchicago.edu+ and copy the swift_cloud directory to your home:
 
-----
-cp -r ~maheshwari/swift_cloud $HOME/
-----
 
-Replace the hosts.txt by adding the address/DNS of instances.
-
 Now that you have all of your configuration files generated, run the following command:
 
 -----



From wilde at ci.uchicago.edu  Fri Jun 14 08:52:12 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Fri, 14 Jun 2013 08:52:12 -0500 (CDT)
Subject: [Swift-commit] r6551 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130614135212.756EA9CC82@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-14 08:52:11 -0500 (Fri, 14 Jun 2013)
New Revision: 6551

Added:
   SwiftTutorials/OHBM_2013-06-16/apps.beagle-scp
   SwiftTutorials/OHBM_2013-06-16/auth.defaults.example
   SwiftTutorials/OHBM_2013-06-16/setup.sh
   SwiftTutorials/OHBM_2013-06-16/swift.properties.ps
Modified:
   SwiftTutorials/OHBM_2013-06-16/README
   SwiftTutorials/OHBM_2013-06-16/TODO
   SwiftTutorials/OHBM_2013-06-16/genatlas.swift
   SwiftTutorials/OHBM_2013-06-16/sites.xml
   SwiftTutorials/OHBM_2013-06-16/swift.properties
Log:
Demo updates; includes provider staging config for midway-to-beagle.

Modified: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	2013-06-14 04:07:57 UTC (rev 6550)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-14 13:52:11 UTC (rev 6551)
@@ -1,7 +1,7 @@
 
 fMRI Data Processing demo for OHBM 2013
 
-Setup
+* Setup
 
   # Get the scripts from svn
 
@@ -11,37 +11,59 @@
   # Set default swift.properties in $HOME/.swift.  Points to "." for apps (tc) and sites.xml
 
   mkdir -p ~/.swift
-  cp ~/.swift/swift.properties ~/.swift/save.swift.properties # If needed, as needed.
-  cp swift.properties ~/.swift
+  cp ~/.swift/swift.properties ~/.swift/swift.properties.save # Backup yours, if needed
 
+  cp swift.properties    ~/.swift   # for ssh staging      (see
+  cp swift.propertes.ps ~/.swift    # for provider staging  below)
+
+  # for scp staging, set your auth.defaults:
+
+  mv auth.defaults.example auth.defaults  # AND EDIT to set your login and ssh key
+  cp $HOME/.ssh/auth.defaults $HOME/.ssh/auth.defaults.save # Backup as needed
+  cp auth.defaults $HOME/.ssh/auth.defaults
+
   # Get swift
 
-  module load swift
+  module load swift  # or set PATH as below
 
-To generate test data directories:
+  # NOTE: CURRENT TESTING SHOULD USE THIS SWIFT: (with the latest provider-staging fixes)
 
-  ./makedata data_100 100 # create 100 anatomical image volumes in directory data_100
+  PATH=/project/wilde/swift/src/0.94/cog/modules/swift/dist/swift-svn/bin:$PATH
 
-To run:
+  # Run setup: sets env var(s) and ensures java is loaded    # <== DONT FORGET !!!
 
- # On localhost:
+  source setup.sh
 
- swift genatlas.swift             # processes data/ directory by default
- swift genatlas.swift -d=data_100 # process data_100/ directory
+* Generate test data directories (example):
 
- # With most parallel work on midway westmere parition:
+  ./makedata data_100 100   # creates 100 anatomical image volumes in directory data_100
 
- swift -tc.file apps.midway genatlas.swift
+The generated data consists of links to a single file, for ease of setup and demo.
 
- # Choices for -tc.file are:
 
- apps         # default, runs on localhost
- apps.beagle  # on beagle, 8 nodes
- apps.midway  # on midway westmere, 1 node
- apps.amazon  # on Amazon EC2 - needs start-coaster-service, see below
- apps.UC3     # submits to UC3, needs apps to be sent.
+* To run:
 
+  # On localhost:
 
+  swift genatlas.swift             # processes data/ directory by default
+  swift genatlas.swift -d=data_100 # process data_100/ directory
+
+  # With most parallel work on midway westmere parition:
+
+  swift -tc.file apps.midway genatlas.swift
+
+  # From midway to beagle using provider staging:
+
+   swift -config swift.properties.ps -tc.file apps.beagle genatlas.swift -d=data_100
+
+  # Choices for -tc.file are:
+
+  apps         # default, runs on localhost
+  apps.beagle  # on beagle, 8 nodes
+  apps.midway  # on midway westmere, 1 node
+  apps.amazon  # on Amazon EC2 - needs start-coaster-service, see below
+  apps.UC3     # submits to UC3, needs apps to be sent.
+
 The output files of the workflow are placed under output/,
 intermediate files under work/.
 
@@ -52,18 +74,10 @@
   http://www.ci.uchicago.edu/~wilde/atlas-y.png
   http://www.ci.uchicago.edu/~wilde/atlas-z.png
 
-Notes:
+* Notes:
 
   The "aligin" initial stage runs 3 AIR tools under as a single shell
   script, to reduce staging between these steps.
 
-TODO
 
-  Show the workflow with the 3 AIR tools expanded as separate workflow
-  steps, and as a Swift procedure.
 
-  Run on other sites and Multisite
-
-  Add performance monitoring and plotting
-
-

Modified: SwiftTutorials/OHBM_2013-06-16/TODO
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/TODO	2013-06-14 04:07:57 UTC (rev 6550)
+++ SwiftTutorials/OHBM_2013-06-16/TODO	2013-06-14 13:52:11 UTC (rev 6551)
@@ -2,4 +2,17 @@
 
 /scratch/midway/wilde/ds107/ds107/sub001/model/model001
 
+Show nested studies
 
+
+Show the workflow with the 3 AIR tools (align.sh) expanded as separate workflow
+steps, and as a Swift procedure.
+
+Run on other sites and Multisite
+
+Add performance monitoring and plotting
+
+
+---
+
+

Added: SwiftTutorials/OHBM_2013-06-16/apps.beagle-scp
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps.beagle-scp	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/apps.beagle-scp	2013-06-14 13:52:11 UTC (rev 6551)
@@ -0,0 +1,4 @@
+beagle-scp sh       /bin/sh null null env::AIR5=/lustre/beagle/wilde/software/AIR5.3.0
+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/auth.defaults.example
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/auth.defaults.example	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/auth.defaults.example	2013-06-14 13:52:11 UTC (rev 6551)
@@ -0,0 +1,4 @@
+login.beagle.ci.uchicago.edu.type=key
+login.beagle.ci.uchicago.edu.username=wilde
+login.beagle.ci.uchicago.edu.key=/home/wilde/.ssh/id_rsa-swift
+login.beagle.ci.uchicago.edu.PROMPT_FOR_passphrase=this is the key

Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-14 04:07:57 UTC (rev 6550)
+++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-14 13:52:11 UTC (rev 6551)
@@ -1,10 +1,14 @@
 type file;
 
+# import fMRIdefs
+
 type Volume {
   file header;
   file image;
 };
 
+# import AIRdefs
+
 app (Volume alignedVol) align (file script, Volume reference, Volume input)
 {
   sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
@@ -25,6 +29,8 @@
   convert @i @o;
 }
 
+# Start code here
+
 string dataDir = @arg("d","data");
 file   alignScript<"align.sh">;
 

Added: SwiftTutorials/OHBM_2013-06-16/setup.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/setup.sh	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/setup.sh	2013-06-14 13:52:11 UTC (rev 6551)
@@ -0,0 +1,7 @@
+export GLOBUS_HOSTNAME=swift.rcc.uchicago.edu
+module load java
+
+if [ $(hostname) != midway001 ]; then
+  echo ERROR: this neesd to run from swift.rcc.uchicago.edu
+  return
+fi

Modified: SwiftTutorials/OHBM_2013-06-16/sites.xml
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/sites.xml	2013-06-14 04:07:57 UTC (rev 6550)
+++ SwiftTutorials/OHBM_2013-06-16/sites.xml	2013-06-14 13:52:11 UTC (rev 6551)
@@ -45,13 +45,13 @@
     <profile namespace="globus" key="lowOverAllocation">100</profile>
     <profile namespace="globus" key="highOverAllocation">100</profile>
     <profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile>
-    <!-- to use a beage reservation, eg:
-         <profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24;pbs.resource_list=advres=wilde.1768</profile>
+    <!-- to use a beage reservation, modify above tag, eg:
+    <... key="providerAttributes">pbs.aprun;pbs.mpp;depth=24;pbs.resource_list=advres=wilde.1768</profile>
     -->
     <profile namespace="globus" key="maxtime">3600</profile>
     <profile namespace="globus" key="maxWalltime">00:05:00</profile>
     <profile namespace="globus" key="userHomeOverride">/lustre/beagle/{env.USER}/swiftwork</profile>
-    <profile namespace="globus" key="slots">20</profile>
+    <profile namespace="globus" key="slots">8</profile>
     <profile namespace="globus" key="maxnodes">1</profile>
     <profile namespace="globus" key="nodeGranularity">1</profile>
     <profile namespace="karajan" key="jobThrottle">4.80</profile>
@@ -59,4 +59,36 @@
     <workdirectory>/tmp/{env.USER}/swiftwork</workdirectory>
   </pool>
 
+  <pool handle="beagle-scp">
+    <execution provider="coaster" jobmanager="ssh-cl:pbs" url="login.beagle.ci.uchicago.edu"/>
+    <profile namespace="globus" key="jobsPerNode">24</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="providerAttributes">pbs.aprun;pbs.mpp;depth=24</profile>
+    <!-- to use a beage reservation, modify above tag, eg:
+    <... key="providerAttributes">pbs.aprun;pbs.mpp;depth=24;pbs.resource_list=advres=wilde.1768</profile>
+    -->
+    <profile namespace="globus" key="maxtime">3600</profile>
+    <profile namespace="globus" key="maxWalltime">00:05:00</profile>
+    <profile namespace="globus" key="userHomeOverride">/lustre/beagle/{env.USER}/swiftwork</profile>
+    <profile namespace="globus" key="slots">4</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="nodeGranularity">1</profile>
+    <profile namespace="karajan" key="jobThrottle">1.00</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+
+    <filesystem provider="ssh" url="login.beagle.ci.uchicago.edu"/>
+    <workdirectory>/lustre/beagle/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="beagle-coast-temp">
+    <execution provider="coaster" jobmanager="ssh:local" url="login.beagle.ci.uchicago.edu"/>
+    <profile namespace="karajan" key="jobThrottle">0</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+
+    <filesystem provider="ssh" url="login.beagle.ci.uchicago.edu"/>
+    <workdirectory>/lustre/beagle/wilde/swiftwork</workdirectory>
+  </pool>
+
+
 </config>

Modified: SwiftTutorials/OHBM_2013-06-16/swift.properties
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/swift.properties	2013-06-14 04:07:57 UTC (rev 6550)
+++ SwiftTutorials/OHBM_2013-06-16/swift.properties	2013-06-14 13:52:11 UTC (rev 6551)
@@ -2,13 +2,94 @@
 sites.file=sites.xml
 tc.file=apps
 
+use.provider.staging=false
+provider.staging.pin.swiftfiles=true
+
+use.wrapper.staging=false
 status.mode=provider
-use.provider.staging=true
-use.wrapper.staging=false
 wrapperlog.always.transfer=true
-execution.retries=0
-lazy.errors=false
-provider.staging.pin.swiftfiles=true
+execution.retries=3
+lazy.errors=true
 sitedir.keep=true
 file.gc.enabled=false
 #tcp.port.range=50000,51000
+
+###########################################################################
+#                          Throttling options                             #
+###########################################################################
+#
+# For the throttling parameters, valid values are either a positive integer
+# or "off" (without the quotes).
+#
+
+#
+# Limits the number of concurrent submissions for a workflow instance. This
+# throttle only limits the number of concurrent tasks (jobs) that are being
+# sent to sites, not the total number of concurrent jobs that can be run.
+# The submission stage in GRAM is one of the most CPU expensive stages (due
+# mostly to the mutual authentication and delegation). Having too many
+# concurrent submissions can overload either or both the submit host CPU
+# and the remote host/head node causing degraded performance.
+#
+# Default: 4
+#
+
+throttle.submit=4
+#throttle.submit=off
+
+#
+# Limits the number of concurrent submissions for any of the sites Swift will
+# try to send jobs to. In other words it guarantees that no more than the
+# value of this throttle jobs sent to any site will be concurrently in a state
+# of being submitted.
+#
+# Default: 2
+#
+
+### throttle.host.submit=2
+#throttle.host.submit=off
+
+#
+# The Swift scheduler has the ability to limit the number of concurrent jobs
+# allowed on a site based on the performance history of that site. Each site
+# is assigned a score (initially 1), which can increase or decrease based
+# on whether the site yields successful or faulty job runs. The score for a
+# site can take values in the (0.1, 100) interval. The number of allowed jobs
+# is calculated using the following formula:
+# 	2 + score*throttle.score.job.factor
+# This means a site will always be allowed at least two concurrent jobs and
+# at most 2 + 100*throttle.score.job.factor. With a default of 4 this means
+# at least 2 jobs and at most 402.
+#
+# Default: 4
+#
+
+### throttle.score.job.factor=0.2
+#throttle.score.job.factor=off
+
+
+#
+# Limits the total number of concurrent file transfers that can happen at any
+# given time. File transfers consume bandwidth. Too many concurrent transfers
+# can cause the network to be overloaded preventing various other signalling
+# traffic from flowing properly.
+#
+# Default: 4
+#
+
+throttle.transfers=1
+#throttle.transfers=off
+
+# Limits the total number of concurrent file operations that can happen at any
+# given time. File operations (like transfers) require an exclusive connection
+# to a site. These connections can be expensive to establish. A large number
+# of concurrent file operations may cause Swift to attempt to establish many
+# such expensive connections to various sites. Limiting the number of concurrent
+# file operations causes Swift to use a small number of cached connections and
+# achieve better overall performance.
+#
+# Default: 8
+#
+
+throttle.file.operations=1
+#throttle.file.operations=off

Added: SwiftTutorials/OHBM_2013-06-16/swift.properties.ps
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/swift.properties.ps	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/swift.properties.ps	2013-06-14 13:52:11 UTC (rev 6551)
@@ -0,0 +1,95 @@
+
+sites.file=sites.xml
+tc.file=apps
+
+use.provider.staging=true
+provider.staging.pin.swiftfiles=true
+
+use.wrapper.staging=false
+status.mode=provider
+wrapperlog.always.transfer=true
+execution.retries=3
+lazy.errors=true
+sitedir.keep=true
+file.gc.enabled=false
+#tcp.port.range=50000,51000
+
+###########################################################################
+#                          Throttling options                             #
+###########################################################################
+#
+# For the throttling parameters, valid values are either a positive integer
+# or "off" (without the quotes).
+#
+
+#
+# Limits the number of concurrent submissions for a workflow instance. This
+# throttle only limits the number of concurrent tasks (jobs) that are being
+# sent to sites, not the total number of concurrent jobs that can be run.
+# The submission stage in GRAM is one of the most CPU expensive stages (due
+# mostly to the mutual authentication and delegation). Having too many
+# concurrent submissions can overload either or both the submit host CPU
+# and the remote host/head node causing degraded performance.
+#
+# Default: 4
+#
+
+throttle.submit=4
+#throttle.submit=off
+
+#
+# Limits the number of concurrent submissions for any of the sites Swift will
+# try to send jobs to. In other words it guarantees that no more than the
+# value of this throttle jobs sent to any site will be concurrently in a state
+# of being submitted.
+#
+# Default: 2
+#
+
+### throttle.host.submit=2
+#throttle.host.submit=off
+
+#
+# The Swift scheduler has the ability to limit the number of concurrent jobs
+# allowed on a site based on the performance history of that site. Each site
+# is assigned a score (initially 1), which can increase or decrease based
+# on whether the site yields successful or faulty job runs. The score for a
+# site can take values in the (0.1, 100) interval. The number of allowed jobs
+# is calculated using the following formula:
+# 	2 + score*throttle.score.job.factor
+# This means a site will always be allowed at least two concurrent jobs and
+# at most 2 + 100*throttle.score.job.factor. With a default of 4 this means
+# at least 2 jobs and at most 402.
+#
+# Default: 4
+#
+
+### throttle.score.job.factor=0.2
+#throttle.score.job.factor=off
+
+
+#
+# Limits the total number of concurrent file transfers that can happen at any
+# given time. File transfers consume bandwidth. Too many concurrent transfers
+# can cause the network to be overloaded preventing various other signalling
+# traffic from flowing properly.
+#
+# Default: 4
+#
+
+throttle.transfers=1
+#throttle.transfers=off
+
+# Limits the total number of concurrent file operations that can happen at any
+# given time. File operations (like transfers) require an exclusive connection
+# to a site. These connections can be expensive to establish. A large number
+# of concurrent file operations may cause Swift to attempt to establish many
+# such expensive connections to various sites. Limiting the number of concurrent
+# file operations causes Swift to use a small number of cached connections and
+# achieve better overall performance.
+#
+# Default: 8
+#
+
+throttle.file.operations=1
+#throttle.file.operations=off



From ketan at ci.uchicago.edu  Fri Jun 14 12:13:55 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Fri, 14 Jun 2013 12:13:55 -0500 (CDT)
Subject: [Swift-commit] r6552 - trunk/docs/siteguide
Message-ID: <20130614171355.585A49CC82@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-14 12:13:55 -0500 (Fri, 14 Jun 2013)
New Revision: 6552

Modified:
   trunk/docs/siteguide/ec2
Log:
updates based on Justin feedback

Modified: trunk/docs/siteguide/ec2
===================================================================
--- trunk/docs/siteguide/ec2	2013-06-14 13:52:11 UTC (rev 6551)
+++ trunk/docs/siteguide/ec2	2013-06-14 17:13:55 UTC (rev 6552)
@@ -106,6 +106,16 @@
 cp -r ~maheshwari/swift_cloud $HOME/
 ----
 
+Make sure Swift module is loaded and your credentials are added as follows:
+
+----
+module load swift
+----
+
+----
+ssh-add
+----
+
 Replace the hosts.txt found in +swift_cloud+ directory by adding the address/DNS of instances.
 
 With the ec2 commandline, the list of ip addresses of running instances can be obtained and added to hosts.txt as follows:



From wilde at ci.uchicago.edu  Fri Jun 14 16:19:58 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Fri, 14 Jun 2013 16:19:58 -0500 (CDT)
Subject: [Swift-commit] r6553 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130614211958.1CA4F9CC82@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-14 16:19:57 -0500 (Fri, 14 Jun 2013)
New Revision: 6553

Modified:
   SwiftTutorials/OHBM_2013-06-16/README
   SwiftTutorials/OHBM_2013-06-16/apps
   SwiftTutorials/OHBM_2013-06-16/apps.beagle
   SwiftTutorials/OHBM_2013-06-16/apps.midway
   SwiftTutorials/OHBM_2013-06-16/genatlas.swift
   SwiftTutorials/OHBM_2013-06-16/sites.xml
   SwiftTutorials/OHBM_2013-06-16/swift.properties
Log:
updates for swift version of align() function. Older function is now align_sh().

Modified: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	2013-06-14 17:13:55 UTC (rev 6552)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-14 21:19:57 UTC (rev 6553)
@@ -48,13 +48,13 @@
   swift genatlas.swift             # processes data/ directory by default
   swift genatlas.swift -d=data_100 # process data_100/ directory
 
-  # With most parallel work on midway westmere parition:
+  # With most parallel work on a midway parition (edit sites.xml to set partition)
 
   swift -tc.file apps.midway genatlas.swift
 
   # From midway to beagle using provider staging:
 
-   swift -config swift.properties.ps -tc.file apps.beagle genatlas.swift -d=data_100
+  swift -config swift.properties.ps -tc.file apps.beagle genatlas.swift -d=data_100
 
   # Choices for -tc.file are:
 
@@ -62,7 +62,7 @@
   apps.beagle  # on beagle, 8 nodes
   apps.midway  # on midway westmere, 1 node
   apps.amazon  # on Amazon EC2 - needs start-coaster-service, see below
-  apps.UC3     # submits to UC3, needs apps to be sent.
+  apps.beagle+midway # both of these
 
 The output files of the workflow are placed under output/,
 intermediate files under work/.
@@ -79,5 +79,5 @@
   The "aligin" initial stage runs 3 AIR tools under as a single shell
   script, to reduce staging between these steps.
 
+  A swift version of this function is included as well
 
-

Modified: SwiftTutorials/OHBM_2013-06-16/apps
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps	2013-06-14 17:13:55 UTC (rev 6552)
+++ SwiftTutorials/OHBM_2013-06-16/apps	2013-06-14 21:19:57 UTC (rev 6553)
@@ -1,5 +1,9 @@
-localhost sh       /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0
-#localhost sh       /bin/sh
-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
+midway sh          /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0
+#localhost sh         /bin/sh
+
+localhost softmean    /home/wilde/software/AIR5.3.0/bin/softmean
+localhost alignlinear /home/wilde/software/AIR5.3.0/bin/alignlinear
+localhost align_warp  /home/wilde/software/AIR5.3.0/bin/align_warp
+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

Modified: SwiftTutorials/OHBM_2013-06-16/apps.beagle
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps.beagle	2013-06-14 17:13:55 UTC (rev 6552)
+++ SwiftTutorials/OHBM_2013-06-16/apps.beagle	2013-06-14 21:19:57 UTC (rev 6553)
@@ -1,4 +1,8 @@
-beagle    sh       /bin/sh null null env::AIR5=/lustre/beagle/wilde/software/AIR5.3.0
-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
+beagle    sh          /bin/sh null null env::AIR5=/lustre/beagle/wilde/software/AIR5.3.0
+beagle    alignlinear /lustre/beagle/wilde/software/AIR5.3.0/bin/alignlinear
+beagle    align_warp  /lustre/beagle/wilde/software/AIR5.3.0/bin/align_warp
+beagle    reslice     /lustre/beagle/wilde/software/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

Modified: SwiftTutorials/OHBM_2013-06-16/apps.midway
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps.midway	2013-06-14 17:13:55 UTC (rev 6552)
+++ SwiftTutorials/OHBM_2013-06-16/apps.midway	2013-06-14 21:19:57 UTC (rev 6553)
@@ -1,4 +1,11 @@
-westmere  sh       /bin/sh
-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
+midway    sh          /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0
+midway    alignlinear /home/wilde/software/AIR5.3.0/bin/alignlinear
+midway    align_warp  /home/wilde/software/AIR5.3.0/bin/align_warp
+midway    reslice     /home/wilde/software/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
+
+
+

Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-14 17:13:55 UTC (rev 6552)
+++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-14 21:19:57 UTC (rev 6553)
@@ -7,13 +7,10 @@
   file image;
 };
 
-# import AIRdefs
 
-app (Volume alignedVol) align (file script, Volume reference, Volume input)
-{
-  sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
-}
 
+# import AIR
+
 app (Volume atlas) softmean (Volume v[])
 {
   softmean @filename(atlas.header) "y" "null" @filenames(v);
@@ -29,10 +26,53 @@
   convert @i @o;
 }
 
+app (file warp) alignlinear (Volume ref, Volume subject, string params[])
+{
+  alignlinear @filename(ref.header) @filename(subject.header) @filename(warp) params;
+}
+
+app (file warp) alignwarp (Volume ref, Volume subject, file initWarp, string params[])
+{
+  align_warp @filename(ref.header) @filename(subject.header) @filename(warp) "-f" @filename(initWarp) params;
+}
+
+app (Volume v) reslice (file warp, Volume subject)
+{
+  reslice @filename(warp) @filename(v.header) "-a" @filename(subject.header);
+}
+
+
+
+# start of genatlas workflow
+
+file   alignScript<"align.sh">;
+  /* This script does:
+  time $AIR5/bin/alignlinear $ref $anat init.warp \
+    -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 
+  time $AIR5/bin/align_warp  $ref $anat refined.warp \
+    -m 1 12 -b1 .1 .1 .1  -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01
+  time $AIR5/bin/reslice refined.warp $resliced -a $anat
+  */
+
+app (Volume alignedVol) align_sh (file script, Volume reference, Volume input)
+{
+  sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
+}
+
+(Volume alignedVol) native_align (Volume ref, Volume subject)
+{
+  file firstwarp = alignlinear(ref, subject,
+                     ["-m","15","-t1","55","-t2","55","-x","1","-r","8","-c","0.1","-h","8"]);
+  file refinedWarp = alignwarp(ref, subject, firstwarp,
+                      ["-m","1","12","-b1",".1",".1",".1","-b2",".1",".1",".1",
+                       "-h","10000","-s","1024","2","2","-c",".01"]);
+  alignedVol = reslice(refinedWarp,subject);
+}
+
+
 # Start code here
 
 string dataDir = @arg("d","data");
-file   alignScript<"align.sh">;
 
 Volume referenceVolume<ext; exec="volmapper",name="data/reference">;
 Volume inputVolumes []<ext; exec="volmapper",prefix=@strcat(dataDir,"/anatomy")>;
@@ -40,7 +80,8 @@
 
 foreach v, i in inputVolumes {
   Volume aligned<ext; exec="volmapper",name=@strcat("work/aligned",i)>;
-  aligned = align(alignScript,referenceVolume, v);
+  // aligned = align(alignScript,referenceVolume, v);
+  aligned = native_align(referenceVolume, v);
   outputVolumes[i] = aligned;
 }
 
@@ -56,6 +97,12 @@
 zSlice = convert(slicer(atlasVolume,"z"));
 
 
+
+
+
+
+
+
 /******* The following code to be removed
 
 string testNames[] = imageNames(outputVolumes);

Modified: SwiftTutorials/OHBM_2013-06-16/sites.xml
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/sites.xml	2013-06-14 17:13:55 UTC (rev 6552)
+++ SwiftTutorials/OHBM_2013-06-16/sites.xml	2013-06-14 21:19:57 UTC (rev 6553)
@@ -9,11 +9,11 @@
     <profile namespace="karajan" key="jobThrottle">.03</profile> <!-- eg .11 -> 12 -->
   </pool>
 
-  <pool handle="westmere">
+  <pool handle="midway">
     <execution provider="coaster" jobmanager="local:slurm"/>
 
     <!-- Set partition and account here: -->
-    <profile namespace="globus" key="queue">westmere</profile>
+    <profile namespace="globus" key="queue">bigmem</profile>
     <profile namespace="globus" key="ppn">12</profile>
     <!-- <profile namespace="globus" key="project">pi-wilde</profile> -->
 

Modified: SwiftTutorials/OHBM_2013-06-16/swift.properties
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/swift.properties	2013-06-14 17:13:55 UTC (rev 6552)
+++ SwiftTutorials/OHBM_2013-06-16/swift.properties	2013-06-14 21:19:57 UTC (rev 6553)
@@ -3,7 +3,7 @@
 tc.file=apps
 
 use.provider.staging=false
-provider.staging.pin.swiftfiles=true
+provider.staging.pin.swiftfiles=false
 
 use.wrapper.staging=false
 status.mode=provider



From wilde at ci.uchicago.edu  Fri Jun 14 16:27:01 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Fri, 14 Jun 2013 16:27:01 -0500 (CDT)
Subject: [Swift-commit] r6554 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130614212701.B064A9CC82@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-14 16:27:01 -0500 (Fri, 14 Jun 2013)
New Revision: 6554

Modified:
   SwiftTutorials/OHBM_2013-06-16/genatlas.swift
Log:
Adjust names for align()

Modified: SwiftTutorials/OHBM_2013-06-16/genatlas.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-14 21:19:57 UTC (rev 6553)
+++ SwiftTutorials/OHBM_2013-06-16/genatlas.swift	2013-06-14 21:27:01 UTC (rev 6554)
@@ -45,13 +45,12 @@
 
 # start of genatlas workflow
 
-file   alignScript<"align.sh">;
-  /* This script does:
-  time $AIR5/bin/alignlinear $ref $anat init.warp \
+file   alignScript<"align.sh">;  /* This script does:
+   alignlinear $ref $anat init.warp \
     -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 
-  time $AIR5/bin/align_warp  $ref $anat refined.warp \
-    -m 1 12 -b1 .1 .1 .1  -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01
-  time $AIR5/bin/reslice refined.warp $resliced -a $anat
+  align_warp  $ref $anat refined.warp \
+    -m 1 12 -b1 .1 .1 .1  -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01
+  reslice refined.warp $resliced -a $anat
   */
 
 app (Volume alignedVol) align_sh (file script, Volume reference, Volume input)
@@ -59,7 +58,7 @@
   sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
 }
 
-(Volume alignedVol) native_align (Volume ref, Volume subject)
+(Volume alignedVol) align (Volume ref, Volume subject)
 {
   file firstwarp = alignlinear(ref, subject,
                      ["-m","15","-t1","55","-t2","55","-x","1","-r","8","-c","0.1","-h","8"]);
@@ -80,8 +79,8 @@
 
 foreach v, i in inputVolumes {
   Volume aligned<ext; exec="volmapper",name=@strcat("work/aligned",i)>;
-  // aligned = align(alignScript,referenceVolume, v);
-  aligned = native_align(referenceVolume, v);
+  // aligned = align_sh(alignScript,referenceVolume, v);
+  aligned = align(referenceVolume, v);
   outputVolumes[i] = aligned;
 }
 
@@ -100,9 +99,6 @@
 
 
 
-
-
-
 /******* The following code to be removed
 
 string testNames[] = imageNames(outputVolumes);



From wilde at ci.uchicago.edu  Fri Jun 14 19:01:57 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Fri, 14 Jun 2013 19:01:57 -0500 (CDT)
Subject: [Swift-commit] r6555 - in SwiftTutorials/OHBM_2013-06-16: . lib
	original
Message-ID: <20130615000157.30FED9CC82@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-14 19:01:57 -0500 (Fri, 14 Jun 2013)
New Revision: 6555

Added:
   SwiftTutorials/OHBM_2013-06-16/atlas00.swift
   SwiftTutorials/OHBM_2013-06-16/atlas01.swift
   SwiftTutorials/OHBM_2013-06-16/atlas02.swift
   SwiftTutorials/OHBM_2013-06-16/atlas03.swift
   SwiftTutorials/OHBM_2013-06-16/lib/
   SwiftTutorials/OHBM_2013-06-16/lib/AIR.swift
   SwiftTutorials/OHBM_2013-06-16/lib/FSL.swift
   SwiftTutorials/OHBM_2013-06-16/lib/ImageMagick.swift
   SwiftTutorials/OHBM_2013-06-16/lib/fMRI.swift
   SwiftTutorials/OHBM_2013-06-16/lib/types.swift
   SwiftTutorials/OHBM_2013-06-16/original/workflow.sh
   SwiftTutorials/OHBM_2013-06-16/original/workflow1.sh
Removed:
   SwiftTutorials/OHBM_2013-06-16/original/workflow.sh
Modified:
   SwiftTutorials/OHBM_2013-06-16/README
   SwiftTutorials/OHBM_2013-06-16/align.sh
   SwiftTutorials/OHBM_2013-06-16/apps
Log:
Checkpoint edits for all 4 demo phases building up to full script: atlas0{0,1,2,3}.swift

Modified: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	2013-06-14 21:27:01 UTC (rev 6554)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-15 00:01:57 UTC (rev 6555)
@@ -48,6 +48,10 @@
   swift genatlas.swift             # processes data/ directory by default
   swift genatlas.swift -d=data_100 # process data_100/ directory
 
+  # While above are running, do this in another window to view its activity:
+
+    watch ps -u $USER -H
+
   # With most parallel work on a midway parition (edit sites.xml to set partition)
 
   swift -tc.file apps.midway genatlas.swift

Modified: SwiftTutorials/OHBM_2013-06-16/align.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/align.sh	2013-06-14 21:27:01 UTC (rev 6554)
+++ SwiftTutorials/OHBM_2013-06-16/align.sh	2013-06-15 00:01:57 UTC (rev 6555)
@@ -1,53 +1,11 @@
 #!/bin/sh
 
-#AIR5=/home/wilde/software/AIR5.3.0
+ref=$1      # Input:  reference volume
+anat=$2     # Input:  subject volume
+resliced=$3 # Ouput:  rrealigned and resliced volume
 
-# Arguments: referenceImage (in) anatomicalImage (in) reslicedImage (out)
-
-ref=$1
-anat=$2
-resliced=$3
-
 time $AIR5/bin/alignlinear $ref $anat init.warp \
   -m 15 -t1 55 -t2 55 -x 1 -r 8 -c 0.1 -h 8 
 time $AIR5/bin/align_warp  $ref $anat refined.warp \
-  -m 1 12 -b1 .1 .1 .1  -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01 # -v -q -s 1024 2 2 -c .01
+  -m 1 12 -b1 .1 .1 .1  -b2 .1 .1 .1 -f init.warp -h 10000 -s 1024 2 2 -c .01
 time $AIR5/bin/reslice refined.warp $resliced -a $anat
-
-exit
-
-
-
-
-
-
-
-fsl=/project/wilde/software/fsl-5.0.4/fsl
-
-clean=y
-
-if [ $clean = y ]; then
-  rm *warp atlas* resliced*
-fi
-
-
-
-if true; then
-
-  warp 1
-  warp 2
-  warp 3
-  warp 4
-
-  time  $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img
-fi
-
-export FSLOUTPUTTYPE=NIFTI
-
-time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm
-time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm
-time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm
-
-time convert atlas-x.pgm atlas-x.gif
-time convert atlas-y.pgm atlas-y.gif
-time convert atlas-z.pgm atlas-z.gif

Modified: SwiftTutorials/OHBM_2013-06-16/apps
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/apps	2013-06-14 21:27:01 UTC (rev 6554)
+++ SwiftTutorials/OHBM_2013-06-16/apps	2013-06-15 00:01:57 UTC (rev 6555)
@@ -1,9 +1,9 @@
 midway sh          /bin/sh null null env::AIR5=/home/wilde/software/AIR5.3.0
 #localhost sh         /bin/sh
 
-localhost softmean    /home/wilde/software/AIR5.3.0/bin/softmean
 localhost alignlinear /home/wilde/software/AIR5.3.0/bin/alignlinear
 localhost align_warp  /home/wilde/software/AIR5.3.0/bin/align_warp
+localhost reslice     /home/wilde/software/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/atlas00.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/atlas00.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/atlas00.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,17 @@
+
+import "lib/types";
+
+app (file warp) alignlinear (file rh, file ri, file sh, file si)
+{
+  alignlinear @rh @sh @warp "-m" "12" "-q";
+}
+
+file refhdr <"data/reference.hdr">;  // Reference volume
+file refimg <"data/reference.img">;
+
+file subhdr <"data/anatomy4.hdr">;   // One subject volume
+file subimg <"data/anatomy4.img">;
+
+file output <"warp.out">;            // Output alignment
+
+output = alignlinear(refhdr,refimg,subhdr,subimg);

Added: SwiftTutorials/OHBM_2013-06-16/atlas01.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/atlas01.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/atlas01.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,24 @@
+
+import "lib/types";
+
+type Volume {
+  file header;
+  file image;
+};
+
+app (file warp) alignlinear (Volume ref, Volume subject, string params[])
+{
+  alignlinear @filename(ref.header) @filename(subject.header) @filename(warp) params;
+}
+
+string dataDir = @arg("d","data");  // Get a command-line argument, -d
+
+file alignment;
+
+Volume refVolume  <ext; exec="volmapper",name="data/reference">;
+Volume subjects[] <ext; exec="volmapper",prefix=@strcat(dataDir,"/anatomy")>;
+file   warps[]    <simple_mapper; location="warps",prefix="warp">;
+
+foreach subjectVolume, i in subjects {
+  warps[i] = alignlinear(refVolume, subjectVolume, ["-m","12","-q"]);
+}

Added: SwiftTutorials/OHBM_2013-06-16/atlas02.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/atlas02.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/atlas02.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,49 @@
+
+import "lib/types";
+import "lib/fMRI";
+import "lib/AIR";
+import "lib/FSL";
+import "lib/ImageMagick";
+
+# Full version of align() function
+
+(Volume alignedVol) align (Volume ref, Volume subject)
+{
+  file firstwarp = alignlinear(ref, subject,
+                     ["-m","15","-t1","55","-t2","55","-x","1","-r","8","-c","0.1","-h","8"]);
+  file refinedWarp = alignwarp(ref, subject, firstwarp,
+                      ["-m","1","12","-b1",".1",".1",".1","-b2",".1",".1",".1",
+                       "-h","10000","-s","1024","2","2","-c",".01"]);
+  alignedVol = reslice(refinedWarp,subject);
+}
+
+string dataDir = @arg("d","data");
+
+Volume referenceVolume <ext; exec="volmapper",name="data/reference">;
+Volume inputVolumes [] <ext; exec="volmapper",prefix=@strcat(dataDir,"/anatomy")>;
+Volume outputVolumes[];
+
+# Align all subjects
+
+foreach v, i in inputVolumes {
+  Volume aligned <ext; exec="volmapper",name=@strcat("work/aligned",i)>;
+  aligned = align(referenceVolume, v);
+  outputVolumes[i] = aligned;
+}
+
+# Create the "averaged" atlas
+
+Volume atlasVolume <ext; exec="volmapper",name="output/atlas">;
+atlasVolume = softmean(outputVolumes);
+
+# Extract x, y, z slices for inspection
+
+file xSlice<"output/atlas-x.png">;
+file ySlice<"output/atlas-y.png">;
+file zSlice<"output/atlas-z.png">;
+
+# Convert x, y, z planes to viewable files
+
+xSlice = convert(slicer(atlasVolume,"x"));
+ySlice = convert(slicer(atlasVolume,"y"));
+zSlice = convert(slicer(atlasVolume,"z"));

Added: SwiftTutorials/OHBM_2013-06-16/atlas03.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/atlas03.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/atlas03.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,38 @@
+
+import "lib/types";
+import "lib/fMRI";
+import "lib/AIR";
+import "lib/FSL";
+import "lib/ImageMagick";
+
+# Perform align() function in an external shell script
+
+file   alignScript<"align.sh">;
+
+app (Volume alignedVol) align_sh (file script, Volume reference, Volume input)
+{
+  sh @script @filename(reference.image) @filename(input.image) @filename(alignedVol.image);
+}
+
+string dataDir = @arg("d","data");
+
+Volume referenceVolume <ext; exec="volmapper",name="data/reference">;
+Volume inputVolumes [] <ext; exec="volmapper",prefix=@strcat(dataDir,"/anatomy")>;
+Volume outputVolumes[];
+
+foreach v, i in inputVolumes {
+  Volume aligned <ext; exec="volmapper",name=@strcat("work/aligned",i)>;
+  aligned = align_sh(alignScript,referenceVolume, v);
+  outputVolumes[i] = aligned;
+}
+
+Volume atlasVolume <ext; exec="volmapper",name="output/atlas">;
+atlasVolume = softmean(outputVolumes);
+
+file xSlice<"output/atlas-x.png">;
+file ySlice<"output/atlas-y.png">;
+file zSlice<"output/atlas-z.png">;
+
+xSlice = convert(slicer(atlasVolume,"x"));
+ySlice = convert(slicer(atlasVolume,"y"));
+zSlice = convert(slicer(atlasVolume,"z"));

Added: SwiftTutorials/OHBM_2013-06-16/lib/AIR.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/lib/AIR.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/lib/AIR.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,20 @@
+
+app (Volume atlas) softmean (Volume v[])
+{
+  softmean @filename(atlas.header) "y" "null" @filenames(v);
+}
+
+app (file warp) alignlinear (Volume ref, Volume subject, string params[])
+{
+  alignlinear @filename(ref.header) @filename(subject.header) @filename(warp) params;
+}
+
+app (file warp) alignwarp (Volume ref, Volume subject, file initWarp, string params[])
+{
+  align_warp @filename(ref.header) @filename(subject.header) @filename(warp) "-f" @filename(initWarp) params;
+}
+
+app (Volume v) reslice (file warp, Volume subject)
+{
+  reslice @filename(warp) @filename(v.header) "-a" @filename(subject.header);
+}

Added: SwiftTutorials/OHBM_2013-06-16/lib/FSL.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/lib/FSL.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/lib/FSL.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,5 @@
+
+app (file pgm) slicer (Volume v, string axis)
+{
+  slicer @filename(v.header) @strcat("-",axis) .5 @filename(pgm);
+}

Added: SwiftTutorials/OHBM_2013-06-16/lib/ImageMagick.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/lib/ImageMagick.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/lib/ImageMagick.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,6 @@
+
+app (file o) convert (file i)
+{
+  convert @i @o;
+}
+

Added: SwiftTutorials/OHBM_2013-06-16/lib/fMRI.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/lib/fMRI.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/lib/fMRI.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,5 @@
+
+type Volume {
+  file header;
+  file image;
+};

Added: SwiftTutorials/OHBM_2013-06-16/lib/types.swift
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/lib/types.swift	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/lib/types.swift	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,2 @@
+
+type file;

Deleted: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/original/workflow.sh	2013-06-14 21:27:01 UTC (rev 6554)
+++ SwiftTutorials/OHBM_2013-06-16/original/workflow.sh	2013-06-15 00:01:57 UTC (rev 6555)
@@ -1,30 +0,0 @@
-#!/bin/sh
-
-AIR5=$HOME/software/AIR5.3.0
-fsl=/project/wilde/software/fsl-5.0.4/fsl
-
-if true; then
-
-#time  $AIR5/bin/align_warp anatomy1.img reference.img warp1.warp -m 1 12 -s 1024 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  -h 10000 -v -j # -q
-
-time  $AIR5/bin/align_warp reference.img anatomy1.img warp1.warp -m 1 12  -b1 .1 .1 .1  -b2 .1 .1 .1  -h 10000 -v -s 1024 2 2 -c .01  -f out # -q -s 1024 2 2 -c .01
-
-
-time  $AIR5/bin/align_warp anatomy2.img reference.img warp2.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
-time  $AIR5/bin/align_warp anatomy3.img reference.img warp3.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
-time  $AIR5/bin/align_warp anatomy4.img reference.img warp4.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
-time  $AIR5/bin/reslice warp1.warp resliced1
-time  $AIR5/bin/reslice warp2.warp resliced2
-time  $AIR5/bin/reslice warp3.warp resliced3
-time  $AIR5/bin/reslice warp4.warp resliced4
-time  $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img
-fi
-
-export FSLOUTPUTTYPE=NIFTI
-
-time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm
-time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm
-time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm
-time convert atlas-x.pgm atlas-x.gif
-time convert atlas-y.pgm atlas-y.gif
-time convert atlas-z.pgm atlas-z.gif

Added: SwiftTutorials/OHBM_2013-06-16/original/workflow.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/original/workflow.sh	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/original/workflow.sh	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,25 @@
+#!/bin/sh
+
+#
+# Original workflow from PC1 and DBIC
+#
+
+AIR5.2.5/bin/align_warp anatomy1.img reference.img warp1.warp -m 12 -q
+AIR5.2.5/bin/align_warp anatomy2.img reference.img warp2.warp -m 12 -q
+AIR5.2.5/bin/align_warp anatomy3.img reference.img warp3.warp -m 12 -q
+AIR5.2.5/bin/align_warp anatomy4.img reference.img warp4.warp -m 12 -q
+
+AIR5.2.5/bin/reslice warp1.warp resliced1
+AIR5.2.5/bin/reslice warp2.warp resliced2
+AIR5.2.5/bin/reslice warp3.warp resliced3
+AIR5.2.5/bin/reslice warp4.warp resliced4
+
+AIR5.2.5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img
+
+fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm
+fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm
+fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm
+
+convert atlas-x.pgm atlas-x.gif
+convert atlas-y.pgm atlas-y.gif
+convert atlas-z.pgm atlas-z.gif

Copied: SwiftTutorials/OHBM_2013-06-16/original/workflow1.sh (from rev 6550, SwiftTutorials/OHBM_2013-06-16/original/workflow.sh)
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/original/workflow1.sh	                        (rev 0)
+++ SwiftTutorials/OHBM_2013-06-16/original/workflow1.sh	2013-06-15 00:01:57 UTC (rev 6555)
@@ -0,0 +1,30 @@
+#!/bin/sh
+
+AIR5=$HOME/software/AIR5.3.0
+fsl=/project/wilde/software/fsl-5.0.4/fsl
+
+if true; then
+
+#time  $AIR5/bin/align_warp anatomy1.img reference.img warp1.warp -m 1 12 -s 1024 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  -h 10000 -v -j # -q
+
+time  $AIR5/bin/align_warp reference.img anatomy1.img warp1.warp -m 1 12  -b1 .1 .1 .1  -b2 .1 .1 .1  -h 10000 -v -s 1024 2 2 -c .01  -f out # -q -s 1024 2 2 -c .01
+
+
+time  $AIR5/bin/align_warp anatomy2.img reference.img warp2.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
+time  $AIR5/bin/align_warp anatomy3.img reference.img warp3.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
+time  $AIR5/bin/align_warp anatomy4.img reference.img warp4.warp -m 1 12 -s 64 2 2 -c .01 -b1 .1 .1 .1 -b2 .1 .1 .1  # -q
+time  $AIR5/bin/reslice warp1.warp resliced1
+time  $AIR5/bin/reslice warp2.warp resliced2
+time  $AIR5/bin/reslice warp3.warp resliced3
+time  $AIR5/bin/reslice warp4.warp resliced4
+time  $AIR5/bin/softmean atlas.hdr y null resliced1.img resliced2.img resliced3.img resliced4.img
+fi
+
+export FSLOUTPUTTYPE=NIFTI
+
+time $fsl/bin/slicer atlas.hdr -x .5 atlas-x.pgm
+time $fsl/bin/slicer atlas.hdr -y .5 atlas-y.pgm
+time $fsl/bin/slicer atlas.hdr -z .5 atlas-z.pgm
+time convert atlas-x.pgm atlas-x.gif
+time convert atlas-y.pgm atlas-y.gif
+time convert atlas-z.pgm atlas-z.gif



From wilde at ci.uchicago.edu  Fri Jun 14 19:14:45 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Fri, 14 Jun 2013 19:14:45 -0500 (CDT)
Subject: [Swift-commit] r6556 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130615001445.1787E9CC82@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-14 19:14:44 -0500 (Fri, 14 Jun 2013)
New Revision: 6556

Modified:
   SwiftTutorials/OHBM_2013-06-16/README
   SwiftTutorials/OHBM_2013-06-16/clean.sh
Log:
Edit README, adjust clean.sh

Modified: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	2013-06-15 00:01:57 UTC (rev 6555)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-15 00:14:44 UTC (rev 6556)
@@ -43,6 +43,18 @@
 
 * To run:
 
+  # Latest demo code versions:
+
+  atlas00.swift:  Just run one app, no Volume struct types
+  atlas01.swift:  Run a loop with volume struct types
+  atlas02.swift:  The fill workflow, with align() as a Swift function (for local execution)
+  atlas03.swift:  Full wowrkflow with align.sh, suitable for remote execution
+
+  genatlas.swift: The original workflow, now obsolete.
+
+  In the examples below, use atlas00.swift through atlas02.swift,
+  and atlas03.swift for all runs on beagle and cloud.
+
   # On localhost:
 
   swift genatlas.swift             # processes data/ directory by default

Modified: SwiftTutorials/OHBM_2013-06-16/clean.sh
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/clean.sh	2013-06-15 00:01:57 UTC (rev 6555)
+++ SwiftTutorials/OHBM_2013-06-16/clean.sh	2013-06-15 00:14:44 UTC (rev 6556)
@@ -1,4 +1,4 @@
 #! /bin/sh
 
-rm -rf _concurrent work/* output/* *.log *.rlog *.d *.kml *.swiftx 
+rm -rf _concurrent work/* output/* warps *.log *.rlog *.d *.kml *.swiftx 
 



From wilde at ci.uchicago.edu  Fri Jun 14 19:29:02 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Fri, 14 Jun 2013 19:29:02 -0500 (CDT)
Subject: [Swift-commit] r6557 - SwiftTutorials/OHBM_2013-06-16
Message-ID: <20130615002902.637749CC82@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-14 19:29:02 -0500 (Fri, 14 Jun 2013)
New Revision: 6557

Modified:
   SwiftTutorials/OHBM_2013-06-16/README
Log:
Add suggested demo sequence to README

Modified: SwiftTutorials/OHBM_2013-06-16/README
===================================================================
--- SwiftTutorials/OHBM_2013-06-16/README	2013-06-15 00:14:44 UTC (rev 6556)
+++ SwiftTutorials/OHBM_2013-06-16/README	2013-06-15 00:29:02 UTC (rev 6557)
@@ -55,15 +55,61 @@
   In the examples below, use atlas00.swift through atlas02.swift,
   and atlas03.swift for all runs on beagle and cloud.
 
+  # APPROXIMATE *SUGGESTED* DEMO SEQUENCE
+
+    # Show first Swift script:
+    
+    ./clean.sh
+    swift atlas00.swift
+
+    # Show struct data types for fMRI "ANALYZE 7.5" Volumes, @arg, and parallel foreach loop
+
+    ./clean.sh
+    ./makedata.sh data_10 10
+    swift atlas01.swift -d=data_10
+
+      # While above are running, do this in another window to view its activity:
+
+      watch ps -u $USER -H
+
+    # Show same script running on a cluster
+
+    ./clean.sh
+    ./makedata.sh data_50 50
+    swift -tc.file apps.midway atlas01.swift -d=data_50
+
+    # Show compound functions, imported libs, and full workflow
+
+    ./clean.sh
+    swift atlas02.swift -d=data_2
+
+    ./clean.sh
+    swift -tc.file apps.midway atlas02.swift -d=data_50
+
+   # Show full script, optimized for remote exec, running on beagle
+
+   ./clean.sh
+   swift -tc.file apps.beagle atlas02.swift -d=data_20
+
+   # Show full script running on Amazon EC2
+
+   ./clean.sh
+   # Start cloud resources and services here (document!)
+   swift -tc.file apps.amazon atlas02.swift -d=data_20
+
+   # Grand finale: show full script running on multiple resources
+
+  ./clean.sh
+   swift -tc.file apps.everywhere atlas02.swift -d=data_20
+
+### Obsolete below this line.... clean up vvvvvv
+
+
   # On localhost:
 
   swift genatlas.swift             # processes data/ directory by default
   swift genatlas.swift -d=data_100 # process data_100/ directory
 
-  # While above are running, do this in another window to view its activity:
-
-    watch ps -u $USER -H
-
   # With most parallel work on a midway parition (edit sites.xml to set partition)
 
   swift -tc.file apps.midway genatlas.swift



From swift at ci.uchicago.edu  Sat Jun 15 18:50:03 2013
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Sat, 15 Jun 2013 18:50:03 -0500 (CDT)
Subject: [Swift-commit] cog r3673
Message-ID: <20130615235003.DD7528D0008D@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3673 | hategan | 2013-06-15 18:48:32 -0500 (Sat, 15 Jun 2013) | 1 line

prevent log configuration warnings when running along with something that replaces the file appender with an async appender (such as swift)
------------------------------------------------------------------------
Index: modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java
===================================================================
--- modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java	(revision 3672)
+++ modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/CoasterService.java	(working copy)
@@ -405,11 +405,8 @@
     }
 
     public static void configureLogName() {
-        FileAppender fa = (FileAppender) getAppender(FileAppender.class);
-        if (fa == null) {
-            logger.warn("Failed to configure log file name");
-        }
-        else {
+        FileAppender fa = (FileAppender) getFileAppender();
+        if (fa != null) {
             fa.setFile(Bootstrap.LOG_DIR + File.separator + makeLogFileName());
             fa.activateOptions();
             
@@ -430,16 +427,23 @@
         root.addAppender(aa);
     }
     
-    @SuppressWarnings({ "rawtypes", "unchecked" })
-    protected static Appender getAppender(Class cls) {
+    @SuppressWarnings("rawtypes")
+    protected static Appender getFileAppender() {
         Logger root = Logger.getRootLogger();
         Enumeration e = root.getAllAppenders();
         while (e.hasMoreElements()) {
             Appender a = (Appender) e.nextElement();
-            if (cls.isAssignableFrom(a.getClass())) {
+            if (a instanceof FileAppender) {
                 return a;
             }
+            if (a instanceof AsyncAppender) {
+                // likely this is running in a JVM in which
+                // the file appender has been replaced with 
+                // an async appender, so don't mess with things
+                return null;
+            }
         }
+        logger.warn("Could not find a file appender to configure");
         return null;
     }
 


From wilde at ci.uchicago.edu  Sun Jun 16 00:11:42 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 16 Jun 2013 00:11:42 -0500 (CDT)
Subject: [Swift-commit] r6558 - SwiftTutorials
Message-ID: <20130616051142.6F30B178884@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-16 00:11:42 -0500 (Sun, 16 Jun 2013)
New Revision: 6558

Added:
   SwiftTutorials/CMTS_2013-06-17/
Log:
Initial dir for CMTS Workshop tutorial 2013.



From wilde at ci.uchicago.edu  Sun Jun 16 11:52:26 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 16 Jun 2013 11:52:26 -0500 (CDT)
Subject: [Swift-commit] r6560 - in
	SwiftTutorials/CMTS_2013-06-17/basic_swift: part01 part02
	part03 part04 part05 part06 part07
Message-ID: <20130616165226.51B439CC8F@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-16 11:52:26 -0500 (Sun, 16 Jun 2013)
New Revision: 6560

Added:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/sites.xml
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/sites.xml
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/sites.xml
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/sites.xml
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/sites.xml
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/sites.xml
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps
Removed:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc
Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README
Log:
Initial revisions for CMTS workshop.

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README	2013-06-16 16:52:26 UTC (rev 6560)
@@ -4,37 +4,41 @@
 
 Verify that random.sh is in your path, and that it works:
 
-$ which random.sh
-$ random.sh
+  $ which random.sh
+  $ random.sh
 
 Study the Swift program:
 
-$ cat p1.swift
+  $ cat p1.swift
 
-Examine the tool catalog file:
+Examine the app location file, telling swift which apps are installed
+and where to find them (e.g., from $PATH or a specific pathname):
 
-$ cat tc
+  $ cat apps
 
 Run the program:
 
-$ swift -tc.file tc p1.swift
+  $ swift p1.swift
 
 Look at the output:
 
-$ cat _concurrent/*
+  $ cat _concurrent/*
 
 Look at the other files generated:
 
-$ ls -l
+  $ ls -l
 
 We'll talk more about these files later
 
-$ cleanup
+This will remove log and temp files, first prompting you for
+confirmation:
 
-Then test the sript a few more times.
+  $ cleanup  
 
-$ swift -tc.file tc p1.swift; cat _concurrent/*
+Then test the sript a few more times:
 
-$ swift -tc.file tc p1.swift; cat _concurrent/*
+  $ swift -tc.file tc p1.swift; cat _concurrent/*
 
-$ swift -tc.file tc p1.swift; cat _concurrent/*
+  $ swift -tc.file tc p1.swift; cat _concurrent/*
+
+  $ swift -tc.file tc p1.swift; cat _concurrent/*

Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc)
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/apps	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1 @@
+localhost random random.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/sites.xml	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,9 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+</config>

Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1 +0,0 @@
-localhost random random.sh

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,33 +1,36 @@
 
-TOPIC: specifying the output filenames
+TOPIC:   Specifying the output filenames
 
+
 Study the Swift program:
 
-$ cat p2.swift
+  $ cat p2.swift
 
 Examine the tool catalog file:
 
-$ cat tc
+  $ cat tc
 
 Run the program:
 
-$ swift -tc.file tc p2.swift
+  $ swift -tc.file tc p2.swift
 
 Look at the output:
 
-$ cat sim.out
+  $ cat sim.out
 
 Then test the sript a few more times.
 
-$ swift -tc.file tc p1.swift; cat sim.out
+  $ swift -tc.file tc p1.swift; cat sim.out
 
-$ swift -tc.file tc p1.swift; cat sim.out
+  $ swift -tc.file tc p1.swift; cat sim.out
 
-$ swift -tc.file tc p1.swift; cat sim.out
+  $ swift -tc.file tc p1.swift; cat sim.out
 
 Things to try:
 
-- change the output filename
+  o change the output filename
 
-- add a dir component to the output filename
+  o add a directory component to the output filename
 
+  o try using fully qualified file names
+

Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc)
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/apps	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1 @@
+localhost random random.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/sites.xml	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,9 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+</config>

Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1 +0,0 @@
-localhost random random.sh

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,20 +1,23 @@
 
-TOPIC: run many instances of a "simulation" program in a foreach() loop
+TOPIC:   Run many instances of a "simulation" program in parallel
+         with a foreach() loop
 
 
 Run the program:
 
-$ swift -tc.file tc p3.swift
+  $ swift p3.swift
 
 Look at the output:
 
-$ cd _concurrent
-$ ls -l
-$ cat *
+  $ cd _concurrent
+  $ ls -l
+  $ cat *
 
 Look at the order in which the files were written:
 
-$ ls -lt
+  $ ls -lt
 
-We'll come back to this...
+Run p3.swift a few more times, noting how the order changes.
 
+Swift runs the apps in a foreach loop with high concurrency:
+you cant count on what order they run in!

Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc)
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/apps	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1 @@
+localhost random random.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/sites.xml	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,9 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+</config>

Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1 +0,0 @@
-localhost random random.sh

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,42 +1,59 @@
 
-TOPIC: run a program in a foreach() loop with explicitly named output files.
+TOPIC:   Run a program in a foreach() loop with explicitly named output files.
 
 
 Study the program:
 
-- @strcat() is a Swift builtin function (the @name() form is used for many but not all builtins)
+  @strcat() is a Swift builtin function (the @name() form is used for many but not all builtins)
 
-- Note that @strcat() coerces numeric args to strings 
+  Note that @strcat() coerces numeric args to strings 
 
-- <"filename"> was a shorthand for <single_file_mapper;...> but the latter is more flexible.
+  <"filename"> was a shorthand for <single_file_mapper;...> but the latter is more flexible.
 
+
 Run the program:
 
-$ swift -tc.file tc p4.swift
+  $ swift -tc.file tc p4.swift
 
 Look at the output:
 
-$ cd output
-$ ls -l
-$ cat *
+  $ cd output
+  $ ls -l
+  $ cat *
 
 
-Try:
+Try these exercises:
 
-- Adjust the script to take the number of simulations to do from the command line
+  o Adjust the script to take the number of simulations to do from the command line
 
-  @arg("argname") returns arguments after the .swift script on the swift command line:
+    @arg("argname") returns arguments after the .swift script on the swift command line:
 
-    swift -tc.file tc p4.swift -myarg1=value1 ...
+      swift -tc.file tc p4.swift -myarg1=value1 ...
 
-  @arg("argname","default") returns "default" if the argname is not given on the command line
+    @arg("argname","default") returns "default" if the argname is not given on the command line
 
-  @toInt() converts strings to integers:
+    @toInt() converts strings to integers:
 
-    @toInt(@arg("myArg1"))
+      @toInt(@arg("myArg1"))
 
 
-- trace(expr1,...) traces expressions on stdout.
+  o Add some output tracing.
 
-  Try inserting a few traces.  But remember: Swift is *very* concurrent!
+    trace(expr1,...) traces expressions on stdout.
 
+    tracef() allows some simple formatting ala printf (but with slighly different codes)
+    see: http://www.swiftlang.org/guides/trunk/userguide/userguide.html#_tracef
+
+    Try inserting a few traces.  But remember: Swift is *very* concurrent!
+
+  o Use readData() to read the output files back in to the Swift script and print their values.
+
+  o Use readData() to read both a scalar and an array
+
+  o create a version of Random that prints pairs, and read these into arrays
+
+  o Experiment with sparse arrays
+
+  o Experiment with string-indexed arrays (hash tables)
+
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/sites.xml	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,9 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+</config>

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,51 +1,39 @@
 
+TOPIC:   Add a program that "analyzes" the output the parallel simulations
 
-TOPIC: Add a program that "analyzes" the output the parallel simulations
 
-
 Study the program:
 
-We added a new app to "analyze" all the simulation outputs:
+  We added a new app to "analyze" all the simulation outputs:
 
-app (file o) analyze (file s[])
-{
-  average @filenames(s) stdout=@filename(o);
-}
+  app (file o) analyze (file s[])
+  {
+    average @filenames(s) stdout=@filename(o);
+  }
 
 Nots that it expects an array of files as its input, and that
 it uses @filenames() to place the names of all the files on 
 the command line to the "average" program.
 
 Average does:  
---------------------
-#! /bin/sh
 
-awk '
-
-{ sum += $1}
-
-END { print sum/NR }
-' $*
--------------------
-
-
+  awk '    { sum += $1}
+       END { print sum/NR } ' $*
+  
 At the end of the script we insert:
 
-file stats<"output/average.out">;
-stats = analyze(sims);
+  file stats<"output/average.out">;
+  stats = analyze(sims);
 
 ...which runs the analysis *after* all the simulations complete.
 
-
 Run the program:
 
-$ swift -tc.file tc p5.swift
+  $ swift p5.swift
 
-Look at the output:
+Inspect the output:
 
-$ cd output
-$ ls -l
-$ cat sim*.out
-$ cat average.out
-
-
+  $ cd output
+  $ ls -l
+  $ cat sim*.out
+  $ cat average.out

Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc)
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/apps	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,2 @@
+localhost random  random.sh
+localhost average avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/sites.xml	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,9 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+</config>

Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,2 +0,0 @@
-localhost random  random.sh
-localhost average avg.sh

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,28 +1,42 @@
 
-TOPIC: add arguments to the "simulation" program
-(to control number of steps, range of output, and number of output lines)
+TOPIC:   Add arguments to the "simulation" program
+         (to control number of steps, range of output, and number of output lines)
 
 
-Test new versions of the "simulation" program:
+Test these new versions of the "simulation" program:
 
   random.sh                            # original
   random2.sh [runtime]                 # runtime in seconds; defaults to 1 sec
   random3.sh [runtime] [range]         # requests random numbers in {0:range-1}
   random4.sh [runtime] [range] [count] # requests "count" random numbers in {0:range}
 
-p6.swift changes to random2 for the simulation program and adds an argument.
+p6.swift uses random2 for the simulation program and adds an argument.
 
 Run the program:
 
-$ swift -tc.file tc p6.swift -steps=3  # each simulation takes 3 seconds
+  $ swift p6.swift -steps=3  # each simulation takes 3 seconds
 
 Next we need to use the parallel cluster for our simulations!
 
-Try:
+Try these exercises:
 
-- change to random3.sh and add the extra argument "range"
+  o Change to random3.sh and add the extra command line argument " -range= "
 
-- change to random4.sh and add yet another argument "count"
+  o Change to random4.sh and add yet another argument " -count= "
 
+Also try adjusting the runtime concurrency throttle for "localhost"
 
+  $ cp sites.xml faster.xml
+  $ vi faster.xml
+  # Add these lines before the </pool> closing tag
+    <profile namespace="karajan" key="initialScore">10000</profile>
+    <profile namespace="karajan" key="jobThrottle">.03</profile> 
+  
+  $ swift -sites.file faster.xml p6.swift
 
+Note the increased number of active jobs
+
+
+
+
+

Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc)
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/apps	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,2 @@
+localhost random2  random2.sh
+localhost average avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/sites.xml	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,9 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+</config>

Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,2 +0,0 @@
-localhost random2  random2.sh
-localhost average avg.sh

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,9 +1,8 @@
 
-TOPIC: Run the "simulations" on the parallel cluster
+TOPIC:   Run the "simulations" on the parallel cluster
 
 
-Til now we've been running our "simulations" on the local login host.
-
+So far we've been running our "simulations" on the local login host.
 Now we'll run them on the parallel cluster.
 
 The script will be the same as previous, but we change the tool catalog to
@@ -12,20 +11,20 @@
 
 We changed file "tc" from:
 
-localhost random4  random4.sh
-localhost average  avg.sh
+  localhost random4  random4.sh
+  localhost average  avg.sh
 
 to:
 
-westmere  random4  random4.sh
-localhost average  avg.sh
+  cmtsworkshop  random4  random4.sh
+  localhost     average  avg.sh
 
-And we added the "sites.xml" file which specifies two "pools" of resources,
-the "local host" pool (which we've been using till now) and the "westmere" pool.
+And we added a pool entry to "sites.xml" file which specifies two "pools" of resources,
+the "local host" pool (which we've been using till now) and the "cmtsworkshop" pool.
 
-To run, we now add the sites.xml file to the swift command line:
+To run:
 
-$ swift -tc.file tc -sites.file sites.xml p7.swift -steps=10 -range=1000 -count=6 -nsim=100
+  $ swift p7.swift -steps=10 -range=1000 -count=6 -nsim=100
 
 Note that we're now asking for 100 simulations to be run, each of which
 is to run for 10 steps (ie 10 seconds).
@@ -40,20 +39,20 @@
     <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
   </pool>
 
-  <pool handle="westmere">
+  <pool handle="cmtsworkshop">
     <execution provider="coaster" jobmanager="local:slurm"/>
 
     <!-- Set partition and account here: -->
-    <profile namespace="globus" key="queue">westmere</profile>
-    <profile namespace="globus" key="ppn">12</profile>
-    <!-- <profile namespace="globus" key="project">pi-wilde</profile> -->
+    <profile namespace="globus" key="queue">cmtsworkshop</profile>
+    <profile namespace="globus" key="ppn">8</profile>
+    <profile namespace="globus" key="project">cmtsworkshop</profile> -->
 
     <!-- Set number of jobs and nodes per job here: -->
     <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="jobsPerNode">12</profile> <!-- apps per node! -->
-    <profile namespace="karajan" key="jobThrottle">.11</profile> <!-- eg .11 -> 12 -->
+    <profile namespace="globus" key="jobsPerNode">8</profile>    <!-- apps per node -->
+    <profile namespace="karajan" key="jobThrottle">.07</profile> <!-- eg .07 -> 8   -->
 
     <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
     <profile namespace="globus" key="maxWalltime">00:15:00</profile>
@@ -74,8 +73,8 @@
 
 Try:
 
-- running more app() calls at once:  change jobsPerNode and jobThrottle
+  o running more app() calls at once:  change jobsPerNode and jobThrottle
 
-- requesting more than 1 slurm job at once: change slots
+  o requesting more than 1 slurm job at once: change slots
 
-- requesting nodes in units greater than 1: change maxnodes and nodeGranularity
+  o requesting nodes in units greater than 1: change maxnodes and nodeGranularity

Copied: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc)
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps	2013-06-16 16:52:26 UTC (rev 6560)
@@ -0,0 +1,2 @@
+westmere  random4  random4.sh
+localhost average  avg.sh

Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc	2013-06-16 13:30:27 UTC (rev 6559)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc	2013-06-16 16:52:26 UTC (rev 6560)
@@ -1,2 +0,0 @@
-westmere  random4  random4.sh
-localhost average  avg.sh



From wilde at ci.uchicago.edu  Sun Jun 16 12:46:23 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 16 Jun 2013 12:46:23 -0500 (CDT)
Subject: [Swift-commit] r6561 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part07
Message-ID: <20130616174623.EC0FC9CC8F@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-16 12:46:23 -0500 (Sun, 16 Jun 2013)
New Revision: 6561

Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml
Log:
Adjust apps and sites for cmtsworkshop.

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps	2013-06-16 16:52:26 UTC (rev 6560)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/apps	2013-06-16 17:46:23 UTC (rev 6561)
@@ -1,2 +1,2 @@
-westmere  random4  random4.sh
-localhost average  avg.sh
+cmtsworkshop random4  random4.sh
+localhost    average  avg.sh

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml	2013-06-16 16:52:26 UTC (rev 6560)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml	2013-06-16 17:46:23 UTC (rev 6561)
@@ -6,20 +6,20 @@
     <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
   </pool>
 
-  <pool handle="westmere">
+  <pool handle="cmtsworkshop">
     <execution provider="coaster" jobmanager="local:slurm"/>
 
     <!-- Set partition and account here: -->
-    <profile namespace="globus" key="queue">westmere</profile>
-    <profile namespace="globus" key="ppn">12</profile>
-    <!-- <profile namespace="globus" key="project">pi-wilde</profile> -->
+    <profile namespace="globus" key="queue">cmtsworkshop</profile>
+    <profile namespace="globus" key="ppn">8</profile>
+    <profile namespace="globus" key="project">cmtsworkshop</profile>
 
     <!-- Set number of jobs and nodes per job here: -->
-    <profile namespace="globus" key="slots">1</profile>
+    <profile namespace="globus" key="slots">4</profile>
     <profile namespace="globus" key="maxnodes">1</profile>
     <profile namespace="globus" key="nodegranularity">1</profile>
-    <profile namespace="globus" key="jobsPerNode">12</profile> <!-- apps per node! -->
-    <profile namespace="karajan" key="jobThrottle">.11</profile> <!-- eg .11 -> 12 -->
+    <profile namespace="globus" key="jobsPerNode">8</profile> <!-- apps per node! -->
+    <profile namespace="karajan" key="jobThrottle">.31</profile> <!-- eg .31 -> 32 -->
 
     <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
     <profile namespace="globus" key="maxWalltime">00:15:00</profile>



From wilde at ci.uchicago.edu  Sun Jun 16 12:50:27 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 16 Jun 2013 12:50:27 -0500 (CDT)
Subject: [Swift-commit] r6562 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part02
Message-ID: <20130616175027.8F7809CC8F@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-16 12:50:27 -0500 (Sun, 16 Jun 2013)
New Revision: 6562

Removed:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift
Log:
Remove this one answer file.  Add answers for all 'eercises' later in a uniform way.

Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift	2013-06-16 17:46:23 UTC (rev 6561)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift	2013-06-16 17:50:27 UTC (rev 6562)
@@ -1,9 +0,0 @@
-type file;
-
-app (file o) mysim ()
-{
-  random stdout=@filename(o);
-}
-
-file f<"output/sim.out">;
-f = mysim();



From wilde at ci.uchicago.edu  Sun Jun 16 13:09:49 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 16 Jun 2013 13:09:49 -0500 (CDT)
Subject: [Swift-commit] r6563 - SwiftTutorials/CMTS_2013-06-17/namd_sweep
Message-ID: <20130616180949.E65AC9CC8F@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-16 13:09:49 -0500 (Sun, 16 Jun 2013)
New Revision: 6563

Added:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps
Removed:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc
Modified:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
Log:
Initial adaptations of rmsd exercise (namd sweep).

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-16 18:09:49 UTC (rev 6563)
@@ -13,5 +13,11 @@
 data in a gnuplot 2D plot data format. This script also prints to screen 
 the minimum RMSD and the parameter values corresponding to that value.
 
--Frank X. Vazquez fxv at uchicago.edu
-7-13-2012
+-Frank X. Vazquez fxv at uchicago.edu  7-13-2012
+
+To Run:
+
+  PATH=$PATH:$PWD  # Note: must use $PWD, not "." !!!
+
+  swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5
+

Copied: SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps (from rev 6559, SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc)
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps	2013-06-16 18:09:49 UTC (rev 6563)
@@ -0,0 +1,5 @@
+
+localhost     gensweep  sweep_pd.pl   null null null
+localhost     analyze   analyze_pd.pl null null null
+
+cmtsworkshop  rmsd      rmsd.sh       null null null

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh	2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh	2013-06-16 18:09:49 UTC (rev 6563)
@@ -1,3 +1,3 @@
 #!/bin/bash
 
-rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/* RMSD/* VMD/* CONF/* OUT/*
+rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/ RMSD/ VMD/ CONF/ OUT/

Deleted: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh	2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh	2013-06-16 18:09:49 UTC (rev 6563)
@@ -1,7 +0,0 @@
-PATH=$PATH:$PWD
-
-# export SBATCH_RESERVATION=swift_test
-
-mkdir  -p CONF PAR VMD RMSD OUT
-
-swift -sites.file sites.xml -tc.file tc -config cf rmsd.swift -cwd=$PWD -max=${1:-0.0} -delta=${2:-0.5}

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml	2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml	2013-06-16 18:09:49 UTC (rev 6563)
@@ -1,11 +1,42 @@
 <config>
 
-  <pool handle="local">
+  <pool handle="localhost">
     <execution provider="local"/>
     <filesystem provider="local"/>
     <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
   </pool>
 
+  <pool handle="cmtsworkshop">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">cmtsworkshop</profile>
+    <profile namespace="globus" key="ppn">8</profile>
+    <profile namespace="globus" key="project">cmtsworkshop</profile>
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <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">.03</profile>
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">true</profile>
+    <profile namespace="globus" key="jobtype">single</profile>
+    <profile namespace="globus" key="jobsPerNode">1</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
   <pool handle="westmere">
     <execution provider="coaster" jobmanager="local:slurm"/>
 

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl	2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl	2013-06-16 18:09:49 UTC (rev 6563)
@@ -10,6 +10,10 @@
 
 chdir($ARGV[0]);
 
+# Create dirs
+
+system("mkdir  -p CONF PAR VMD RMSD OUT");
+
 # Bead names
 
 my $b1name = "PX";

Deleted: SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc	2013-06-16 17:50:27 UTC (rev 6562)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc	2013-06-16 18:09:49 UTC (rev 6563)
@@ -1,8 +0,0 @@
-
-local     gensweep  sweep_pd.pl   null null null
-local     analyze   analyze_pd.pl null null null
-
-#bigmem   rmsd      rmsd.sh       null null null
-#sandyb   rmsd      rmsd.sh       null null null
-#trestles rmsd      rmsd.sh       null null null
-westmere  rmsd      rmsd.sh       null null null



From wilde at ci.uchicago.edu  Sun Jun 16 13:15:26 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 16 Jun 2013 13:15:26 -0500 (CDT)
Subject: [Swift-commit] r6564 - SwiftTutorials/CMTS_2013-06-17/namd_sweep
Message-ID: <20130616181526.B71FC9CC8F@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-16 13:15:26 -0500 (Sun, 16 Jun 2013)
New Revision: 6564

Modified:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift
Log:
Update README with run instructions; pretty up the trace.

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-16 18:09:49 UTC (rev 6563)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-16 18:15:26 UTC (rev 6564)
@@ -19,5 +19,8 @@
 
   PATH=$PATH:$PWD  # Note: must use $PWD, not "." !!!
 
-  swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5
+  swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5  # 1 param set
 
+  swift rmsd.swift -cwd=$PWD -max=1.0 -delta=0.5  # 9 param sets (3 x 3)
+
+

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift	2013-06-16 18:09:49 UTC (rev 6563)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift	2013-06-16 18:15:26 UTC (rev 6564)
@@ -26,7 +26,6 @@
 
 string beadids[] = readData(genConfigs(sweepMax, sweepDelta));
 
-trace("Processing these bead IDs:", beadids);
 
 foreach beadid, i in beadids {
   file conf   <single_file_mapper; file=@strcat("CONF/",beadid,".conf")>;
@@ -36,6 +35,8 @@
   file log    <single_file_mapper; file=@strcat("OUT/", beadid,".log")>;
   file dat    <single_file_mapper; file=@strcat("RMSD/",beadid,".dat")>;
 
+  tracef("Processing bead ID %s\n", beadid);
+
   (log,dat) = rmsd([conf,pdb,psf,inp,vmdtcl], beadid);
   rmsds[i] = dat;
 }



From davidk at ci.uchicago.edu  Mon Jun 17 10:25:19 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 10:25:19 -0500 (CDT)
Subject: [Swift-commit] r6565 - in
	SwiftTutorials/CMTS_2013-06-17/basic_swift: part01 part02
	part04 part07
Message-ID: <20130617152520.047399CC43@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 10:25:18 -0500 (Mon, 17 Jun 2013)
New Revision: 6565

Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift
Log:
Fix some inconsistencies with tc/app files, fix scope warning in p7.swift


Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README	2013-06-16 18:15:26 UTC (rev 6564)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README	2013-06-17 15:25:18 UTC (rev 6565)
@@ -37,8 +37,8 @@
 
 Then test the sript a few more times:
 
-  $ swift -tc.file tc p1.swift; cat _concurrent/*
+  $ swift p1.swift; cat _concurrent/*
 
-  $ swift -tc.file tc p1.swift; cat _concurrent/*
+  $ swift p1.swift; cat _concurrent/*
 
-  $ swift -tc.file tc p1.swift; cat _concurrent/*
+  $ swift p1.swift; cat _concurrent/*

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README	2013-06-16 18:15:26 UTC (rev 6564)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README	2013-06-17 15:25:18 UTC (rev 6565)
@@ -8,11 +8,11 @@
 
 Examine the tool catalog file:
 
-  $ cat tc
+  $ cat apps
 
 Run the program:
 
-  $ swift -tc.file tc p2.swift
+  $ swift p2.swift
 
 Look at the output:
 
@@ -20,11 +20,11 @@
 
 Then test the sript a few more times.
 
-  $ swift -tc.file tc p1.swift; cat sim.out
+  $ swift p2.swift; cat sim.out
 
-  $ swift -tc.file tc p1.swift; cat sim.out
+  $ swift p2.swift; cat sim.out
 
-  $ swift -tc.file tc p1.swift; cat sim.out
+  $ swift p2.swift; cat sim.out
 
 Things to try:
 

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README	2013-06-16 18:15:26 UTC (rev 6564)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README	2013-06-17 15:25:18 UTC (rev 6565)
@@ -13,7 +13,7 @@
 
 Run the program:
 
-  $ swift -tc.file tc p4.swift
+  $ swift p4.swift
 
 Look at the output:
 

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README	2013-06-16 18:15:26 UTC (rev 6564)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README	2013-06-17 15:25:18 UTC (rev 6565)
@@ -9,7 +9,7 @@
 indicate that our "simulation app" (random4.sh) should be run on the
 "westmere" partition of the Midway cluster using the "slurm" scheduler:
 
-We changed file "tc" from:
+We changed file "apps" from:
 
   localhost random4  random4.sh
   localhost average  avg.sh

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift	2013-06-16 18:15:26 UTC (rev 6564)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift	2013-06-17 15:25:18 UTC (rev 6565)
@@ -1,8 +1,8 @@
 type file;
 
-app (file o) mysim4 (int timesteps, int range, int count)
+app (file o) mysim4 (int timesteps, int range_value, int count_value)
 {
-  random4 timesteps range count stdout=@filename(o);
+  random4 timesteps range_value count_value stdout=@filename(o);
 }
 
 app (file o) analyze (file s[])
@@ -12,7 +12,6 @@
 
 file sims[];
 int  nsim  = @toInt(@arg("nsim",  "10"));
-
 int  steps = @toInt(@arg("steps", "1"));
 int  range = @toInt(@arg("range", "100"));
 int  count = @toInt(@arg("count", "10"));



From davidk at ci.uchicago.edu  Mon Jun 17 10:44:26 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 10:44:26 -0500 (CDT)
Subject: [Swift-commit] r6566 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part04
Message-ID: <20130617154426.9D6069CC43@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 10:44:26 -0500 (Mon, 17 Jun 2013)
New Revision: 6566

Added:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/apps
Log:
apps


Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/apps
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/apps	2013-06-17 15:44:26 UTC (rev 6566)
@@ -0,0 +1 @@
+localhost random random.sh



From davidk at ci.uchicago.edu  Mon Jun 17 10:44:54 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 10:44:54 -0500 (CDT)
Subject: [Swift-commit] r6567 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part04
Message-ID: <20130617154454.502DC9CC43@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 10:44:54 -0500 (Mon, 17 Jun 2013)
New Revision: 6567

Removed:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc
Log:
Remove tc


Deleted: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc	2013-06-17 15:44:26 UTC (rev 6566)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc	2013-06-17 15:44:54 UTC (rev 6567)
@@ -1 +0,0 @@
-localhost random random.sh



From ketan at ci.uchicago.edu  Mon Jun 17 10:48:16 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 10:48:16 -0500 (CDT)
Subject: [Swift-commit] r6568 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part05
Message-ID: <20130617154816.05F589CC45@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-17 10:48:15 -0500 (Mon, 17 Jun 2013)
New Revision: 6568

Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README
Log:
small typo



Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README	2013-06-17 15:44:54 UTC (rev 6567)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README	2013-06-17 15:48:15 UTC (rev 6568)
@@ -11,7 +11,7 @@
     average @filenames(s) stdout=@filename(o);
   }
 
-Nots that it expects an array of files as its input, and that
+Note that it expects an array of files as its input, and that
 it uses @filenames() to place the names of all the files on 
 the command line to the "average" program.
 



From wilde at ci.uchicago.edu  Mon Jun 17 13:10:43 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 13:10:43 -0500 (CDT)
Subject: [Swift-commit] r6569 - SwiftTutorials/CMTS_2013-06-17
Message-ID: <20130617181043.83D2A9CC45@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-17 13:10:43 -0500 (Mon, 17 Jun 2013)
New Revision: 6569

Modified:
   SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
Log:
Presented version of Swift lecture.

Modified: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
===================================================================
(Binary files differ)



From davidk at ci.uchicago.edu  Mon Jun 17 13:42:31 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 13:42:31 -0500 (CDT)
Subject: [Swift-commit] r6570 - in
	SwiftTutorials/CMTS_2013-06-17/basic_swift: . part08
Message-ID: <20130617184231.684AF9CC45@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 13:42:31 -0500 (Mon, 17 Jun 2013)
New Revision: 6570

Added:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/sites.xml
Log:
Part08


Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README	2013-06-17 18:42:31 UTC (rev 6570)
@@ -0,0 +1,80 @@
+
+TOPIC: Example pipelines 
+
+
+So far we've been running our "simulations" on the local login host.
+Now we'll run them on the parallel cluster.
+
+The script will be the same as previous, but we change the tool catalog to
+indicate that our "simulation app" (random4.sh) should be run on the
+"westmere" partition of the Midway cluster using the "slurm" scheduler:
+
+We changed file "apps" from:
+
+  localhost random4  random4.sh
+  localhost average  avg.sh
+
+to:
+
+  cmtsworkshop  random4  random4.sh
+  localhost     average  avg.sh
+
+And we added a pool entry to "sites.xml" file which specifies two "pools" of resources,
+the "local host" pool (which we've been using till now) and the "cmtsworkshop" pool.
+
+To run:
+
+  $ swift p7.swift -steps=10 -range=1000 -count=6 -nsim=100
+
+Note that we're now asking for 100 simulations to be run, each of which
+is to run for 10 steps (ie 10 seconds).
+
+The sites file looks like this:
+
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="cmtsworkshop">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">cmtsworkshop</profile>
+    <profile namespace="globus" key="ppn">8</profile>
+    <profile namespace="globus" key="project">cmtsworkshop</profile> -->
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <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="jobsPerNode">8</profile>    <!-- apps per node -->
+    <profile namespace="karajan" key="jobThrottle">.07</profile> <!-- eg .07 -> 8   -->
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+  </pool>
+
+</config>
+
+Try:
+
+  o running more app() calls at once:  change jobsPerNode and jobThrottle
+
+  o requesting more than 1 slurm job at once: change slots
+
+  o requesting nodes in units greater than 1: change maxnodes and nodeGranularity

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/apps
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/apps	2013-06-17 18:42:31 UTC (rev 6570)
@@ -0,0 +1,2 @@
+cmtsworkshop random4  random4.sh
+localhost    average  avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift	2013-06-17 18:42:31 UTC (rev 6570)
@@ -0,0 +1,36 @@
+type file;
+
+app (file o) mysim4 (int timesteps, int range_value, int count_value)
+{
+  random4 timesteps range_value count_value stdout=@filename(o);
+}
+
+app (file o) mysim4_filename (int timesteps, file range_value, int count_value)
+{
+   random4 timesteps @filename(range_value) count_value stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+  average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+int  nsim  = @toInt(@arg("nsim",  "10"));
+int  steps = @toInt(@arg("steps", "1"));
+int  range = @toInt(@arg("range", "100"));
+int  count = @toInt(@arg("count", "10"));
+
+foreach i in [0:nsim-1] {
+
+  file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+  simout = mysim4(steps, range, 1);
+
+  file simout2 <single_file_mapper; file=@strcat("output/sim_", i, ".tmp.out")>;
+  simout2 = mysim4_filename(steps, simout, nsim);
+  
+  sims[i] = simout2;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/sites.xml	2013-06-17 18:42:31 UTC (rev 6570)
@@ -0,0 +1,39 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="cmtsworkshop">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">cmtsworkshop</profile>
+    <profile namespace="globus" key="ppn">8</profile>
+    <profile namespace="globus" key="project">cmtsworkshop</profile>
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <profile namespace="globus" key="slots">4</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="nodegranularity">1</profile>
+    <profile namespace="globus" key="jobsPerNode">8</profile> <!-- apps per node! -->
+    <profile namespace="karajan" key="jobThrottle">.31</profile> <!-- eg .31 -> 32 -->
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+  </pool>
+
+</config>



From davidk at ci.uchicago.edu  Mon Jun 17 13:48:50 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 13:48:50 -0500 (CDT)
Subject: [Swift-commit] r6571 - SwiftTutorials/CMTS_2013-06-17/bin
Message-ID: <20130617184850.2023C9CC43@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 13:48:50 -0500 (Mon, 17 Jun 2013)
New Revision: 6571

Modified:
   SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
Log:
updated random4


Modified: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random4.sh	2013-06-17 18:42:31 UTC (rev 6570)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random4.sh	2013-06-17 18:48:50 UTC (rev 6571)
@@ -4,6 +4,10 @@
 range=${2:-30000}
 n=${3:-10}
 
+if [ -f "$2" ]; then
+   range=$( cat $2 )
+fi
+
 sleep $runtime
 
 for ((i=0;i<n;i++)); do



From ketan at ci.uchicago.edu  Mon Jun 17 14:14:57 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 14:14:57 -0500 (CDT)
Subject: [Swift-commit] r6572 - in
	SwiftTutorials/CMTS_2013-06-17/basic_swift: . swift10
Message-ID: <20130617191457.A2CE69CC43@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-17 14:14:57 -0500 (Mon, 17 Jun 2013)
New Revision: 6572

Added:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_5nm.coor
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_qvals.txt
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/p10.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/particles.dat
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/sites.xml
Log:
TJ Lane's example

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/README	2013-06-17 19:14:57 UTC (rev 6572)
@@ -0,0 +1,25 @@
+
+TOPIC: Example illustrating readData from a file with multiple fields
+
+To run:
+
+  $ swift p10.swift 
+
+In this example, multiple fields from a file are read into a Swift struct
+variable. The file particles.dat contains eight fields corresponding to eight
+members in the struct type defined in p10.swift as follows:
+
+type shootargs{
+    string coords;
+    string qvals;
+    int numphi;
+    int numshots;
+    int nummolec;
+    float photons;
+    int parallel;
+    string output_filename;
+}
+
+Note that the first row in the particles.dat corresponds to the member names in
+the shootargs type which is how Swift assigns values to structure member
+variables.

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/apps
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/apps	2013-06-17 19:14:57 UTC (rev 6572)
@@ -0,0 +1,3 @@
+cmtsworkshop random4  random4.sh
+cmtsworkshop echo  echo
+localhost    average  avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_5nm.coor
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_5nm.coor	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_5nm.coor	2013-06-17 19:14:57 UTC (rev 6572)
@@ -0,0 +1,3 @@
+====
+Test.
+====

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_qvals.txt
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_qvals.txt	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/gold_qvals.txt	2013-06-17 19:14:57 UTC (rev 6572)
@@ -0,0 +1,3 @@
+=====
+Hello
+=====

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/p10.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/p10.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/p10.swift	2013-06-17 19:14:57 UTC (rev 6572)
@@ -0,0 +1,30 @@
+type qvalfile;
+type coordfile;
+type shotfile;
+
+type shootargs{
+    string coords;
+    string qvals;
+    int numphi;
+    int numshots;
+    int nummolec;
+    float photons;
+    int parallel;
+    string output_filename;
+}
+
+app (shotfile outfile) shootsim (shootargs args, coordfile coords, qvalfile qvals) {
+     echo "polshoot" "-s" @coords "-f" @qvals "-x" args.numphi "-n" args.numshots
+                     "-m" args.nummolec "-g" args.photons "-p" args.parallel "-o" @outfile
+                     stdout=@outfile; # Note double use of outfile, just for testing/demo
+}
+
+shootargs myargs[] = readData("particles.dat");
+
+foreach a in myargs {
+    shotfile  output <single_file_mapper; file=a.output_filename>;
+    coordfile coords <single_file_mapper; file=a.coords>;
+    qvalfile  qvals  <single_file_mapper; file=a.qvals>;
+    output = shootsim(a, coords, qvals);
+}
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/particles.dat
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/particles.dat	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/particles.dat	2013-06-17 19:14:57 UTC (rev 6572)
@@ -0,0 +1,6 @@
+coords        qvals          numphi numshots nummolec photons parallel output_filename
+gold_5nm.coor gold_qvals.txt 3600   10       1        0.25    12       out0.ring
+gold_5nm.coor gold_qvals.txt 3600   10       2        0.5     12       out1.ring
+gold_5nm.coor gold_qvals.txt 3600   10       4        1.0     12       out2.ring
+gold_5nm.coor gold_qvals.txt 3600   10       8        2.0     12       out3.ring
+gold_5nm.coor gold_qvals.txt 3600   10       16       4.0     12       out4.ring

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/sites.xml	2013-06-17 19:14:57 UTC (rev 6572)
@@ -0,0 +1,39 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="cmtsworkshop">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">cmtsworkshop</profile>
+    <profile namespace="globus" key="ppn">8</profile>
+    <profile namespace="globus" key="project">cmtsworkshop</profile>
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <profile namespace="globus" key="slots">4</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="nodegranularity">1</profile>
+    <profile namespace="globus" key="jobsPerNode">8</profile> <!-- apps per node! -->
+    <profile namespace="karajan" key="jobThrottle">.31</profile> <!-- eg .31 -> 32 -->
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+  </pool>
+
+</config>



From ketan at ci.uchicago.edu  Mon Jun 17 14:16:19 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 14:16:19 -0500 (CDT)
Subject: [Swift-commit] r6573 - SwiftTutorials/CMTS_2013-06-17/basic_swift
Message-ID: <20130617191619.B9F109CC43@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-17 14:16:19 -0500 (Mon, 17 Jun 2013)
New Revision: 6573

Added:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/
Removed:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/swift10/
Log:
renamed for consistency



From ketan at ci.uchicago.edu  Mon Jun 17 14:18:14 2013
From: ketan at ci.uchicago.edu (ketan at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 14:18:14 -0500 (CDT)
Subject: [Swift-commit] r6574 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part10
Message-ID: <20130617191814.957F29CC43@svn.ci.uchicago.edu>

Author: ketan
Date: 2013-06-17 14:18:14 -0500 (Mon, 17 Jun 2013)
New Revision: 6574

Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/README
Log:
 

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/README	2013-06-17 19:16:19 UTC (rev 6573)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part10/README	2013-06-17 19:18:14 UTC (rev 6574)
@@ -23,3 +23,4 @@
 Note that the first row in the particles.dat corresponds to the member names in
 the shootargs type which is how Swift assigns values to structure member
 variables.
+



From davidk at ci.uchicago.edu  Mon Jun 17 14:19:36 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 14:19:36 -0500 (CDT)
Subject: [Swift-commit] r6575 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part08
Message-ID: <20130617191936.3219D9CC43@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 14:19:36 -0500 (Mon, 17 Jun 2013)
New Revision: 6575

Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift
Log:
Use random number to determine how many random numbers to generate. Updated README.


Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README	2013-06-17 19:18:14 UTC (rev 6574)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README	2013-06-17 19:19:36 UTC (rev 6575)
@@ -1,80 +1,14 @@
 
-TOPIC: Example pipelines 
+TOPIC: Example pipeline 
 
+This example shows combining two app calls in a pipeline. There are two apps
+defined in this script: mysim4, and mysim4_filename. 
 
-So far we've been running our "simulations" on the local login host.
-Now we'll run them on the parallel cluster.
+mysim4 takes integer to determine the number of random numbers to generate.
+mysim4_filename reads a file to determine the number of random numbers to generate
 
-The script will be the same as previous, but we change the tool catalog to
-indicate that our "simulation app" (random4.sh) should be run on the
-"westmere" partition of the Midway cluster using the "slurm" scheduler:
+In this example, we use mysim4 to generate a random number. The output of mysim4
+get passed as input to mysim4_filename.
 
-We changed file "apps" from:
-
-  localhost random4  random4.sh
-  localhost average  avg.sh
-
-to:
-
-  cmtsworkshop  random4  random4.sh
-  localhost     average  avg.sh
-
-And we added a pool entry to "sites.xml" file which specifies two "pools" of resources,
-the "local host" pool (which we've been using till now) and the "cmtsworkshop" pool.
-
-To run:
-
-  $ swift p7.swift -steps=10 -range=1000 -count=6 -nsim=100
-
-Note that we're now asking for 100 simulations to be run, each of which
-is to run for 10 steps (ie 10 seconds).
-
-The sites file looks like this:
-
-<config>
-
-  <pool handle="localhost">
-    <execution provider="local"/>
-    <filesystem provider="local"/>
-    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
-  </pool>
-
-  <pool handle="cmtsworkshop">
-    <execution provider="coaster" jobmanager="local:slurm"/>
-
-    <!-- Set partition and account here: -->
-    <profile namespace="globus" key="queue">cmtsworkshop</profile>
-    <profile namespace="globus" key="ppn">8</profile>
-    <profile namespace="globus" key="project">cmtsworkshop</profile> -->
-
-    <!-- Set number of jobs and nodes per job here: -->
-    <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="jobsPerNode">8</profile>    <!-- apps per node -->
-    <profile namespace="karajan" key="jobThrottle">.07</profile> <!-- eg .07 -> 8   -->
-
-    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
-    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
-    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
-
-    <!-- Set data staging model and work dir here: -->
-    <filesystem provider="local"/>
-    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
-
-    <!-- Typically leave these constant: -->
-    <profile namespace="globus" key="slurm.exclusive">false</profile>
-    <profile namespace="globus" key="highOverAllocation">100</profile>
-    <profile namespace="globus" key="lowOverAllocation">100</profile>
-    <profile namespace="karajan" key="initialScore">10000</profile>
-  </pool>
-
-</config>
-
-Try:
-
-  o running more app() calls at once:  change jobsPerNode and jobThrottle
-
-  o requesting more than 1 slurm job at once: change slots
-
-  o requesting nodes in units greater than 1: change maxnodes and nodeGranularity
+To run
+$ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift	2013-06-17 19:18:14 UTC (rev 6574)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p8.swift	2013-06-17 19:19:36 UTC (rev 6575)
@@ -5,9 +5,9 @@
   random4 timesteps range_value count_value stdout=@filename(o);
 }
 
-app (file o) mysim4_filename (int timesteps, file range_value, int count_value)
+app (file o) mysim4_filename (int timesteps, int range_value, file count_value)
 {
-   random4 timesteps @filename(range_value) count_value stdout=@filename(o);
+   random4 timesteps range_value @filename(count_value) stdout=@filename(o);
 }
 
 app (file o) analyze (file s[])
@@ -23,13 +23,13 @@
 
 foreach i in [0:nsim-1] {
 
-  file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
-  simout = mysim4(steps, range, 1);
+  file random <single_file_mapper; file=@strcat("output/sim_", i, ".random.out")>;
+  random = mysim4(steps, range, 1);
 
-  file simout2 <single_file_mapper; file=@strcat("output/sim_", i, ".tmp.out")>;
-  simout2 = mysim4_filename(steps, simout, nsim);
+  file simout <single_file_mapper; file=@strcat("output/sim_", i, ".out")>;
+  simout = mysim4_filename(steps, range, random);
   
-  sims[i] = simout2;
+  sims[i] = simout;
 }
 
 file stats<"output/average.out">;



From davidk at ci.uchicago.edu  Mon Jun 17 14:21:41 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 14:21:41 -0500 (CDT)
Subject: [Swift-commit] r6576 - SwiftTutorials/CMTS_2013-06-17/bin
Message-ID: <20130617192141.E20EB9CC43@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 14:21:41 -0500 (Mon, 17 Jun 2013)
New Revision: 6576

Modified:
   SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
Log:
Updated random4.sh for checking for files


Modified: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random4.sh	2013-06-17 19:19:36 UTC (rev 6575)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random4.sh	2013-06-17 19:21:41 UTC (rev 6576)
@@ -4,8 +4,8 @@
 range=${2:-30000}
 n=${3:-10}
 
-if [ -f "$2" ]; then
-   range=$( cat $2 )
+if [ -f "$3" ]; then
+   n=$( cat $3 )
 fi
 
 sleep $runtime



From wilde at ci.uchicago.edu  Mon Jun 17 14:37:38 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 14:37:38 -0500 (CDT)
Subject: [Swift-commit] r6579 - SwiftTutorials/CMTS_2013-06-17/namd_sweep
Message-ID: <20130617193738.38FFC9CC43@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-17 14:37:38 -0500 (Mon, 17 Jun 2013)
New Revision: 6579

Modified:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
Log:
Updates for faster namd runs with correct vmd extraction.  Changes initfrm and drops minimize.

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf	2013-06-17 19:37:11 UTC (rev 6578)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf	2013-06-17 19:37:38 UTC (rev 6579)
@@ -84,7 +84,7 @@
 #langevinTemp $temperature
 
 
-minimize            10000
+#minimize            10000
 #reinitvels          $temperature
 #run 		    1000000 desired, 200000 min to get non-zero RMSDs
-run                 20000
+run                 10000

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl	2013-06-17 19:37:11 UTC (rev 6578)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl	2013-06-17 19:37:38 UTC (rev 6579)
@@ -13,6 +13,7 @@
 
 # Set the initial frame
 set inifrm 200
+set inifrm 1
 
 set psf cg_clath_cage.psf
 set pdb cg_clath_cage.pdb

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml	2013-06-17 19:37:11 UTC (rev 6578)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml	2013-06-17 19:37:38 UTC (rev 6579)
@@ -16,9 +16,9 @@
 
     <!-- Set number of jobs and nodes per job here: -->
     <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">.03</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="nodegranularity">1</profile>
+    <profile namespace="karajan" key="jobThrottle">.15</profile>
 
     <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
     <profile namespace="globus" key="maxWalltime">00:15:00</profile>



From wilde at ci.uchicago.edu  Mon Jun 17 14:55:09 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 14:55:09 -0500 (CDT)
Subject: [Swift-commit] r6581 - SwiftTutorials/CMTS_2013-06-17/namd_sweep
Message-ID: <20130617195509.3A9729CC43@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-17 14:55:09 -0500 (Mon, 17 Jun 2013)
New Revision: 6581

Modified:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps
Log:
minor edits

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-17 19:40:34 UTC (rev 6580)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-17 19:55:09 UTC (rev 6581)
@@ -21,6 +21,8 @@
 
   swift rmsd.swift -cwd=$PWD -max=0.0 -delta=0.5  # 1 param set
 
+  swift rmsd.swift -cwd=$PWD -max=0.5 -delta=0.5  # 4 param sets (2 x 2)
+
   swift rmsd.swift -cwd=$PWD -max=1.0 -delta=0.5  # 9 param sets (3 x 3)
 
 

Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps	2013-06-17 19:40:34 UTC (rev 6580)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/apps	2013-06-17 19:55:09 UTC (rev 6581)
@@ -1,5 +1,6 @@
+localhost     sh        /bin/bash
+localhost     gensweep  sweep_pd.pl
+localhost     analyze   analyze_pd.pl
 
-localhost     gensweep  sweep_pd.pl   null null null
-localhost     analyze   analyze_pd.pl null null null
+cmtsworkshop  rmsd      rmsd.sh
 
-cmtsworkshop  rmsd      rmsd.sh       null null null



From davidk at ci.uchicago.edu  Mon Jun 17 14:55:12 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 14:55:12 -0500 (CDT)
Subject: [Swift-commit] r6582 - SwiftTutorials/CMTS_2013-06-17/basic_swift
Message-ID: <20130617195512.52F2D9CC43@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 14:55:12 -0500 (Mon, 17 Jun 2013)
New Revision: 6582

Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/README
Log:
Updating list of applications


Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/README	2013-06-17 19:55:09 UTC (rev 6581)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/README	2013-06-17 19:55:12 UTC (rev 6582)
@@ -50,3 +50,10 @@
 part06: Add arguments to the "simulation" program
 
 part07: Run the "simulations" on the parallel cluster
+
+part08: Example of pipeline - sending output of one app to the input of another app
+
+part09: Example pipeline using readData
+
+part10: Example readData to read file with multiple fields into a struct
+



From davidk at ci.uchicago.edu  Mon Jun 17 15:17:58 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 15:17:58 -0500 (CDT)
Subject: [Swift-commit] r6584 - in
	SwiftTutorials/CMTS_2013-06-17/basic_swift: . part08 part11
Message-ID: <20130617201758.AF1979CC43@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-17 15:17:58 -0500 (Mon, 17 Jun 2013)
New Revision: 6584

Added:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/p11.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/sites.xml
Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README
Log:
Part11


Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/README	2013-06-17 20:01:51 UTC (rev 6583)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/README	2013-06-17 20:17:58 UTC (rev 6584)
@@ -57,3 +57,4 @@
 
 part10: Example readData to read file with multiple fields into a struct
 
+part11: Example using composite functions

Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README	2013-06-17 20:01:51 UTC (rev 6583)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README	2013-06-17 20:17:58 UTC (rev 6584)
@@ -10,3 +10,4 @@
 
 To run
 $ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/README	2013-06-17 20:17:58 UTC (rev 6584)
@@ -0,0 +1,16 @@
+
+TOPIC: Example pipeline showing composite functions
+
+This example shows composite functions. The function called generate_randoms
+combines two app calls and returns only the result we care about.
+
+(file o) generate_randoms (int timesteps, int range_value, int count_value)
+{
+  file tmp;
+  tmp = mysim4(timesteps, range_value, 1);
+  int rand = readData(tmp);
+  o = mysim4(timesteps, range_value, rand);
+}
+
+To run
+$ swift p11.swift -steps=10 -range=100 -count=6 -nsim=1

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/apps
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/apps	2013-06-17 20:17:58 UTC (rev 6584)
@@ -0,0 +1,2 @@
+cmtsworkshop random4  random4.sh
+localhost    average  avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/p11.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/p11.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/p11.swift	2013-06-17 20:17:58 UTC (rev 6584)
@@ -0,0 +1,35 @@
+type file;
+
+app (file o) mysim4 (int timesteps, int range_value, int count_value)
+{
+  random4 timesteps range_value count_value stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+  average @filenames(s) stdout=@filename(o);
+}
+
+(file o) generate_randoms (int timesteps, int range_value, int count_value)
+{
+  file tmp;
+  tmp = mysim4(timesteps, range_value, 1);
+  int rand = readData(tmp);
+  o = mysim4(timesteps, range_value, rand);
+}
+
+
+file sims[];
+int  nsim  = @toInt(@arg("nsim",  "10"));
+int  steps = @toInt(@arg("steps", "1"));
+int  range = @toInt(@arg("range", "100"));
+int  count = @toInt(@arg("count", "10"));
+
+foreach i in [0:nsim-1] {
+  file simout <single_file_mapper; file=@strcat("output/sim_", i, ".tmp.out")>;
+  simout = generate_randoms(steps, range, count);
+  sims[i] = simout;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part11/sites.xml	2013-06-17 20:17:58 UTC (rev 6584)
@@ -0,0 +1,39 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="cmtsworkshop">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">cmtsworkshop</profile>
+    <profile namespace="globus" key="ppn">8</profile>
+    <profile namespace="globus" key="project">cmtsworkshop</profile>
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <profile namespace="globus" key="slots">4</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="nodegranularity">1</profile>
+    <profile namespace="globus" key="jobsPerNode">8</profile> <!-- apps per node! -->
+    <profile namespace="karajan" key="jobThrottle">.31</profile> <!-- eg .31 -> 32 -->
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+  </pool>
+
+</config>



From wilde at ci.uchicago.edu  Mon Jun 17 15:23:15 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 15:23:15 -0500 (CDT)
Subject: [Swift-commit] r6585 - SwiftTutorials/CMTS_2013-06-17/namd_sweep
Message-ID: <20130617202315.2FEAB9CC43@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-17 15:23:15 -0500 (Mon, 17 Jun 2013)
New Revision: 6585

Added:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsdx2.swift
Log:
new example.

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsdx2.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsdx2.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsdx2.swift	2013-06-17 20:23:15 UTC (rev 6585)
@@ -0,0 +1,56 @@
+type file;
+
+global string cwd = @arg("cwd",".");
+
+app (file blist) genConfigs (dir, string max, string delta)
+{
+  gensweep dir max delta stdout=@blist;
+}
+
+app (file rmsdout, file rmsd) rmsd (file i[], string id)
+{
+  rmsd id;
+}
+
+app (file plot_data) analyze (file[] rmsdfiles)
+{
+  analyze @filenames(rmsdfiles) stdout=@plot_data;
+}
+
+global file pdb      <"cg_clath_cage.pdb">;
+global file psf      <"cg_clath_cage.psf">;
+
+string sweepMax=@arg("max","0.6"), sweepDelta=@arg("delta","0.5");
+
+sweep(string beads[],string set)
+{
+  file rmsds[];
+  foreach beadid, i in beads {
+    file conf   <single_file_mapper; file=@strcat(set,"/CONF/",beadid,".conf")>;
+    file inp    <single_file_mapper; file=@strcat(set,"/PAR/", beadid,".inp")>;
+    file vmdtcl <single_file_mapper; file=@strcat(set,"/VMD/", beadid,".tcl")>;
+  
+    file log    <single_file_mapper; file=@strcat(set,"/OUT/", beadid,".log")>;
+    file dat    <single_file_mapper; file=@strcat(set,"/RMSD/",beadid,".dat")>;
+  
+    tracef("Processing bead ID %s\n", beadid);
+  
+    (log,dat) = rmsd([conf,pdb,psf,inp,vmdtcl], beadid);
+    rmsds[i] = dat;
+  }
+   
+  file plot_out <single_file_mapper; file=@strcat(set,"/OUT/plot_pd.txt")>;
+  plot_out = analyze(rmsds);
+}
+
+
+string bead_set_1[] = readData(genConfigs("0.2", "0.1"));
+
+# string bead_set_2[] = readData(genConfigs("0.5", "0.5"));
+
+sweep(bead_set_1,"set1");
+
+
+
+
+



From swift at ci.uchicago.edu  Thu Jun 20 02:15:02 2013
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Thu, 20 Jun 2013 02:15:02 -0500 (CDT)
Subject: [Swift-commit] cog r3674
Message-ID: <20130620071502.E91E28D0009E@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3674 | hategan | 2013-06-20 02:11:48 -0500 (Thu, 20 Jun 2013) | 1 line

expose cwd as a global variable
------------------------------------------------------------------------
Index: modules/karajan/src/org/globus/cog/karajan/workflow/ExecutionContext.java
===================================================================
--- modules/karajan/src/org/globus/cog/karajan/workflow/ExecutionContext.java	(revision 3673)
+++ modules/karajan/src/org/globus/cog/karajan/workflow/ExecutionContext.java	(working copy)
@@ -147,6 +147,7 @@
 		stack.setVar("user.home", System.getProperty("user.home"));
 		stack.setVar("user.name", System.getProperty("user.name"));
 		stack.setVar(CMDLINE_ARGS, arguments);
+		stack.setVar("cwd", cwd);
 		setEnvironmentVariables(stack);
 	}
 


From wilde at ci.uchicago.edu  Tue Jun 25 15:06:02 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Tue, 25 Jun 2013 15:06:02 -0500 (CDT)
Subject: [Swift-commit] r6588 - SwiftTutorials/CMTS_2013-06-17
Message-ID: <20130625200602.C3F9A9CCC2@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-25 15:06:02 -0500 (Tue, 25 Jun 2013)
New Revision: 6588

Modified:
   SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
Log:
Final presentation, for web posting.

Modified: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
===================================================================
(Binary files differ)



From davidk at ci.uchicago.edu  Thu Jun 27 15:45:29 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Thu, 27 Jun 2013 15:45:29 -0500 (CDT)
Subject: [Swift-commit] r6589 - SwiftApps
Message-ID: <20130627204529.8595D9CCC2@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-27 15:45:29 -0500 (Thu, 27 Jun 2013)
New Revision: 6589

Added:
   SwiftApps/FitPosOrStrains/
Log:
FitPosOrStrains 




From davidk at ci.uchicago.edu  Thu Jun 27 15:54:53 2013
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Thu, 27 Jun 2013 15:54:53 -0500 (CDT)
Subject: [Swift-commit] r6590 - SwiftApps
Message-ID: <20130627205453.606A29CC92@svn.ci.uchicago.edu>

Author: davidk
Date: 2013-06-27 15:54:53 -0500 (Thu, 27 Jun 2013)
New Revision: 6590

Added:
   SwiftApps/strains/
Removed:
   SwiftApps/FitPosOrStrains/
Log:
Rename - directory can't have a capital 'S' in it




From wilde at ci.uchicago.edu  Sun Jun 16 08:30:30 2013
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 16 Jun 2013 13:30:30 -0000
Subject: [Swift-commit] r6559 - in SwiftTutorials/CMTS_2013-06-17: .
	basic_swift basic_swift/data basic_swift/part01
	basic_swift/part02 basic_swift/part03 basic_swift/part04
	basic_swift/part05 basic_swift/part06 basic_swift/part07 bin
	namd_sweep
Message-ID: <20130616133029.069F09CC8F@svn.ci.uchicago.edu>

Author: wilde
Date: 2013-06-16 08:30:27 -0500 (Sun, 16 Jun 2013)
New Revision: 6559

Added:
   SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
   SwiftTutorials/CMTS_2013-06-17/basic_swift/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/data/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc
   SwiftTutorials/CMTS_2013-06-17/bin/
   SwiftTutorials/CMTS_2013-06-17/bin/avg.sh
   SwiftTutorials/CMTS_2013-06-17/bin/cleanup
   SwiftTutorials/CMTS_2013-06-17/bin/highest.sh
   SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh
   SwiftTutorials/CMTS_2013-06-17/bin/makeinput
   SwiftTutorials/CMTS_2013-06-17/bin/myapp
   SwiftTutorials/CMTS_2013-06-17/bin/random.sh
   SwiftTutorials/CMTS_2013-06-17/bin/random2.sh
   SwiftTutorials/CMTS_2013-06-17/bin/random3.sh
   SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc
   SwiftTutorials/CMTS_2013-06-17/setup.csh
   SwiftTutorials/CMTS_2013-06-17/setup.sh
Log:
Initial revision for this tutorial.

Added: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,52 @@
+
+INTRODUCTION TO SWIFT
+
+SETUP
+
+Obtain the tutorial package
+
+Change directory into the created directory called "tutorial"
+
+This directory contains:
+
+bin:     script tools for the tutorial
+scripts: Swift scripts for the tutorial
+
+TO START, do:
+
+$ source setup.sh # to add tutorial programs to your PATH
+
+...and then verify:
+
+$ random.sh # should be found in your PATH now
+
+
+
+The tutorial is arranged in parts.  To begin:
+
+$ cd part01
+$ cat README
+
+When finished:
+
+$ cd ../part02  # etc
+
+In each part, you can type "cleanup" after running a few swift scripts
+to remove the old logs that build up, and (usually) the output files.
+
+
+The topics of the tutorial parts are:
+
+part01: First Swift script - run a "simulation" program, random.sh
+
+part02: Specifying the output filenames
+
+part03: Run many instances of a "simulation" program in a foreach() loop
+
+part04: run a program in a foreach() loop with explicitly named output files.
+
+part05: Add a program that "analyzes" the output the parallel simulations
+
+part06: Add arguments to the "simulation" program
+
+part07: Run the "simulations" on the parallel cluster

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+Hi Swift!

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,40 @@
+
+TOPIC: First Swift script - run a "simulation" program, random.sh
+
+
+Verify that random.sh is in your path, and that it works:
+
+$ which random.sh
+$ random.sh
+
+Study the Swift program:
+
+$ cat p1.swift
+
+Examine the tool catalog file:
+
+$ cat tc
+
+Run the program:
+
+$ swift -tc.file tc p1.swift
+
+Look at the output:
+
+$ cat _concurrent/*
+
+Look at the other files generated:
+
+$ ls -l
+
+We'll talk more about these files later
+
+$ cleanup
+
+Then test the sript a few more times.
+
+$ swift -tc.file tc p1.swift; cat _concurrent/*
+
+$ swift -tc.file tc p1.swift; cat _concurrent/*
+
+$ swift -tc.file tc p1.swift; cat _concurrent/*

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,8 @@
+type file;
+
+app (file o) mysim ()
+{
+  random stdout=@filename(o);
+}
+
+file f = mysim();

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+localhost random random.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,33 @@
+
+TOPIC: specifying the output filenames
+
+Study the Swift program:
+
+$ cat p2.swift
+
+Examine the tool catalog file:
+
+$ cat tc
+
+Run the program:
+
+$ swift -tc.file tc p2.swift
+
+Look at the output:
+
+$ cat sim.out
+
+Then test the sript a few more times.
+
+$ swift -tc.file tc p1.swift; cat sim.out
+
+$ swift -tc.file tc p1.swift; cat sim.out
+
+$ swift -tc.file tc p1.swift; cat sim.out
+
+Things to try:
+
+- change the output filename
+
+- add a dir component to the output filename
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,9 @@
+type file;
+
+app (file o) mysim ()
+{
+  random stdout=@filename(o);
+}
+
+file f<"sim.out">;
+f = mysim();

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,9 @@
+type file;
+
+app (file o) mysim ()
+{
+  random stdout=@filename(o);
+}
+
+file f<"output/sim.out">;
+f = mysim();

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+localhost random random.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,20 @@
+
+TOPIC: run many instances of a "simulation" program in a foreach() loop
+
+
+Run the program:
+
+$ swift -tc.file tc p3.swift
+
+Look at the output:
+
+$ cd _concurrent
+$ ls -l
+$ cat *
+
+Look at the order in which the files were written:
+
+$ ls -lt
+
+We'll come back to this...
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,11 @@
+type file;
+
+app (file o) mysim ()
+{
+  random stdout=@filename(o);
+}
+
+foreach i in [0:9] {
+  file f = mysim();
+}
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+localhost random random.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,42 @@
+
+TOPIC: run a program in a foreach() loop with explicitly named output files.
+
+
+Study the program:
+
+- @strcat() is a Swift builtin function (the @name() form is used for many but not all builtins)
+
+- Note that @strcat() coerces numeric args to strings 
+
+- <"filename"> was a shorthand for <single_file_mapper;...> but the latter is more flexible.
+
+Run the program:
+
+$ swift -tc.file tc p4.swift
+
+Look at the output:
+
+$ cd output
+$ ls -l
+$ cat *
+
+
+Try:
+
+- Adjust the script to take the number of simulations to do from the command line
+
+  @arg("argname") returns arguments after the .swift script on the swift command line:
+
+    swift -tc.file tc p4.swift -myarg1=value1 ...
+
+  @arg("argname","default") returns "default" if the argname is not given on the command line
+
+  @toInt() converts strings to integers:
+
+    @toInt(@arg("myArg1"))
+
+
+- trace(expr1,...) traces expressions on stdout.
+
+  Try inserting a few traces.  But remember: Swift is *very* concurrent!
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,12 @@
+type file;
+
+app (file o) mysim ()
+{
+  random stdout=@filename(o);
+}
+
+foreach i in [0:9] {
+  file f <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+  f = mysim();
+}
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+localhost random random.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,51 @@
+
+
+TOPIC: Add a program that "analyzes" the output the parallel simulations
+
+
+Study the program:
+
+We added a new app to "analyze" all the simulation outputs:
+
+app (file o) analyze (file s[])
+{
+  average @filenames(s) stdout=@filename(o);
+}
+
+Nots that it expects an array of files as its input, and that
+it uses @filenames() to place the names of all the files on 
+the command line to the "average" program.
+
+Average does:  
+--------------------
+#! /bin/sh
+
+awk '
+
+{ sum += $1}
+
+END { print sum/NR }
+' $*
+-------------------
+
+
+At the end of the script we insert:
+
+file stats<"output/average.out">;
+stats = analyze(sims);
+
+...which runs the analysis *after* all the simulations complete.
+
+
+Run the program:
+
+$ swift -tc.file tc p5.swift
+
+Look at the output:
+
+$ cd output
+$ ls -l
+$ cat sim*.out
+$ cat average.out
+
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,24 @@
+type file;
+
+app (file o) mysim ()
+{
+  random stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+  average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+
+int nsim = @toInt(@arg("nsim","10"));
+
+foreach i in [0:nsim-1] {
+  file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+  simout = mysim();
+  sims[i] = simout;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+localhost random  random.sh
+localhost average avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,28 @@
+
+TOPIC: add arguments to the "simulation" program
+(to control number of steps, range of output, and number of output lines)
+
+
+Test new versions of the "simulation" program:
+
+  random.sh                            # original
+  random2.sh [runtime]                 # runtime in seconds; defaults to 1 sec
+  random3.sh [runtime] [range]         # requests random numbers in {0:range-1}
+  random4.sh [runtime] [range] [count] # requests "count" random numbers in {0:range}
+
+p6.swift changes to random2 for the simulation program and adds an argument.
+
+Run the program:
+
+$ swift -tc.file tc p6.swift -steps=3  # each simulation takes 3 seconds
+
+Next we need to use the parallel cluster for our simulations!
+
+Try:
+
+- change to random3.sh and add the extra argument "range"
+
+- change to random4.sh and add yet another argument "count"
+
+
+

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,25 @@
+type file;
+
+app (file o) mysim2 (int timesteps)
+{
+  random2 timesteps stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+  average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+int  nsim = @toInt(@arg("nsim","10"));
+
+int steps = @toInt(@arg("steps","1"));
+
+foreach i in [0:nsim-1] {
+  file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+  simout = mysim2(steps);
+  sims[i] = simout;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+localhost random2  random2.sh
+localhost average avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,81 @@
+
+TOPIC: Run the "simulations" on the parallel cluster
+
+
+Til now we've been running our "simulations" on the local login host.
+
+Now we'll run them on the parallel cluster.
+
+The script will be the same as previous, but we change the tool catalog to
+indicate that our "simulation app" (random4.sh) should be run on the
+"westmere" partition of the Midway cluster using the "slurm" scheduler:
+
+We changed file "tc" from:
+
+localhost random4  random4.sh
+localhost average  avg.sh
+
+to:
+
+westmere  random4  random4.sh
+localhost average  avg.sh
+
+And we added the "sites.xml" file which specifies two "pools" of resources,
+the "local host" pool (which we've been using till now) and the "westmere" pool.
+
+To run, we now add the sites.xml file to the swift command line:
+
+$ swift -tc.file tc -sites.file sites.xml p7.swift -steps=10 -range=1000 -count=6 -nsim=100
+
+Note that we're now asking for 100 simulations to be run, each of which
+is to run for 10 steps (ie 10 seconds).
+
+The sites file looks like this:
+
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="westmere">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">westmere</profile>
+    <profile namespace="globus" key="ppn">12</profile>
+    <!-- <profile namespace="globus" key="project">pi-wilde</profile> -->
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <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="jobsPerNode">12</profile> <!-- apps per node! -->
+    <profile namespace="karajan" key="jobThrottle">.11</profile> <!-- eg .11 -> 12 -->
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+  </pool>
+
+</config>
+
+Try:
+
+- running more app() calls at once:  change jobsPerNode and jobThrottle
+
+- requesting more than 1 slurm job at once: change slots
+
+- requesting nodes in units greater than 1: change maxnodes and nodeGranularity

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,27 @@
+type file;
+
+app (file o) mysim4 (int timesteps, int range, int count)
+{
+  random4 timesteps range count stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+  average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+int  nsim  = @toInt(@arg("nsim",  "10"));
+
+int  steps = @toInt(@arg("steps", "1"));
+int  range = @toInt(@arg("range", "100"));
+int  count = @toInt(@arg("count", "10"));
+
+foreach i in [0:nsim-1] {
+  file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+  simout = mysim4(steps,range,count);
+  sims[i] = simout;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,39 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="westmere">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">westmere</profile>
+    <profile namespace="globus" key="ppn">12</profile>
+    <!-- <profile namespace="globus" key="project">pi-wilde</profile> -->
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <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="jobsPerNode">12</profile> <!-- apps per node! -->
+    <profile namespace="karajan" key="jobThrottle">.11</profile> <!-- eg .11 -> 12 -->
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+  </pool>
+
+</config>

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+westmere  random4  random4.sh
+localhost average  avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/bin/avg.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/avg.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/avg.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,9 @@
+#! /bin/sh
+
+awk '
+
+{ sum += $1}
+
+END { print sum/NR }
+' $*
+


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/avg.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/cleanup
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/cleanup	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/cleanup	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+echo Removing:
+echo
+ls -ltd *log *.d swiftwork _concurrent output *.kml *.swiftx swift.log 2>/dev/null
+echo
+echo Enter y to proceed:
+read ok
+if [ _$ok = _y -o _$ok = _Y -o _$ok = _yes ]; then
+  echo
+  set -x
+  rm -rf *log *.d swiftwork _concurrent output *.kml *.swiftx swift.log
+else
+  echo
+  echo No files removed.
+fi
+


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/cleanup
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/highest.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/highest.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/highest.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+#! /bin/sh
+sort -nr | head -$1


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/highest.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,5 @@
+#! /bin/sh
+
+# Print the lowest N numbers from standard input (deafult: lowest 3)
+
+sort -n | head -${1:-3}


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/makeinput
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/makeinput	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/makeinput	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,22 @@
+#! /bin/sh
+
+nfiles=${1:-10}
+
+rm -rf input
+mkdir input
+cp ../data/sat/t? input/
+( cd input
+  n=0
+  for h in $(seq -w 00 99); do
+    for v in $(seq -w 00 99); do
+      n=$((n+1))
+      if [ $n -gt $nfiles ]; then
+        break;
+      else
+        f=t$(($RANDOM%10))
+        ln $f h${h}v${v}.rgb
+      fi
+    done
+  done
+  rm t?
+)


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/makeinput
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/myapp
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/myapp	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/myapp	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+hostname -f
+date
+sleep 3
+ps -u $USER -H -f


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/myapp
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/random.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+#! /bin/sh
+echo $RANDOM


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/random2.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random2.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random2.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,7 @@
+#! /bin/sh
+
+runtime=${1:-0}
+
+sleep $runtime
+
+echo $(($RANDOM))


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random2.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/random3.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random3.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random3.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,10 @@
+#! /bin/sh
+
+runtime=${1:-0}
+range=${2:-30000}
+
+sleep $runtime
+
+echo $(($RANDOM%range))
+
+


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random3.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random4.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random4.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,12 @@
+#! /bin/sh
+
+runtime=${1:-0}
+range=${2:-30000}
+n=${3:-10}
+
+sleep $runtime
+
+for ((i=0;i<n;i++)); do
+  echo $(($RANDOM%range))
+done
+


Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,17 @@
+?These files perform a brute force parameter search in two dimensions
+in order to find the parameters that minimize the root mean square 
+deviation (RMSD) of the system from an ideal structure.
+
+sweep_pd.pl ? Loops over all possible parameter pairs, creates from 
+templates a parameter file (par_cg_clath.temp.inp), a NAMD input file 
+(cg_clath_cage.temp.conf), and a VMD script (rmsd.temp.tcl) for 
+calculating the RMSD. The script then submits a single pbs job (pxdt.pbs) 
+for each parameter pair. 
+
+plot_pd.pl ? After all of the simulations have been performed, this 
+script reads in the RMSD values for each parameter pair and writes the 
+data in a gnuplot 2D plot data format. This script also prints to screen 
+the minimum RMSD and the parameter values corresponding to that value.
+
+-Frank X. Vazquez fxv at uchicago.edu
+7-13-2012

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,5 @@
+Swift in PATH
+
+swift module
+
+account to use  - pi_gavoth
\ No newline at end of file

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,40 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my $rmsdmin = 123456789.0;  # Set large number to find min RMSD
+my $b1rmsdmin=0.0;
+my $b2rmsdmin=0.0;
+my $b1name;
+my $b2name;
+
+for(my $i=0; $i<=$#ARGV; $i++) {
+
+  my $filename =  $ARGV[$i];
+  my $basename = basename($filename,".dat");
+  my @params = split(/_/,$basename);
+
+  $b1name = $params[0];
+  my $b1 =  $params[1];
+  $b2name = $params[2];
+  my $b2 =  $params[3];
+
+  open(INPUT, "<", $filename);
+  my $_ = <INPUT>;
+  my @data = split(/ +/,$_);
+  my $rmsd=$data[2]*1.0;
+			
+  # Find Minimum
+  if ($rmsd<$rmsdmin) {
+    $rmsdmin=$rmsd;
+    $b1rmsdmin=$b1;
+    $b2rmsdmin=$b2;
+  }
+	
+  printf "%0.3f %0.3f %0.9f\n", $b1, $b2, $rmsd;			
+  close(INPUT);
+}		
+
+printf "\nMinimum Values: RMSD=%0.9f eps_$b1name=%0.3f eps_$b2name=%0.3f\n", $rmsdmin, $b1rmsdmin, $b2rmsdmin; 


Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,7 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=false
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,470 @@
+REMARK original generated coordinate pdb file
+ATOM      1  HB0 CLA X   1      92.981 164.025 331.473  1.00  0.00      A0    
+ATOM      2  PX1 CLA X   1     136.274 211.422 275.579  1.00  0.00      A0    
+ATOM      3  DT1 CLA X   1     200.662 208.148 159.192  1.00  0.00      A0    
+ATOM      4  AK1 CLA X   1     243.304 111.359  96.656  1.00  0.00      A0    
+ATOM      5  LT1 CLA X   1     223.763  18.662  85.497  1.00  0.00      A0    
+ATOM      6  PX2 CLA X   1     126.815  89.000 352.917  1.00  0.00      A0    
+ATOM      7  DT2 CLA X   1     128.673 -47.724 333.137  1.00  0.00      A0    
+ATOM      8  AK2 CLA X   1      49.929-132.718 287.973  1.00  0.00      A0    
+ATOM      9  LT2 CLA X   1     -24.828-143.462 235.435  1.00  0.00      A0    
+ATOM     10  PX3 CLA X   1      10.483 180.619 340.613  1.00  0.00      A0    
+ATOM     11  DT3 CLA X   1     -95.424 204.239 265.860  1.00  0.00      A0    
+ATOM     12  AK3 CLA X   1    -101.877 231.712 146.926  1.00  0.00      A0    
+ATOM     13  LT3 CLA X   1     -58.664 217.336  66.678  1.00  0.00      A0    
+ATOM     14  HB0 CLA X   1     152.597 263.250 182.367  1.00  0.00      B0    
+ATOM     15  PX1 CLA X   1     120.437 238.824 256.749  1.00  0.00      B0    
+ATOM     16  DT1 CLA X   1      18.642 174.399 313.695  1.00  0.00      B0    
+ATOM     17  AK1 CLA X   1     -88.420 151.452 262.690  1.00  0.00      B0    
+ATOM     18  LT1 CLA X   1    -128.527 143.156 177.443  1.00  0.00      B0    
+ATOM     19  PX2 CLA X   1      99.230 306.155 133.576  1.00  0.00      B0    
+ATOM     20  DT2 CLA X   1      21.433 316.316  21.125  1.00  0.00      B0    
+ATOM     21  AK2 CLA X   1      26.263 266.923 -95.151  1.00  0.00      B0    
+ATOM     22  LT2 CLA X   1      58.151 195.850-145.576  1.00  0.00      B0    
+ATOM     23  PX3 CLA X   1     223.451 225.604 155.002  1.00  0.00      B0    
+ATOM     24  DT3 CLA X   1     275.701 105.136 138.751  1.00  0.00      B0    
+ATOM     25  AK3 CLA X   1     235.267   1.374 186.863  1.00  0.00      B0    
+ATOM     26  LT3 CLA X   1     155.819 -36.632 217.712  1.00  0.00      B0    
+ATOM     27  HB0 CLA X   1     286.805 165.855  93.118  1.00  0.00      C0    
+ATOM     28  PX1 CLA X   1     303.935 101.204 144.420  1.00  0.00      C0    
+ATOM     29  DT1 CLA X   1     251.178  21.712 232.998  1.00  0.00      C0    
+ATOM     30  AK1 CLA X   1     142.263  28.038 287.691  1.00  0.00      C0    
+ATOM     31  LT1 CLA X   1      50.945  58.195 270.101  1.00  0.00      C0    
+ATOM     32  PX2 CLA X   1     234.620 227.534 121.486  1.00  0.00      C0    
+ATOM     33  DT2 CLA X   1     104.398 278.700 124.820  1.00  0.00      C0    
+ATOM     34  AK2 CLA X   1       0.965 276.330  50.135  1.00  0.00      C0    
+ATOM     35  LT2 CLA X   1     -42.600 228.187 -18.776  1.00  0.00      C0    
+ATOM     36  PX3 CLA X   1     303.934 158.846  11.493  1.00  0.00      C0    
+ATOM     37  DT3 CLA X   1     291.514  88.537-103.359  1.00  0.00      C0    
+ATOM     38  AK3 CLA X   1     250.991 -24.248-144.395  1.00  0.00      C0    
+ATOM     39  LT3 CLA X   1     191.706 -94.728-126.760  1.00  0.00      C0    
+ATOM     40  HB0 CLA X   1     -95.559 162.537 331.473  1.00  0.00      A1    
+ATOM     41  PX1 CLA X   1    -114.959 223.728 275.579  1.00  0.00      A1    
+ATOM     42  DT1 CLA X   1     -79.930 277.853 159.192  1.00  0.00      A1    
+ATOM     43  AK1 CLA X   1      25.213 266.386  96.656  1.00  0.00      A1    
+ATOM     44  LT1 CLA X   1      95.719 203.115  85.497  1.00  0.00      A1    
+ATOM     45  PX2 CLA X   1     -13.669 154.325 352.917  1.00  0.00      A1    
+ATOM     46  DT2 CLA X   1     105.666  87.572 333.137  1.00  0.00      A1    
+ATOM     47  AK2 CLA X   1     139.902 -23.120 287.973  1.00  0.00      A1    
+ATOM     48  LT2 CLA X   1     111.827 -93.233 235.435  1.00  0.00      A1    
+ATOM     49  PX3 CLA X   1    -151.180  99.388 340.613  1.00  0.00      A1    
+ATOM     50  DT3 CLA X   1    -224.588  19.480 265.860  1.00  0.00      A1    
+ATOM     51  AK3 CLA X   1    -251.607  27.627 146.926  1.00  0.00      A1    
+ATOM     52  LT3 CLA X   1    -217.550  57.864  66.678  1.00  0.00      A1    
+ATOM     53  HB0 CLA X   1    -151.683 263.777 182.367  1.00  0.00      B1    
+ATOM     54  PX1 CLA X   1    -146.609 223.714 256.749  1.00  0.00      B1    
+ATOM     55  DT1 CLA X   1    -141.713 103.344 313.695  1.00  0.00      B1    
+ATOM     56  AK1 CLA X   1    -175.371  -0.848 262.690  1.00  0.00      B1    
+ATOM     57  LT1 CLA X   1    -188.241 -39.730 177.443  1.00  0.00      B1    
+ATOM     58  PX2 CLA X   1    -215.523 239.014 133.576  1.00  0.00      B1    
+ATOM     59  DT2 CLA X   1    -263.221 176.720  21.125  1.00  0.00      B1    
+ATOM     60  AK2 CLA X   1    -218.030 156.206 -95.151  1.00  0.00      B1    
+ATOM     61  LT2 CLA X   1    -140.536 148.285-145.576  1.00  0.00      B1    
+ATOM     62  PX3 CLA X   1     -83.654 306.316 155.002  1.00  0.00      B1    
+ATOM     63  DT3 CLA X   1      46.800 291.332 138.751  1.00  0.00      B1    
+ATOM     64  AK3 CLA X   1     116.444 204.434 186.863  1.00  0.00      B1    
+ATOM     65  LT3 CLA X   1     109.634 116.627 217.712  1.00  0.00      B1    
+ATOM     66  HB0 CLA X   1      -0.232 331.308  93.118  1.00  0.00      C1    
+ATOM     67  PX1 CLA X   1      64.322 313.817 144.420  1.00  0.00      C1    
+ATOM     68  DT1 CLA X   1     106.786 228.382 232.998  1.00  0.00      C1    
+ATOM     69  AK1 CLA X   1      46.850 137.222 287.691  1.00  0.00      C1    
+ATOM     70  LT1 CLA X   1     -24.926  73.217 270.101  1.00  0.00      C1    
+ATOM     71  PX2 CLA X   1     -79.740 316.953 121.486  1.00  0.00      C1    
+ATOM     72  DT2 CLA X   1    -189.163 229.761 124.820  1.00  0.00      C1    
+ATOM     73  AK2 CLA X   1    -238.827 139.001  50.135  1.00  0.00      C1    
+ATOM     74  LT2 CLA X   1    -218.915  77.201 -18.776  1.00  0.00      C1    
+ATOM     75  PX3 CLA X   1      14.402 342.637  11.493  1.00  0.00      C1    
+ATOM     76  DT3 CLA X   1      69.082 296.727-103.359  1.00  0.00      C1    
+ATOM     77  AK3 CLA X   1     146.495 205.240-144.395  1.00  0.00      C1    
+ATOM     78  LT3 CLA X   1     177.890 118.659-126.760  1.00  0.00      C1    
+ATOM     79  HB0 CLA X   1    -188.541  -1.488 331.473  1.00  0.00      A2    
+ATOM     80  PX1 CLA X   1    -251.234  12.306 275.579  1.00  0.00      A2    
+ATOM     81  DT1 CLA X   1    -280.592  69.705 159.192  1.00  0.00      A2    
+ATOM     82  AK1 CLA X   1    -218.091 155.028  96.656  1.00  0.00      A2    
+ATOM     83  LT1 CLA X   1    -128.043 184.453  85.497  1.00  0.00      A2    
+ATOM     84  PX2 CLA X   1    -140.484  65.324 352.917  1.00  0.00      A2    
+ATOM     85  DT2 CLA X   1     -23.007 135.296 333.137  1.00  0.00      A2    
+ATOM     86  AK2 CLA X   1      89.973 109.599 287.973  1.00  0.00      A2    
+ATOM     87  LT2 CLA X   1     136.656  50.229 235.435  1.00  0.00      A2    
+ATOM     88  PX3 CLA X   1    -161.662 -81.231 340.613  1.00  0.00      A2    
+ATOM     89  DT3 CLA X   1    -129.164-184.759 265.860  1.00  0.00      A2    
+ATOM     90  AK3 CLA X   1    -149.729-204.084 146.926  1.00  0.00      A2    
+ATOM     91  LT3 CLA X   1    -158.887-159.472  66.678  1.00  0.00      A2    
+ATOM     92  HB0 CLA X   1    -304.279   0.528 182.367  1.00  0.00      B2    
+ATOM     93  PX1 CLA X   1    -267.047 -15.111 256.749  1.00  0.00      B2    
+ATOM     94  DT1 CLA X   1    -160.355 -71.055 313.695  1.00  0.00      B2    
+ATOM     95  AK1 CLA X   1     -86.951-152.300 262.690  1.00  0.00      B2    
+ATOM     96  LT1 CLA X   1     -59.713-182.886 177.443  1.00  0.00      B2    
+ATOM     97  PX2 CLA X   1    -314.754 -67.142 133.576  1.00  0.00      B2    
+ATOM     98  DT2 CLA X   1    -284.654-139.597  21.125  1.00  0.00      B2    
+ATOM     99  AK2 CLA X   1    -244.294-110.717 -95.151  1.00  0.00      B2    
+ATOM    100  LT2 CLA X   1    -198.687 -47.565-145.576  1.00  0.00      B2    
+ATOM    101  PX3 CLA X   1    -307.104  80.712 155.002  1.00  0.00      B2    
+ATOM    102  DT3 CLA X   1    -228.901 186.196 138.751  1.00  0.00      B2    
+ATOM    103  AK3 CLA X   1    -118.823 203.060 186.863  1.00  0.00      B2    
+ATOM    104  LT3 CLA X   1     -46.185 153.259 217.712  1.00  0.00      B2    
+ATOM    105  HB0 CLA X   1    -287.037 165.452  93.118  1.00  0.00      C2    
+ATOM    106  PX1 CLA X   1    -239.613 212.613 144.420  1.00  0.00      C2    
+ATOM    107  DT1 CLA X   1    -144.392 206.670 232.998  1.00  0.00      C2    
+ATOM    108  AK1 CLA X   1     -95.413 109.184 287.691  1.00  0.00      C2    
+ATOM    109  LT1 CLA X   1     -75.871  15.022 270.101  1.00  0.00      C2    
+ATOM    110  PX2 CLA X   1    -314.360  89.420 121.486  1.00  0.00      C2    
+ATOM    111  DT2 CLA X   1    -293.560 -48.939 124.820  1.00  0.00      C2    
+ATOM    112  AK2 CLA X   1    -239.791-137.330  50.135  1.00  0.00      C2    
+ATOM    113  LT2 CLA X   1    -176.315-150.986 -18.776  1.00  0.00      C2    
+ATOM    114  PX3 CLA X   1    -289.532 183.791  11.493  1.00  0.00      C2    
+ATOM    115  DT3 CLA X   1    -222.432 208.190-103.359  1.00  0.00      C2    
+ATOM    116  AK3 CLA X   1    -104.496 229.489-144.395  1.00  0.00      C2    
+ATOM    117  LT3 CLA X   1     -13.817 213.386-126.760  1.00  0.00      C2    
+ATOM    118  HB0 CLA X   1     -92.981-164.025 331.473  1.00  0.00      A3    
+ATOM    119  PX1 CLA X   1    -136.274-211.422 275.579  1.00  0.00      A3    
+ATOM    120  DT1 CLA X   1    -200.662-208.148 159.192  1.00  0.00      A3    
+ATOM    121  AK1 CLA X   1    -243.304-111.359  96.656  1.00  0.00      A3    
+ATOM    122  LT1 CLA X   1    -223.763 -18.662  85.497  1.00  0.00      A3    
+ATOM    123  PX2 CLA X   1    -126.815 -89.000 352.917  1.00  0.00      A3    
+ATOM    124  DT2 CLA X   1    -128.673  47.724 333.137  1.00  0.00      A3    
+ATOM    125  AK2 CLA X   1     -49.929 132.718 287.973  1.00  0.00      A3    
+ATOM    126  LT2 CLA X   1      24.828 143.462 235.435  1.00  0.00      A3    
+ATOM    127  PX3 CLA X   1     -10.483-180.619 340.613  1.00  0.00      A3    
+ATOM    128  DT3 CLA X   1      95.424-204.239 265.860  1.00  0.00      A3    
+ATOM    129  AK3 CLA X   1     101.877-231.712 146.926  1.00  0.00      A3    
+ATOM    130  LT3 CLA X   1      58.664-217.336  66.678  1.00  0.00      A3    
+ATOM    131  HB0 CLA X   1    -152.597-263.250 182.367  1.00  0.00      B3    
+ATOM    132  PX1 CLA X   1    -120.437-238.824 256.749  1.00  0.00      B3    
+ATOM    133  DT1 CLA X   1     -18.642-174.399 313.695  1.00  0.00      B3    
+ATOM    134  AK1 CLA X   1      88.420-151.452 262.690  1.00  0.00      B3    
+ATOM    135  LT1 CLA X   1     128.527-143.156 177.443  1.00  0.00      B3    
+ATOM    136  PX2 CLA X   1     -99.230-306.155 133.576  1.00  0.00      B3    
+ATOM    137  DT2 CLA X   1     -21.433-316.316  21.125  1.00  0.00      B3    
+ATOM    138  AK2 CLA X   1     -26.263-266.923 -95.151  1.00  0.00      B3    
+ATOM    139  LT2 CLA X   1     -58.151-195.850-145.576  1.00  0.00      B3    
+ATOM    140  PX3 CLA X   1    -223.451-225.604 155.002  1.00  0.00      B3    
+ATOM    141  DT3 CLA X   1    -275.701-105.136 138.751  1.00  0.00      B3    
+ATOM    142  AK3 CLA X   1    -235.267  -1.374 186.863  1.00  0.00      B3    
+ATOM    143  LT3 CLA X   1    -155.819  36.632 217.712  1.00  0.00      B3    
+ATOM    144  HB0 CLA X   1    -286.805-165.855  93.118  1.00  0.00      C3    
+ATOM    145  PX1 CLA X   1    -303.935-101.204 144.420  1.00  0.00      C3    
+ATOM    146  DT1 CLA X   1    -251.178 -21.712 232.998  1.00  0.00      C3    
+ATOM    147  AK1 CLA X   1    -142.263 -28.038 287.691  1.00  0.00      C3    
+ATOM    148  LT1 CLA X   1     -50.945 -58.195 270.101  1.00  0.00      C3    
+ATOM    149  PX2 CLA X   1    -234.620-227.534 121.486  1.00  0.00      C3    
+ATOM    150  DT2 CLA X   1    -104.398-278.700 124.820  1.00  0.00      C3    
+ATOM    151  AK2 CLA X   1      -0.965-276.330  50.135  1.00  0.00      C3    
+ATOM    152  LT2 CLA X   1      42.600-228.187 -18.776  1.00  0.00      C3    
+ATOM    153  PX3 CLA X   1    -303.934-158.846  11.493  1.00  0.00      C3    
+ATOM    154  DT3 CLA X   1    -291.514 -88.537-103.359  1.00  0.00      C3    
+ATOM    155  AK3 CLA X   1    -250.991  24.248-144.395  1.00  0.00      C3    
+ATOM    156  LT3 CLA X   1    -191.706  94.728-126.760  1.00  0.00      C3    
+ATOM    157  HB0 CLA X   1      95.559-162.537 331.473  1.00  0.00      A4    
+ATOM    158  PX1 CLA X   1     114.959-223.728 275.579  1.00  0.00      A4    
+ATOM    159  DT1 CLA X   1      79.930-277.853 159.192  1.00  0.00      A4    
+ATOM    160  AK1 CLA X   1     -25.213-266.386  96.656  1.00  0.00      A4    
+ATOM    161  LT1 CLA X   1     -95.719-203.115  85.497  1.00  0.00      A4    
+ATOM    162  PX2 CLA X   1      13.669-154.325 352.917  1.00  0.00      A4    
+ATOM    163  DT2 CLA X   1    -105.666 -87.572 333.137  1.00  0.00      A4    
+ATOM    164  AK2 CLA X   1    -139.902  23.120 287.973  1.00  0.00      A4    
+ATOM    165  LT2 CLA X   1    -111.827  93.233 235.435  1.00  0.00      A4    
+ATOM    166  PX3 CLA X   1     151.180 -99.388 340.613  1.00  0.00      A4    
+ATOM    167  DT3 CLA X   1     224.588 -19.480 265.860  1.00  0.00      A4    
+ATOM    168  AK3 CLA X   1     251.607 -27.627 146.926  1.00  0.00      A4    
+ATOM    169  LT3 CLA X   1     217.550 -57.864  66.678  1.00  0.00      A4    
+ATOM    170  HB0 CLA X   1     151.683-263.777 182.367  1.00  0.00      B4    
+ATOM    171  PX1 CLA X   1     146.609-223.714 256.749  1.00  0.00      B4    
+ATOM    172  DT1 CLA X   1     141.713-103.344 313.695  1.00  0.00      B4    
+ATOM    173  AK1 CLA X   1     175.371   0.848 262.690  1.00  0.00      B4    
+ATOM    174  LT1 CLA X   1     188.241  39.730 177.443  1.00  0.00      B4    
+ATOM    175  PX2 CLA X   1     215.523-239.014 133.576  1.00  0.00      B4    
+ATOM    176  DT2 CLA X   1     263.221-176.720  21.125  1.00  0.00      B4    
+ATOM    177  AK2 CLA X   1     218.030-156.206 -95.151  1.00  0.00      B4    
+ATOM    178  LT2 CLA X   1     140.536-148.285-145.576  1.00  0.00      B4    
+ATOM    179  PX3 CLA X   1      83.654-306.316 155.002  1.00  0.00      B4    
+ATOM    180  DT3 CLA X   1     -46.800-291.332 138.751  1.00  0.00      B4    
+ATOM    181  AK3 CLA X   1    -116.444-204.434 186.863  1.00  0.00      B4    
+ATOM    182  LT3 CLA X   1    -109.634-116.627 217.712  1.00  0.00      B4    
+ATOM    183  HB0 CLA X   1       0.232-331.308  93.118  1.00  0.00      C4    
+ATOM    184  PX1 CLA X   1     -64.322-313.817 144.420  1.00  0.00      C4    
+ATOM    185  DT1 CLA X   1    -106.786-228.382 232.998  1.00  0.00      C4    
+ATOM    186  AK1 CLA X   1     -46.850-137.222 287.691  1.00  0.00      C4    
+ATOM    187  LT1 CLA X   1      24.926 -73.217 270.101  1.00  0.00      C4    
+ATOM    188  PX2 CLA X   1      79.740-316.953 121.486  1.00  0.00      C4    
+ATOM    189  DT2 CLA X   1     189.163-229.761 124.820  1.00  0.00      C4    
+ATOM    190  AK2 CLA X   1     238.827-139.001  50.135  1.00  0.00      C4    
+ATOM    191  LT2 CLA X   1     218.915 -77.201 -18.776  1.00  0.00      C4    
+ATOM    192  PX3 CLA X   1     -14.402-342.637  11.493  1.00  0.00      C4    
+ATOM    193  DT3 CLA X   1     -69.082-296.727-103.359  1.00  0.00      C4    
+ATOM    194  AK3 CLA X   1    -146.495-205.240-144.395  1.00  0.00      C4    
+ATOM    195  LT3 CLA X   1    -177.890-118.659-126.760  1.00  0.00      C4    
+ATOM    196  HB0 CLA X   1     188.541   1.488 331.473  1.00  0.00      A5    
+ATOM    197  PX1 CLA X   1     251.234 -12.306 275.579  1.00  0.00      A5    
+ATOM    198  DT1 CLA X   1     280.592 -69.705 159.192  1.00  0.00      A5    
+ATOM    199  AK1 CLA X   1     218.091-155.028  96.656  1.00  0.00      A5    
+ATOM    200  LT1 CLA X   1     128.043-184.453  85.497  1.00  0.00      A5    
+ATOM    201  PX2 CLA X   1     140.484 -65.324 352.917  1.00  0.00      A5    
+ATOM    202  DT2 CLA X   1      23.007-135.296 333.137  1.00  0.00      A5    
+ATOM    203  AK2 CLA X   1     -89.973-109.599 287.973  1.00  0.00      A5    
+ATOM    204  LT2 CLA X   1    -136.656 -50.229 235.435  1.00  0.00      A5    
+ATOM    205  PX3 CLA X   1     161.662  81.231 340.613  1.00  0.00      A5    
+ATOM    206  DT3 CLA X   1     129.164 184.759 265.860  1.00  0.00      A5    
+ATOM    207  AK3 CLA X   1     149.729 204.084 146.926  1.00  0.00      A5    
+ATOM    208  LT3 CLA X   1     158.887 159.472  66.678  1.00  0.00      A5    
+ATOM    209  HB0 CLA X   1     304.279  -0.528 182.367  1.00  0.00      B5    
+ATOM    210  PX1 CLA X   1     267.047  15.111 256.749  1.00  0.00      B5    
+ATOM    211  DT1 CLA X   1     160.355  71.055 313.695  1.00  0.00      B5    
+ATOM    212  AK1 CLA X   1      86.951 152.300 262.690  1.00  0.00      B5    
+ATOM    213  LT1 CLA X   1      59.713 182.886 177.443  1.00  0.00      B5    
+ATOM    214  PX2 CLA X   1     314.754  67.142 133.576  1.00  0.00      B5    
+ATOM    215  DT2 CLA X   1     284.654 139.597  21.125  1.00  0.00      B5    
+ATOM    216  AK2 CLA X   1     244.294 110.717 -95.151  1.00  0.00      B5    
+ATOM    217  LT2 CLA X   1     198.687  47.565-145.576  1.00  0.00      B5    
+ATOM    218  PX3 CLA X   1     307.104 -80.712 155.002  1.00  0.00      B5    
+ATOM    219  DT3 CLA X   1     228.901-186.196 138.751  1.00  0.00      B5    
+ATOM    220  AK3 CLA X   1     118.823-203.060 186.863  1.00  0.00      B5    
+ATOM    221  LT3 CLA X   1      46.185-153.259 217.712  1.00  0.00      B5    
+ATOM    222  HB0 CLA X   1     287.037-165.452  93.118  1.00  0.00      C5    
+ATOM    223  PX1 CLA X   1     239.613-212.613 144.420  1.00  0.00      C5    
+ATOM    224  DT1 CLA X   1     144.392-206.670 232.998  1.00  0.00      C5    
+ATOM    225  AK1 CLA X   1      95.413-109.184 287.691  1.00  0.00      C5    
+ATOM    226  LT1 CLA X   1      75.871 -15.022 270.101  1.00  0.00      C5    
+ATOM    227  PX2 CLA X   1     314.360 -89.420 121.486  1.00  0.00      C5    
+ATOM    228  DT2 CLA X   1     293.560  48.939 124.820  1.00  0.00      C5    
+ATOM    229  AK2 CLA X   1     239.791 137.330  50.135  1.00  0.00      C5    
+ATOM    230  LT2 CLA X   1     176.315 150.986 -18.776  1.00  0.00      C5    
+ATOM    231  PX3 CLA X   1     289.532-183.791  11.493  1.00  0.00      C5    
+ATOM    232  DT3 CLA X   1     222.432-208.190-103.359  1.00  0.00      C5    
+ATOM    233  AK3 CLA X   1     104.496-229.489-144.395  1.00  0.00      C5    
+ATOM    234  LT3 CLA X   1      13.817-213.386-126.760  1.00  0.00      C5    
+ATOM    235  HB0 CLA X   1      95.559 162.537-331.473  1.00  0.00      A6    
+ATOM    236  PX1 CLA X   1     114.959 223.728-275.579  1.00  0.00      A6    
+ATOM    237  DT1 CLA X   1      79.930 277.853-159.192  1.00  0.00      A6    
+ATOM    238  AK1 CLA X   1     -25.213 266.386 -96.656  1.00  0.00      A6    
+ATOM    239  LT1 CLA X   1     -95.719 203.115 -85.497  1.00  0.00      A6    
+ATOM    240  PX2 CLA X   1      13.669 154.325-352.917  1.00  0.00      A6    
+ATOM    241  DT2 CLA X   1    -105.666  87.572-333.137  1.00  0.00      A6    
+ATOM    242  AK2 CLA X   1    -139.902 -23.120-287.973  1.00  0.00      A6    
+ATOM    243  LT2 CLA X   1    -111.827 -93.233-235.435  1.00  0.00      A6    
+ATOM    244  PX3 CLA X   1     151.180  99.388-340.613  1.00  0.00      A6    
+ATOM    245  DT3 CLA X   1     224.588  19.480-265.860  1.00  0.00      A6    
+ATOM    246  AK3 CLA X   1     251.607  27.627-146.926  1.00  0.00      A6    
+ATOM    247  LT3 CLA X   1     217.550  57.864 -66.678  1.00  0.00      A6    
+ATOM    248  HB0 CLA X   1     151.683 263.777-182.367  1.00  0.00      B6    
+ATOM    249  PX1 CLA X   1     146.609 223.714-256.749  1.00  0.00      B6    
+ATOM    250  DT1 CLA X   1     141.713 103.344-313.695  1.00  0.00      B6    
+ATOM    251  AK1 CLA X   1     175.371  -0.848-262.690  1.00  0.00      B6    
+ATOM    252  LT1 CLA X   1     188.241 -39.730-177.443  1.00  0.00      B6    
+ATOM    253  PX2 CLA X   1     215.523 239.014-133.576  1.00  0.00      B6    
+ATOM    254  DT2 CLA X   1     263.221 176.720 -21.125  1.00  0.00      B6    
+ATOM    255  AK2 CLA X   1     218.030 156.206  95.151  1.00  0.00      B6    
+ATOM    256  LT2 CLA X   1     140.536 148.285 145.576  1.00  0.00      B6    
+ATOM    257  PX3 CLA X   1      83.654 306.316-155.002  1.00  0.00      B6    
+ATOM    258  DT3 CLA X   1     -46.800 291.332-138.751  1.00  0.00      B6    
+ATOM    259  AK3 CLA X   1    -116.444 204.434-186.863  1.00  0.00      B6    
+ATOM    260  LT3 CLA X   1    -109.634 116.627-217.712  1.00  0.00      B6    
+ATOM    261  HB0 CLA X   1       0.232 331.308 -93.118  1.00  0.00      C6    
+ATOM    262  PX1 CLA X   1     -64.322 313.817-144.420  1.00  0.00      C6    
+ATOM    263  DT1 CLA X   1    -106.786 228.382-232.998  1.00  0.00      C6    
+ATOM    264  AK1 CLA X   1     -46.850 137.222-287.691  1.00  0.00      C6    
+ATOM    265  LT1 CLA X   1      24.926  73.217-270.101  1.00  0.00      C6    
+ATOM    266  PX2 CLA X   1      79.740 316.953-121.486  1.00  0.00      C6    
+ATOM    267  DT2 CLA X   1     189.163 229.761-124.820  1.00  0.00      C6    
+ATOM    268  AK2 CLA X   1     238.827 139.001 -50.135  1.00  0.00      C6    
+ATOM    269  LT2 CLA X   1     218.915  77.201  18.776  1.00  0.00      C6    
+ATOM    270  PX3 CLA X   1     -14.402 342.637 -11.493  1.00  0.00      C6    
+ATOM    271  DT3 CLA X   1     -69.082 296.727 103.359  1.00  0.00      C6    
+ATOM    272  AK3 CLA X   1    -146.495 205.240 144.395  1.00  0.00      C6    
+ATOM    273  LT3 CLA X   1    -177.890 118.659 126.760  1.00  0.00      C6    
+ATOM    274  HB0 CLA X   1     188.541  -1.488-331.473  1.00  0.00      A7    
+ATOM    275  PX1 CLA X   1     251.234  12.306-275.579  1.00  0.00      A7    
+ATOM    276  DT1 CLA X   1     280.592  69.705-159.192  1.00  0.00      A7    
+ATOM    277  AK1 CLA X   1     218.091 155.028 -96.656  1.00  0.00      A7    
+ATOM    278  LT1 CLA X   1     128.043 184.453 -85.497  1.00  0.00      A7    
+ATOM    279  PX2 CLA X   1     140.484  65.324-352.917  1.00  0.00      A7    
+ATOM    280  DT2 CLA X   1      23.007 135.296-333.137  1.00  0.00      A7    
+ATOM    281  AK2 CLA X   1     -89.973 109.599-287.973  1.00  0.00      A7    
+ATOM    282  LT2 CLA X   1    -136.656  50.229-235.435  1.00  0.00      A7    
+ATOM    283  PX3 CLA X   1     161.662 -81.231-340.613  1.00  0.00      A7    
+ATOM    284  DT3 CLA X   1     129.164-184.759-265.860  1.00  0.00      A7    
+ATOM    285  AK3 CLA X   1     149.729-204.084-146.926  1.00  0.00      A7    
+ATOM    286  LT3 CLA X   1     158.887-159.472 -66.678  1.00  0.00      A7    
+ATOM    287  HB0 CLA X   1     304.279   0.528-182.367  1.00  0.00      B7    
+ATOM    288  PX1 CLA X   1     267.047 -15.111-256.749  1.00  0.00      B7    
+ATOM    289  DT1 CLA X   1     160.355 -71.055-313.695  1.00  0.00      B7    
+ATOM    290  AK1 CLA X   1      86.951-152.300-262.690  1.00  0.00      B7    
+ATOM    291  LT1 CLA X   1      59.713-182.886-177.443  1.00  0.00      B7    
+ATOM    292  PX2 CLA X   1     314.754 -67.142-133.576  1.00  0.00      B7    
+ATOM    293  DT2 CLA X   1     284.654-139.597 -21.125  1.00  0.00      B7    
+ATOM    294  AK2 CLA X   1     244.294-110.717  95.151  1.00  0.00      B7    
+ATOM    295  LT2 CLA X   1     198.687 -47.565 145.576  1.00  0.00      B7    
+ATOM    296  PX3 CLA X   1     307.104  80.712-155.002  1.00  0.00      B7    
+ATOM    297  DT3 CLA X   1     228.901 186.196-138.751  1.00  0.00      B7    
+ATOM    298  AK3 CLA X   1     118.823 203.060-186.863  1.00  0.00      B7    
+ATOM    299  LT3 CLA X   1      46.185 153.259-217.712  1.00  0.00      B7    
+ATOM    300  HB0 CLA X   1     287.037 165.452 -93.118  1.00  0.00      C7    
+ATOM    301  PX1 CLA X   1     239.613 212.613-144.420  1.00  0.00      C7    
+ATOM    302  DT1 CLA X   1     144.392 206.670-232.998  1.00  0.00      C7    
+ATOM    303  AK1 CLA X   1      95.413 109.184-287.691  1.00  0.00      C7    
+ATOM    304  LT1 CLA X   1      75.871  15.022-270.101  1.00  0.00      C7    
+ATOM    305  PX2 CLA X   1     314.360  89.420-121.486  1.00  0.00      C7    
+ATOM    306  DT2 CLA X   1     293.560 -48.939-124.820  1.00  0.00      C7    
+ATOM    307  AK2 CLA X   1     239.791-137.330 -50.135  1.00  0.00      C7    
+ATOM    308  LT2 CLA X   1     176.315-150.986  18.776  1.00  0.00      C7    
+ATOM    309  PX3 CLA X   1     289.532 183.791 -11.493  1.00  0.00      C7    
+ATOM    310  DT3 CLA X   1     222.432 208.190 103.359  1.00  0.00      C7    
+ATOM    311  AK3 CLA X   1     104.496 229.489 144.395  1.00  0.00      C7    
+ATOM    312  LT3 CLA X   1      13.817 213.386 126.760  1.00  0.00      C7    
+ATOM    313  HB0 CLA X   1      92.981-164.025-331.473  1.00  0.00      A8    
+ATOM    314  PX1 CLA X   1     136.274-211.422-275.579  1.00  0.00      A8    
+ATOM    315  DT1 CLA X   1     200.662-208.148-159.192  1.00  0.00      A8    
+ATOM    316  AK1 CLA X   1     243.304-111.359 -96.656  1.00  0.00      A8    
+ATOM    317  LT1 CLA X   1     223.763 -18.662 -85.497  1.00  0.00      A8    
+ATOM    318  PX2 CLA X   1     126.815 -89.000-352.917  1.00  0.00      A8    
+ATOM    319  DT2 CLA X   1     128.673  47.724-333.137  1.00  0.00      A8    
+ATOM    320  AK2 CLA X   1      49.929 132.718-287.973  1.00  0.00      A8    
+ATOM    321  LT2 CLA X   1     -24.828 143.462-235.435  1.00  0.00      A8    
+ATOM    322  PX3 CLA X   1      10.483-180.619-340.613  1.00  0.00      A8    
+ATOM    323  DT3 CLA X   1     -95.424-204.239-265.860  1.00  0.00      A8    
+ATOM    324  AK3 CLA X   1    -101.877-231.712-146.926  1.00  0.00      A8    
+ATOM    325  LT3 CLA X   1     -58.664-217.336 -66.678  1.00  0.00      A8    
+ATOM    326  HB0 CLA X   1     152.597-263.250-182.367  1.00  0.00      B8    
+ATOM    327  PX1 CLA X   1     120.437-238.824-256.749  1.00  0.00      B8    
+ATOM    328  DT1 CLA X   1      18.642-174.399-313.695  1.00  0.00      B8    
+ATOM    329  AK1 CLA X   1     -88.420-151.452-262.690  1.00  0.00      B8    
+ATOM    330  LT1 CLA X   1    -128.527-143.156-177.443  1.00  0.00      B8    
+ATOM    331  PX2 CLA X   1      99.230-306.155-133.576  1.00  0.00      B8    
+ATOM    332  DT2 CLA X   1      21.433-316.316 -21.125  1.00  0.00      B8    
+ATOM    333  AK2 CLA X   1      26.263-266.923  95.151  1.00  0.00      B8    
+ATOM    334  LT2 CLA X   1      58.151-195.850 145.576  1.00  0.00      B8    
+ATOM    335  PX3 CLA X   1     223.451-225.604-155.002  1.00  0.00      B8    
+ATOM    336  DT3 CLA X   1     275.701-105.136-138.751  1.00  0.00      B8    
+ATOM    337  AK3 CLA X   1     235.267  -1.374-186.863  1.00  0.00      B8    
+ATOM    338  LT3 CLA X   1     155.819  36.632-217.712  1.00  0.00      B8    
+ATOM    339  HB0 CLA X   1     286.805-165.855 -93.118  1.00  0.00      C8    
+ATOM    340  PX1 CLA X   1     303.935-101.204-144.420  1.00  0.00      C8    
+ATOM    341  DT1 CLA X   1     251.178 -21.712-232.998  1.00  0.00      C8    
+ATOM    342  AK1 CLA X   1     142.263 -28.038-287.691  1.00  0.00      C8    
+ATOM    343  LT1 CLA X   1      50.945 -58.195-270.101  1.00  0.00      C8    
+ATOM    344  PX2 CLA X   1     234.620-227.534-121.486  1.00  0.00      C8    
+ATOM    345  DT2 CLA X   1     104.398-278.700-124.820  1.00  0.00      C8    
+ATOM    346  AK2 CLA X   1       0.965-276.330 -50.135  1.00  0.00      C8    
+ATOM    347  LT2 CLA X   1     -42.600-228.187  18.776  1.00  0.00      C8    
+ATOM    348  PX3 CLA X   1     303.934-158.846 -11.493  1.00  0.00      C8    
+ATOM    349  DT3 CLA X   1     291.514 -88.537 103.359  1.00  0.00      C8    
+ATOM    350  AK3 CLA X   1     250.991  24.248 144.395  1.00  0.00      C8    
+ATOM    351  LT3 CLA X   1     191.706  94.728 126.760  1.00  0.00      C8    
+ATOM    352  HB0 CLA X   1     -95.559-162.537-331.473  1.00  0.00      A9    
+ATOM    353  PX1 CLA X   1    -114.959-223.728-275.579  1.00  0.00      A9    
+ATOM    354  DT1 CLA X   1     -79.930-277.853-159.192  1.00  0.00      A9    
+ATOM    355  AK1 CLA X   1      25.213-266.386 -96.656  1.00  0.00      A9    
+ATOM    356  LT1 CLA X   1      95.719-203.115 -85.497  1.00  0.00      A9    
+ATOM    357  PX2 CLA X   1     -13.669-154.325-352.917  1.00  0.00      A9    
+ATOM    358  DT2 CLA X   1     105.666 -87.572-333.137  1.00  0.00      A9    
+ATOM    359  AK2 CLA X   1     139.902  23.120-287.973  1.00  0.00      A9    
+ATOM    360  LT2 CLA X   1     111.827  93.233-235.435  1.00  0.00      A9    
+ATOM    361  PX3 CLA X   1    -151.180 -99.388-340.613  1.00  0.00      A9    
+ATOM    362  DT3 CLA X   1    -224.588 -19.480-265.860  1.00  0.00      A9    
+ATOM    363  AK3 CLA X   1    -251.607 -27.627-146.926  1.00  0.00      A9    
+ATOM    364  LT3 CLA X   1    -217.550 -57.864 -66.678  1.00  0.00      A9    
+ATOM    365  HB0 CLA X   1    -151.683-263.777-182.367  1.00  0.00      B9    
+ATOM    366  PX1 CLA X   1    -146.609-223.714-256.749  1.00  0.00      B9    
+ATOM    367  DT1 CLA X   1    -141.713-103.344-313.695  1.00  0.00      B9    
+ATOM    368  AK1 CLA X   1    -175.371   0.848-262.690  1.00  0.00      B9    
+ATOM    369  LT1 CLA X   1    -188.241  39.730-177.443  1.00  0.00      B9    
+ATOM    370  PX2 CLA X   1    -215.523-239.014-133.576  1.00  0.00      B9    
+ATOM    371  DT2 CLA X   1    -263.221-176.720 -21.125  1.00  0.00      B9    
+ATOM    372  AK2 CLA X   1    -218.030-156.206  95.151  1.00  0.00      B9    
+ATOM    373  LT2 CLA X   1    -140.536-148.285 145.576  1.00  0.00      B9    
+ATOM    374  PX3 CLA X   1     -83.654-306.316-155.002  1.00  0.00      B9    
+ATOM    375  DT3 CLA X   1      46.800-291.332-138.751  1.00  0.00      B9    
+ATOM    376  AK3 CLA X   1     116.444-204.434-186.863  1.00  0.00      B9    
+ATOM    377  LT3 CLA X   1     109.634-116.627-217.712  1.00  0.00      B9    
+ATOM    378  HB0 CLA X   1      -0.232-331.308 -93.118  1.00  0.00      C9    
+ATOM    379  PX1 CLA X   1      64.322-313.817-144.420  1.00  0.00      C9    
+ATOM    380  DT1 CLA X   1     106.786-228.382-232.998  1.00  0.00      C9    
+ATOM    381  AK1 CLA X   1      46.850-137.222-287.691  1.00  0.00      C9    
+ATOM    382  LT1 CLA X   1     -24.926 -73.217-270.101  1.00  0.00      C9    
+ATOM    383  PX2 CLA X   1     -79.740-316.953-121.486  1.00  0.00      C9    
+ATOM    384  DT2 CLA X   1    -189.163-229.761-124.820  1.00  0.00      C9    
+ATOM    385  AK2 CLA X   1    -238.827-139.001 -50.135  1.00  0.00      C9    
+ATOM    386  LT2 CLA X   1    -218.915 -77.201  18.776  1.00  0.00      C9    
+ATOM    387  PX3 CLA X   1      14.402-342.637 -11.493  1.00  0.00      C9    
+ATOM    388  DT3 CLA X   1      69.082-296.727 103.359  1.00  0.00      C9    
+ATOM    389  AK3 CLA X   1     146.495-205.240 144.395  1.00  0.00      C9    
+ATOM    390  LT3 CLA X   1     177.890-118.659 126.760  1.00  0.00      C9    
+ATOM    391  HB0 CLA X   1    -188.541   1.488-331.473  1.00  0.00      A10   
+ATOM    392  PX1 CLA X   1    -251.234 -12.306-275.579  1.00  0.00      A10   
+ATOM    393  DT1 CLA X   1    -280.592 -69.705-159.192  1.00  0.00      A10   
+ATOM    394  AK1 CLA X   1    -218.091-155.028 -96.656  1.00  0.00      A10   
+ATOM    395  LT1 CLA X   1    -128.043-184.453 -85.497  1.00  0.00      A10   
+ATOM    396  PX2 CLA X   1    -140.484 -65.324-352.917  1.00  0.00      A10   
+ATOM    397  DT2 CLA X   1     -23.007-135.296-333.137  1.00  0.00      A10   
+ATOM    398  AK2 CLA X   1      89.973-109.599-287.973  1.00  0.00      A10   
+ATOM    399  LT2 CLA X   1     136.656 -50.229-235.435  1.00  0.00      A10   
+ATOM    400  PX3 CLA X   1    -161.662  81.231-340.613  1.00  0.00      A10   
+ATOM    401  DT3 CLA X   1    -129.164 184.759-265.860  1.00  0.00      A10   
+ATOM    402  AK3 CLA X   1    -149.729 204.084-146.926  1.00  0.00      A10   
+ATOM    403  LT3 CLA X   1    -158.887 159.472 -66.678  1.00  0.00      A10   
+ATOM    404  HB0 CLA X   1    -304.279  -0.528-182.367  1.00  0.00      B10   
+ATOM    405  PX1 CLA X   1    -267.047  15.111-256.749  1.00  0.00      B10   
+ATOM    406  DT1 CLA X   1    -160.355  71.055-313.695  1.00  0.00      B10   
+ATOM    407  AK1 CLA X   1     -86.951 152.300-262.690  1.00  0.00      B10   
+ATOM    408  LT1 CLA X   1     -59.713 182.886-177.443  1.00  0.00      B10   
+ATOM    409  PX2 CLA X   1    -314.754  67.142-133.576  1.00  0.00      B10   
+ATOM    410  DT2 CLA X   1    -284.654 139.597 -21.125  1.00  0.00      B10   
+ATOM    411  AK2 CLA X   1    -244.294 110.717  95.151  1.00  0.00      B10   
+ATOM    412  LT2 CLA X   1    -198.687  47.565 145.576  1.00  0.00      B10   
+ATOM    413  PX3 CLA X   1    -307.104 -80.712-155.002  1.00  0.00      B10   
+ATOM    414  DT3 CLA X   1    -228.901-186.196-138.751  1.00  0.00      B10   
+ATOM    415  AK3 CLA X   1    -118.823-203.060-186.863  1.00  0.00      B10   
+ATOM    416  LT3 CLA X   1     -46.185-153.259-217.712  1.00  0.00      B10   
+ATOM    417  HB0 CLA X   1    -287.037-165.452 -93.118  1.00  0.00      C10   
+ATOM    418  PX1 CLA X   1    -239.613-212.613-144.420  1.00  0.00      C10   
+ATOM    419  DT1 CLA X   1    -144.392-206.670-232.998  1.00  0.00      C10   
+ATOM    420  AK1 CLA X   1     -95.413-109.184-287.691  1.00  0.00      C10   
+ATOM    421  LT1 CLA X   1     -75.871 -15.022-270.101  1.00  0.00      C10   
+ATOM    422  PX2 CLA X   1    -314.360 -89.420-121.486  1.00  0.00      C10   
+ATOM    423  DT2 CLA X   1    -293.560  48.939-124.820  1.00  0.00      C10   
+ATOM    424  AK2 CLA X   1    -239.791 137.330 -50.135  1.00  0.00      C10   
+ATOM    425  LT2 CLA X   1    -176.315 150.986  18.776  1.00  0.00      C10   
+ATOM    426  PX3 CLA X   1    -289.532-183.791 -11.493  1.00  0.00      C10   
+ATOM    427  DT3 CLA X   1    -222.432-208.190 103.359  1.00  0.00      C10   
+ATOM    428  AK3 CLA X   1    -104.496-229.489 144.395  1.00  0.00      C10   
+ATOM    429  LT3 CLA X   1     -13.817-213.386 126.760  1.00  0.00      C10   
+ATOM    430  HB0 CLA X   1     -92.981 164.025-331.473  1.00  0.00      A11   
+ATOM    431  PX1 CLA X   1    -136.274 211.422-275.579  1.00  0.00      A11   
+ATOM    432  DT1 CLA X   1    -200.662 208.148-159.192  1.00  0.00      A11   
+ATOM    433  AK1 CLA X   1    -243.304 111.359 -96.656  1.00  0.00      A11   
+ATOM    434  LT1 CLA X   1    -223.763  18.662 -85.497  1.00  0.00      A11   
+ATOM    435  PX2 CLA X   1    -126.815  89.000-352.917  1.00  0.00      A11   
+ATOM    436  DT2 CLA X   1    -128.673 -47.724-333.137  1.00  0.00      A11   
+ATOM    437  AK2 CLA X   1     -49.929-132.718-287.973  1.00  0.00      A11   
+ATOM    438  LT2 CLA X   1      24.828-143.462-235.435  1.00  0.00      A11   
+ATOM    439  PX3 CLA X   1     -10.483 180.619-340.613  1.00  0.00      A11   
+ATOM    440  DT3 CLA X   1      95.424 204.239-265.860  1.00  0.00      A11   
+ATOM    441  AK3 CLA X   1     101.877 231.712-146.926  1.00  0.00      A11   
+ATOM    442  LT3 CLA X   1      58.664 217.336 -66.678  1.00  0.00      A11   
+ATOM    443  HB0 CLA X   1    -152.597 263.250-182.367  1.00  0.00      B11   
+ATOM    444  PX1 CLA X   1    -120.437 238.824-256.749  1.00  0.00      B11   
+ATOM    445  DT1 CLA X   1     -18.642 174.399-313.695  1.00  0.00      B11   
+ATOM    446  AK1 CLA X   1      88.420 151.452-262.690  1.00  0.00      B11   
+ATOM    447  LT1 CLA X   1     128.527 143.156-177.443  1.00  0.00      B11   
+ATOM    448  PX2 CLA X   1     -99.230 306.155-133.576  1.00  0.00      B11   
+ATOM    449  DT2 CLA X   1     -21.433 316.316 -21.125  1.00  0.00      B11   
+ATOM    450  AK2 CLA X   1     -26.263 266.923  95.151  1.00  0.00      B11   
+ATOM    451  LT2 CLA X   1     -58.151 195.850 145.576  1.00  0.00      B11   
+ATOM    452  PX3 CLA X   1    -223.451 225.604-155.002  1.00  0.00      B11   
+ATOM    453  DT3 CLA X   1    -275.701 105.136-138.751  1.00  0.00      B11   
+ATOM    454  AK3 CLA X   1    -235.267   1.374-186.863  1.00  0.00      B11   
+ATOM    455  LT3 CLA X   1    -155.819 -36.632-217.712  1.00  0.00      B11   
+ATOM    456  HB0 CLA X   1    -286.805 165.855 -93.118  1.00  0.00      C11   
+ATOM    457  PX1 CLA X   1    -303.935 101.204-144.420  1.00  0.00      C11   
+ATOM    458  DT1 CLA X   1    -251.178  21.712-232.998  1.00  0.00      C11   
+ATOM    459  AK1 CLA X   1    -142.263  28.038-287.691  1.00  0.00      C11   
+ATOM    460  LT1 CLA X   1     -50.945  58.195-270.101  1.00  0.00      C11   
+ATOM    461  PX2 CLA X   1    -234.620 227.534-121.486  1.00  0.00      C11   
+ATOM    462  DT2 CLA X   1    -104.398 278.700-124.820  1.00  0.00      C11   
+ATOM    463  AK2 CLA X   1      -0.965 276.330 -50.135  1.00  0.00      C11   
+ATOM    464  LT2 CLA X   1      42.600 228.187  18.776  1.00  0.00      C11   
+ATOM    465  PX3 CLA X   1    -303.934 158.846 -11.493  1.00  0.00      C11   
+ATOM    466  DT3 CLA X   1    -291.514  88.537 103.359  1.00  0.00      C11   
+ATOM    467  AK3 CLA X   1    -250.991 -24.248 144.395  1.00  0.00      C11   
+ATOM    468  LT3 CLA X   1    -191.706 -94.728 126.760  1.00  0.00      C11   
+END

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,1078 @@
+PSF
+
+      38 !NTITLE
+ REMARKS original generated structure x-plor psf file
+ REMARKS topology top_cg_clath.impr.inp 
+ REMARKS segment A0 { first NONE; last NONE; auto angles  }
+ REMARKS segment B0 { first NONE; last NONE; auto angles  }
+ REMARKS segment C0 { first NONE; last NONE; auto angles  }
+ REMARKS segment A1 { first NONE; last NONE; auto angles  }
+ REMARKS segment B1 { first NONE; last NONE; auto angles  }
+ REMARKS segment C1 { first NONE; last NONE; auto angles  }
+ REMARKS segment A2 { first NONE; last NONE; auto angles  }
+ REMARKS segment B2 { first NONE; last NONE; auto angles  }
+ REMARKS segment C2 { first NONE; last NONE; auto angles  }
+ REMARKS segment A3 { first NONE; last NONE; auto angles  }
+ REMARKS segment B3 { first NONE; last NONE; auto angles  }
+ REMARKS segment C3 { first NONE; last NONE; auto angles  }
+ REMARKS segment A4 { first NONE; last NONE; auto angles  }
+ REMARKS segment B4 { first NONE; last NONE; auto angles  }
+ REMARKS segment C4 { first NONE; last NONE; auto angles  }
+ REMARKS segment A5 { first NONE; last NONE; auto angles  }
+ REMARKS segment B5 { first NONE; last NONE; auto angles  }
+ REMARKS segment C5 { first NONE; last NONE; auto angles  }
+ REMARKS segment A6 { first NONE; last NONE; auto angles  }
+ REMARKS segment B6 { first NONE; last NONE; auto angles  }
+ REMARKS segment C6 { first NONE; last NONE; auto angles  }
+ REMARKS segment A7 { first NONE; last NONE; auto angles  }
+ REMARKS segment B7 { first NONE; last NONE; auto angles  }
+ REMARKS segment C7 { first NONE; last NONE; auto angles  }
+ REMARKS segment A8 { first NONE; last NONE; auto angles  }
+ REMARKS segment B8 { first NONE; last NONE; auto angles  }
+ REMARKS segment C8 { first NONE; last NONE; auto angles  }
+ REMARKS segment A9 { first NONE; last NONE; auto angles  }
+ REMARKS segment B9 { first NONE; last NONE; auto angles  }
+ REMARKS segment C9 { first NONE; last NONE; auto angles  }
+ REMARKS segment A10 { first NONE; last NONE; auto angles  }
+ REMARKS segment B10 { first NONE; last NONE; auto angles  }
+ REMARKS segment C10 { first NONE; last NONE; auto angles  }
+ REMARKS segment A11 { first NONE; last NONE; auto angles  }
+ REMARKS segment B11 { first NONE; last NONE; auto angles  }
+ REMARKS segment C11 { first NONE; last NONE; auto angles  }
+
+     468 !NATOM
+       1 A0   1    CLA  HB0  HB     0.000000     30478.0300           0
+       2 A0   1    CLA  PX1  PX     0.000000     46422.2000           0
+       3 A0   1    CLA  DT1  DT     0.000000     49195.2000           0
+       4 A0   1    CLA  AK1  AK     0.000000     34620.7800           0
+       5 A0   1    CLA  LT1  LT     0.000000     55013.7800           0
+       6 A0   1    CLA  PX2  PX     0.000000     46422.2000           0
+       7 A0   1    CLA  DT2  DT     0.000000     49195.2000           0
+       8 A0   1    CLA  AK2  AK     0.000000     34620.7800           0
+       9 A0   1    CLA  LT2  LT     0.000000     55013.7800           0
+      10 A0   1    CLA  PX3  PX     0.000000     46422.2000           0
+      11 A0   1    CLA  DT3  DT     0.000000     49195.2000           0
+      12 A0   1    CLA  AK3  AK     0.000000     34620.7800           0
+      13 A0   1    CLA  LT3  LT     0.000000     55013.7800           0
+      14 B0   1    CLA  HB0  HB     0.000000     30478.0300           0
+      15 B0   1    CLA  PX1  PX     0.000000     46422.2000           0
+      16 B0   1    CLA  DT1  DT     0.000000     49195.2000           0
+      17 B0   1    CLA  AK1  AK     0.000000     34620.7800           0
+      18 B0   1    CLA  LT1  LT     0.000000     55013.7800           0
+      19 B0   1    CLA  PX2  PX     0.000000     46422.2000           0
+      20 B0   1    CLA  DT2  DT     0.000000     49195.2000           0
+      21 B0   1    CLA  AK2  AK     0.000000     34620.7800           0
+      22 B0   1    CLA  LT2  LT     0.000000     55013.7800           0
+      23 B0   1    CLA  PX3  PX     0.000000     46422.2000           0
+      24 B0   1    CLA  DT3  DT     0.000000     49195.2000           0
+      25 B0   1    CLA  AK3  AK     0.000000     34620.7800           0
+      26 B0   1    CLA  LT3  LT     0.000000     55013.7800           0
+      27 C0   1    CLA  HB0  HB     0.000000     30478.0300           0
+      28 C0   1    CLA  PX1  PX     0.000000     46422.2000           0
+      29 C0   1    CLA  DT1  DT     0.000000     49195.2000           0
+      30 C0   1    CLA  AK1  AK     0.000000     34620.7800           0
+      31 C0   1    CLA  LT1  LT     0.000000     55013.7800           0
+      32 C0   1    CLA  PX2  PX     0.000000     46422.2000           0
+      33 C0   1    CLA  DT2  DT     0.000000     49195.2000           0
+      34 C0   1    CLA  AK2  AK     0.000000     34620.7800           0
+      35 C0   1    CLA  LT2  LT     0.000000     55013.7800           0
+      36 C0   1    CLA  PX3  PX     0.000000     46422.2000           0
+      37 C0   1    CLA  DT3  DT     0.000000     49195.2000           0
+      38 C0   1    CLA  AK3  AK     0.000000     34620.7800           0
+      39 C0   1    CLA  LT3  LT     0.000000     55013.7800           0
+      40 A1   1    CLA  HB0  HB     0.000000     30478.0300           0
+      41 A1   1    CLA  PX1  PX     0.000000     46422.2000           0
+      42 A1   1    CLA  DT1  DT     0.000000     49195.2000           0
+      43 A1   1    CLA  AK1  AK     0.000000     34620.7800           0
+      44 A1   1    CLA  LT1  LT     0.000000     55013.7800           0
+      45 A1   1    CLA  PX2  PX     0.000000     46422.2000           0
+      46 A1   1    CLA  DT2  DT     0.000000     49195.2000           0
+      47 A1   1    CLA  AK2  AK     0.000000     34620.7800           0
+      48 A1   1    CLA  LT2  LT     0.000000     55013.7800           0
+      49 A1   1    CLA  PX3  PX     0.000000     46422.2000           0
+      50 A1   1    CLA  DT3  DT     0.000000     49195.2000           0
+      51 A1   1    CLA  AK3  AK     0.000000     34620.7800           0
+      52 A1   1    CLA  LT3  LT     0.000000     55013.7800           0
+      53 B1   1    CLA  HB0  HB     0.000000     30478.0300           0
+      54 B1   1    CLA  PX1  PX     0.000000     46422.2000           0
+      55 B1   1    CLA  DT1  DT     0.000000     49195.2000           0
+      56 B1   1    CLA  AK1  AK     0.000000     34620.7800           0
+      57 B1   1    CLA  LT1  LT     0.000000     55013.7800           0
+      58 B1   1    CLA  PX2  PX     0.000000     46422.2000           0
+      59 B1   1    CLA  DT2  DT     0.000000     49195.2000           0
+      60 B1   1    CLA  AK2  AK     0.000000     34620.7800           0
+      61 B1   1    CLA  LT2  LT     0.000000     55013.7800           0
+      62 B1   1    CLA  PX3  PX     0.000000     46422.2000           0
+      63 B1   1    CLA  DT3  DT     0.000000     49195.2000           0
+      64 B1   1    CLA  AK3  AK     0.000000     34620.7800           0
+      65 B1   1    CLA  LT3  LT     0.000000     55013.7800           0
+      66 C1   1    CLA  HB0  HB     0.000000     30478.0300           0
+      67 C1   1    CLA  PX1  PX     0.000000     46422.2000           0
+      68 C1   1    CLA  DT1  DT     0.000000     49195.2000           0
+      69 C1   1    CLA  AK1  AK     0.000000     34620.7800           0
+      70 C1   1    CLA  LT1  LT     0.000000     55013.7800           0
+      71 C1   1    CLA  PX2  PX     0.000000     46422.2000           0
+      72 C1   1    CLA  DT2  DT     0.000000     49195.2000           0
+      73 C1   1    CLA  AK2  AK     0.000000     34620.7800           0
+      74 C1   1    CLA  LT2  LT     0.000000     55013.7800           0
+      75 C1   1    CLA  PX3  PX     0.000000     46422.2000           0
+      76 C1   1    CLA  DT3  DT     0.000000     49195.2000           0
+      77 C1   1    CLA  AK3  AK     0.000000     34620.7800           0
+      78 C1   1    CLA  LT3  LT     0.000000     55013.7800           0
+      79 A2   1    CLA  HB0  HB     0.000000     30478.0300           0
+      80 A2   1    CLA  PX1  PX     0.000000     46422.2000           0
+      81 A2   1    CLA  DT1  DT     0.000000     49195.2000           0
+      82 A2   1    CLA  AK1  AK     0.000000     34620.7800           0
+      83 A2   1    CLA  LT1  LT     0.000000     55013.7800           0
+      84 A2   1    CLA  PX2  PX     0.000000     46422.2000           0
+      85 A2   1    CLA  DT2  DT     0.000000     49195.2000           0
+      86 A2   1    CLA  AK2  AK     0.000000     34620.7800           0
+      87 A2   1    CLA  LT2  LT     0.000000     55013.7800           0
+      88 A2   1    CLA  PX3  PX     0.000000     46422.2000           0
+      89 A2   1    CLA  DT3  DT     0.000000     49195.2000           0
+      90 A2   1    CLA  AK3  AK     0.000000     34620.7800           0
+      91 A2   1    CLA  LT3  LT     0.000000     55013.7800           0
+      92 B2   1    CLA  HB0  HB     0.000000     30478.0300           0
+      93 B2   1    CLA  PX1  PX     0.000000     46422.2000           0
+      94 B2   1    CLA  DT1  DT     0.000000     49195.2000           0
+      95 B2   1    CLA  AK1  AK     0.000000     34620.7800           0
+      96 B2   1    CLA  LT1  LT     0.000000     55013.7800           0
+      97 B2   1    CLA  PX2  PX     0.000000     46422.2000           0
+      98 B2   1    CLA  DT2  DT     0.000000     49195.2000           0
+      99 B2   1    CLA  AK2  AK     0.000000     34620.7800           0
+     100 B2   1    CLA  LT2  LT     0.000000     55013.7800           0
+     101 B2   1    CLA  PX3  PX     0.000000     46422.2000           0
+     102 B2   1    CLA  DT3  DT     0.000000     49195.2000           0
+     103 B2   1    CLA  AK3  AK     0.000000     34620.7800           0
+     104 B2   1    CLA  LT3  LT     0.000000     55013.7800           0
+     105 C2   1    CLA  HB0  HB     0.000000     30478.0300           0
+     106 C2   1    CLA  PX1  PX     0.000000     46422.2000           0
+     107 C2   1    CLA  DT1  DT     0.000000     49195.2000           0
+     108 C2   1    CLA  AK1  AK     0.000000     34620.7800           0
+     109 C2   1    CLA  LT1  LT     0.000000     55013.7800           0
+     110 C2   1    CLA  PX2  PX     0.000000     46422.2000           0
+     111 C2   1    CLA  DT2  DT     0.000000     49195.2000           0
+     112 C2   1    CLA  AK2  AK     0.000000     34620.7800           0
+     113 C2   1    CLA  LT2  LT     0.000000     55013.7800           0
+     114 C2   1    CLA  PX3  PX     0.000000     46422.2000           0
+     115 C2   1    CLA  DT3  DT     0.000000     49195.2000           0
+     116 C2   1    CLA  AK3  AK     0.000000     34620.7800           0
+     117 C2   1    CLA  LT3  LT     0.000000     55013.7800           0
+     118 A3   1    CLA  HB0  HB     0.000000     30478.0300           0
+     119 A3   1    CLA  PX1  PX     0.000000     46422.2000           0
+     120 A3   1    CLA  DT1  DT     0.000000     49195.2000           0
+     121 A3   1    CLA  AK1  AK     0.000000     34620.7800           0
+     122 A3   1    CLA  LT1  LT     0.000000     55013.7800           0
+     123 A3   1    CLA  PX2  PX     0.000000     46422.2000           0
+     124 A3   1    CLA  DT2  DT     0.000000     49195.2000           0
+     125 A3   1    CLA  AK2  AK     0.000000     34620.7800           0
+     126 A3   1    CLA  LT2  LT     0.000000     55013.7800           0
+     127 A3   1    CLA  PX3  PX     0.000000     46422.2000           0
+     128 A3   1    CLA  DT3  DT     0.000000     49195.2000           0
+     129 A3   1    CLA  AK3  AK     0.000000     34620.7800           0
+     130 A3   1    CLA  LT3  LT     0.000000     55013.7800           0
+     131 B3   1    CLA  HB0  HB     0.000000     30478.0300           0
+     132 B3   1    CLA  PX1  PX     0.000000     46422.2000           0
+     133 B3   1    CLA  DT1  DT     0.000000     49195.2000           0
+     134 B3   1    CLA  AK1  AK     0.000000     34620.7800           0
+     135 B3   1    CLA  LT1  LT     0.000000     55013.7800           0
+     136 B3   1    CLA  PX2  PX     0.000000     46422.2000           0
+     137 B3   1    CLA  DT2  DT     0.000000     49195.2000           0
+     138 B3   1    CLA  AK2  AK     0.000000     34620.7800           0
+     139 B3   1    CLA  LT2  LT     0.000000     55013.7800           0
+     140 B3   1    CLA  PX3  PX     0.000000     46422.2000           0
+     141 B3   1    CLA  DT3  DT     0.000000     49195.2000           0
+     142 B3   1    CLA  AK3  AK     0.000000     34620.7800           0
+     143 B3   1    CLA  LT3  LT     0.000000     55013.7800           0
+     144 C3   1    CLA  HB0  HB     0.000000     30478.0300           0
+     145 C3   1    CLA  PX1  PX     0.000000     46422.2000           0
+     146 C3   1    CLA  DT1  DT     0.000000     49195.2000           0
+     147 C3   1    CLA  AK1  AK     0.000000     34620.7800           0
+     148 C3   1    CLA  LT1  LT     0.000000     55013.7800           0
+     149 C3   1    CLA  PX2  PX     0.000000     46422.2000           0
+     150 C3   1    CLA  DT2  DT     0.000000     49195.2000           0
+     151 C3   1    CLA  AK2  AK     0.000000     34620.7800           0
+     152 C3   1    CLA  LT2  LT     0.000000     55013.7800           0
+     153 C3   1    CLA  PX3  PX     0.000000     46422.2000           0
+     154 C3   1    CLA  DT3  DT     0.000000     49195.2000           0
+     155 C3   1    CLA  AK3  AK     0.000000     34620.7800           0
+     156 C3   1    CLA  LT3  LT     0.000000     55013.7800           0
+     157 A4   1    CLA  HB0  HB     0.000000     30478.0300           0
+     158 A4   1    CLA  PX1  PX     0.000000     46422.2000           0
+     159 A4   1    CLA  DT1  DT     0.000000     49195.2000           0
+     160 A4   1    CLA  AK1  AK     0.000000     34620.7800           0
+     161 A4   1    CLA  LT1  LT     0.000000     55013.7800           0
+     162 A4   1    CLA  PX2  PX     0.000000     46422.2000           0
+     163 A4   1    CLA  DT2  DT     0.000000     49195.2000           0
+     164 A4   1    CLA  AK2  AK     0.000000     34620.7800           0
+     165 A4   1    CLA  LT2  LT     0.000000     55013.7800           0
+     166 A4   1    CLA  PX3  PX     0.000000     46422.2000           0
+     167 A4   1    CLA  DT3  DT     0.000000     49195.2000           0
+     168 A4   1    CLA  AK3  AK     0.000000     34620.7800           0
+     169 A4   1    CLA  LT3  LT     0.000000     55013.7800           0
+     170 B4   1    CLA  HB0  HB     0.000000     30478.0300           0
+     171 B4   1    CLA  PX1  PX     0.000000     46422.2000           0
+     172 B4   1    CLA  DT1  DT     0.000000     49195.2000           0
+     173 B4   1    CLA  AK1  AK     0.000000     34620.7800           0
+     174 B4   1    CLA  LT1  LT     0.000000     55013.7800           0
+     175 B4   1    CLA  PX2  PX     0.000000     46422.2000           0
+     176 B4   1    CLA  DT2  DT     0.000000     49195.2000           0
+     177 B4   1    CLA  AK2  AK     0.000000     34620.7800           0
+     178 B4   1    CLA  LT2  LT     0.000000     55013.7800           0
+     179 B4   1    CLA  PX3  PX     0.000000     46422.2000           0
+     180 B4   1    CLA  DT3  DT     0.000000     49195.2000           0
+     181 B4   1    CLA  AK3  AK     0.000000     34620.7800           0
+     182 B4   1    CLA  LT3  LT     0.000000     55013.7800           0
+     183 C4   1    CLA  HB0  HB     0.000000     30478.0300           0
+     184 C4   1    CLA  PX1  PX     0.000000     46422.2000           0
+     185 C4   1    CLA  DT1  DT     0.000000     49195.2000           0
+     186 C4   1    CLA  AK1  AK     0.000000     34620.7800           0
+     187 C4   1    CLA  LT1  LT     0.000000     55013.7800           0
+     188 C4   1    CLA  PX2  PX     0.000000     46422.2000           0
+     189 C4   1    CLA  DT2  DT     0.000000     49195.2000           0
+     190 C4   1    CLA  AK2  AK     0.000000     34620.7800           0
+     191 C4   1    CLA  LT2  LT     0.000000     55013.7800           0
+     192 C4   1    CLA  PX3  PX     0.000000     46422.2000           0
+     193 C4   1    CLA  DT3  DT     0.000000     49195.2000           0
+     194 C4   1    CLA  AK3  AK     0.000000     34620.7800           0
+     195 C4   1    CLA  LT3  LT     0.000000     55013.7800           0
+     196 A5   1    CLA  HB0  HB     0.000000     30478.0300           0
+     197 A5   1    CLA  PX1  PX     0.000000     46422.2000           0
+     198 A5   1    CLA  DT1  DT     0.000000     49195.2000           0
+     199 A5   1    CLA  AK1  AK     0.000000     34620.7800           0
+     200 A5   1    CLA  LT1  LT     0.000000     55013.7800           0
+     201 A5   1    CLA  PX2  PX     0.000000     46422.2000           0
+     202 A5   1    CLA  DT2  DT     0.000000     49195.2000           0
+     203 A5   1    CLA  AK2  AK     0.000000     34620.7800           0
+     204 A5   1    CLA  LT2  LT     0.000000     55013.7800           0
+     205 A5   1    CLA  PX3  PX     0.000000     46422.2000           0
+     206 A5   1    CLA  DT3  DT     0.000000     49195.2000           0
+     207 A5   1    CLA  AK3  AK     0.000000     34620.7800           0
+     208 A5   1    CLA  LT3  LT     0.000000     55013.7800           0
+     209 B5   1    CLA  HB0  HB     0.000000     30478.0300           0
+     210 B5   1    CLA  PX1  PX     0.000000     46422.2000           0
+     211 B5   1    CLA  DT1  DT     0.000000     49195.2000           0
+     212 B5   1    CLA  AK1  AK     0.000000     34620.7800           0
+     213 B5   1    CLA  LT1  LT     0.000000     55013.7800           0
+     214 B5   1    CLA  PX2  PX     0.000000     46422.2000           0
+     215 B5   1    CLA  DT2  DT     0.000000     49195.2000           0
+     216 B5   1    CLA  AK2  AK     0.000000     34620.7800           0
+     217 B5   1    CLA  LT2  LT     0.000000     55013.7800           0
+     218 B5   1    CLA  PX3  PX     0.000000     46422.2000           0
+     219 B5   1    CLA  DT3  DT     0.000000     49195.2000           0
+     220 B5   1    CLA  AK3  AK     0.000000     34620.7800           0
+     221 B5   1    CLA  LT3  LT     0.000000     55013.7800           0
+     222 C5   1    CLA  HB0  HB     0.000000     30478.0300           0
+     223 C5   1    CLA  PX1  PX     0.000000     46422.2000           0
+     224 C5   1    CLA  DT1  DT     0.000000     49195.2000           0
+     225 C5   1    CLA  AK1  AK     0.000000     34620.7800           0
+     226 C5   1    CLA  LT1  LT     0.000000     55013.7800           0
+     227 C5   1    CLA  PX2  PX     0.000000     46422.2000           0
+     228 C5   1    CLA  DT2  DT     0.000000     49195.2000           0
+     229 C5   1    CLA  AK2  AK     0.000000     34620.7800           0
+     230 C5   1    CLA  LT2  LT     0.000000     55013.7800           0
+     231 C5   1    CLA  PX3  PX     0.000000     46422.2000           0
+     232 C5   1    CLA  DT3  DT     0.000000     49195.2000           0
+     233 C5   1    CLA  AK3  AK     0.000000     34620.7800           0
+     234 C5   1    CLA  LT3  LT     0.000000     55013.7800           0
+     235 A6   1    CLA  HB0  HB     0.000000     30478.0300           0
+     236 A6   1    CLA  PX1  PX     0.000000     46422.2000           0
+     237 A6   1    CLA  DT1  DT     0.000000     49195.2000           0
+     238 A6   1    CLA  AK1  AK     0.000000     34620.7800           0
+     239 A6   1    CLA  LT1  LT     0.000000     55013.7800           0
+     240 A6   1    CLA  PX2  PX     0.000000     46422.2000           0
+     241 A6   1    CLA  DT2  DT     0.000000     49195.2000           0
+     242 A6   1    CLA  AK2  AK     0.000000     34620.7800           0
+     243 A6   1    CLA  LT2  LT     0.000000     55013.7800           0
+     244 A6   1    CLA  PX3  PX     0.000000     46422.2000           0
+     245 A6   1    CLA  DT3  DT     0.000000     49195.2000           0
+     246 A6   1    CLA  AK3  AK     0.000000     34620.7800           0
+     247 A6   1    CLA  LT3  LT     0.000000     55013.7800           0
+     248 B6   1    CLA  HB0  HB     0.000000     30478.0300           0
+     249 B6   1    CLA  PX1  PX     0.000000     46422.2000           0
+     250 B6   1    CLA  DT1  DT     0.000000     49195.2000           0
+     251 B6   1    CLA  AK1  AK     0.000000     34620.7800           0
+     252 B6   1    CLA  LT1  LT     0.000000     55013.7800           0
+     253 B6   1    CLA  PX2  PX     0.000000     46422.2000           0
+     254 B6   1    CLA  DT2  DT     0.000000     49195.2000           0
+     255 B6   1    CLA  AK2  AK     0.000000     34620.7800           0
+     256 B6   1    CLA  LT2  LT     0.000000     55013.7800           0
+     257 B6   1    CLA  PX3  PX     0.000000     46422.2000           0
+     258 B6   1    CLA  DT3  DT     0.000000     49195.2000           0
+     259 B6   1    CLA  AK3  AK     0.000000     34620.7800           0
+     260 B6   1    CLA  LT3  LT     0.000000     55013.7800           0
+     261 C6   1    CLA  HB0  HB     0.000000     30478.0300           0
+     262 C6   1    CLA  PX1  PX     0.000000     46422.2000           0
+     263 C6   1    CLA  DT1  DT     0.000000     49195.2000           0
+     264 C6   1    CLA  AK1  AK     0.000000     34620.7800           0
+     265 C6   1    CLA  LT1  LT     0.000000     55013.7800           0
+     266 C6   1    CLA  PX2  PX     0.000000     46422.2000           0
+     267 C6   1    CLA  DT2  DT     0.000000     49195.2000           0
+     268 C6   1    CLA  AK2  AK     0.000000     34620.7800           0
+     269 C6   1    CLA  LT2  LT     0.000000     55013.7800           0
+     270 C6   1    CLA  PX3  PX     0.000000     46422.2000           0
+     271 C6   1    CLA  DT3  DT     0.000000     49195.2000           0
+     272 C6   1    CLA  AK3  AK     0.000000     34620.7800           0
+     273 C6   1    CLA  LT3  LT     0.000000     55013.7800           0
+     274 A7   1    CLA  HB0  HB     0.000000     30478.0300           0
+     275 A7   1    CLA  PX1  PX     0.000000     46422.2000           0
+     276 A7   1    CLA  DT1  DT     0.000000     49195.2000           0
+     277 A7   1    CLA  AK1  AK     0.000000     34620.7800           0
+     278 A7   1    CLA  LT1  LT     0.000000     55013.7800           0
+     279 A7   1    CLA  PX2  PX     0.000000     46422.2000           0
+     280 A7   1    CLA  DT2  DT     0.000000     49195.2000           0
+     281 A7   1    CLA  AK2  AK     0.000000     34620.7800           0
+     282 A7   1    CLA  LT2  LT     0.000000     55013.7800           0
+     283 A7   1    CLA  PX3  PX     0.000000     46422.2000           0
+     284 A7   1    CLA  DT3  DT     0.000000     49195.2000           0
+     285 A7   1    CLA  AK3  AK     0.000000     34620.7800           0
+     286 A7   1    CLA  LT3  LT     0.000000     55013.7800           0
+     287 B7   1    CLA  HB0  HB     0.000000     30478.0300           0
+     288 B7   1    CLA  PX1  PX     0.000000     46422.2000           0
+     289 B7   1    CLA  DT1  DT     0.000000     49195.2000           0
+     290 B7   1    CLA  AK1  AK     0.000000     34620.7800           0
+     291 B7   1    CLA  LT1  LT     0.000000     55013.7800           0
+     292 B7   1    CLA  PX2  PX     0.000000     46422.2000           0
+     293 B7   1    CLA  DT2  DT     0.000000     49195.2000           0
+     294 B7   1    CLA  AK2  AK     0.000000     34620.7800           0
+     295 B7   1    CLA  LT2  LT     0.000000     55013.7800           0
+     296 B7   1    CLA  PX3  PX     0.000000     46422.2000           0
+     297 B7   1    CLA  DT3  DT     0.000000     49195.2000           0
+     298 B7   1    CLA  AK3  AK     0.000000     34620.7800           0
+     299 B7   1    CLA  LT3  LT     0.000000     55013.7800           0
+     300 C7   1    CLA  HB0  HB     0.000000     30478.0300           0
+     301 C7   1    CLA  PX1  PX     0.000000     46422.2000           0
+     302 C7   1    CLA  DT1  DT     0.000000     49195.2000           0
+     303 C7   1    CLA  AK1  AK     0.000000     34620.7800           0
+     304 C7   1    CLA  LT1  LT     0.000000     55013.7800           0
+     305 C7   1    CLA  PX2  PX     0.000000     46422.2000           0
+     306 C7   1    CLA  DT2  DT     0.000000     49195.2000           0
+     307 C7   1    CLA  AK2  AK     0.000000     34620.7800           0
+     308 C7   1    CLA  LT2  LT     0.000000     55013.7800           0
+     309 C7   1    CLA  PX3  PX     0.000000     46422.2000           0
+     310 C7   1    CLA  DT3  DT     0.000000     49195.2000           0
+     311 C7   1    CLA  AK3  AK     0.000000     34620.7800           0
+     312 C7   1    CLA  LT3  LT     0.000000     55013.7800           0
+     313 A8   1    CLA  HB0  HB     0.000000     30478.0300           0
+     314 A8   1    CLA  PX1  PX     0.000000     46422.2000           0
+     315 A8   1    CLA  DT1  DT     0.000000     49195.2000           0
+     316 A8   1    CLA  AK1  AK     0.000000     34620.7800           0
+     317 A8   1    CLA  LT1  LT     0.000000     55013.7800           0
+     318 A8   1    CLA  PX2  PX     0.000000     46422.2000           0
+     319 A8   1    CLA  DT2  DT     0.000000     49195.2000           0
+     320 A8   1    CLA  AK2  AK     0.000000     34620.7800           0
+     321 A8   1    CLA  LT2  LT     0.000000     55013.7800           0
+     322 A8   1    CLA  PX3  PX     0.000000     46422.2000           0
+     323 A8   1    CLA  DT3  DT     0.000000     49195.2000           0
+     324 A8   1    CLA  AK3  AK     0.000000     34620.7800           0
+     325 A8   1    CLA  LT3  LT     0.000000     55013.7800           0
+     326 B8   1    CLA  HB0  HB     0.000000     30478.0300           0
+     327 B8   1    CLA  PX1  PX     0.000000     46422.2000           0
+     328 B8   1    CLA  DT1  DT     0.000000     49195.2000           0
+     329 B8   1    CLA  AK1  AK     0.000000     34620.7800           0
+     330 B8   1    CLA  LT1  LT     0.000000     55013.7800           0
+     331 B8   1    CLA  PX2  PX     0.000000     46422.2000           0
+     332 B8   1    CLA  DT2  DT     0.000000     49195.2000           0
+     333 B8   1    CLA  AK2  AK     0.000000     34620.7800           0
+     334 B8   1    CLA  LT2  LT     0.000000     55013.7800           0
+     335 B8   1    CLA  PX3  PX     0.000000     46422.2000           0
+     336 B8   1    CLA  DT3  DT     0.000000     49195.2000           0
+     337 B8   1    CLA  AK3  AK     0.000000     34620.7800           0
+     338 B8   1    CLA  LT3  LT     0.000000     55013.7800           0
+     339 C8   1    CLA  HB0  HB     0.000000     30478.0300           0
+     340 C8   1    CLA  PX1  PX     0.000000     46422.2000           0
+     341 C8   1    CLA  DT1  DT     0.000000     49195.2000           0
+     342 C8   1    CLA  AK1  AK     0.000000     34620.7800           0
+     343 C8   1    CLA  LT1  LT     0.000000     55013.7800           0
+     344 C8   1    CLA  PX2  PX     0.000000     46422.2000           0
+     345 C8   1    CLA  DT2  DT     0.000000     49195.2000           0
+     346 C8   1    CLA  AK2  AK     0.000000     34620.7800           0
+     347 C8   1    CLA  LT2  LT     0.000000     55013.7800           0
+     348 C8   1    CLA  PX3  PX     0.000000     46422.2000           0
+     349 C8   1    CLA  DT3  DT     0.000000     49195.2000           0
+     350 C8   1    CLA  AK3  AK     0.000000     34620.7800           0
+     351 C8   1    CLA  LT3  LT     0.000000     55013.7800           0
+     352 A9   1    CLA  HB0  HB     0.000000     30478.0300           0
+     353 A9   1    CLA  PX1  PX     0.000000     46422.2000           0
+     354 A9   1    CLA  DT1  DT     0.000000     49195.2000           0
+     355 A9   1    CLA  AK1  AK     0.000000     34620.7800           0
+     356 A9   1    CLA  LT1  LT     0.000000     55013.7800           0
+     357 A9   1    CLA  PX2  PX     0.000000     46422.2000           0
+     358 A9   1    CLA  DT2  DT     0.000000     49195.2000           0
+     359 A9   1    CLA  AK2  AK     0.000000     34620.7800           0
+     360 A9   1    CLA  LT2  LT     0.000000     55013.7800           0
+     361 A9   1    CLA  PX3  PX     0.000000     46422.2000           0
+     362 A9   1    CLA  DT3  DT     0.000000     49195.2000           0
+     363 A9   1    CLA  AK3  AK     0.000000     34620.7800           0
+     364 A9   1    CLA  LT3  LT     0.000000     55013.7800           0
+     365 B9   1    CLA  HB0  HB     0.000000     30478.0300           0
+     366 B9   1    CLA  PX1  PX     0.000000     46422.2000           0
+     367 B9   1    CLA  DT1  DT     0.000000     49195.2000           0
+     368 B9   1    CLA  AK1  AK     0.000000     34620.7800           0
+     369 B9   1    CLA  LT1  LT     0.000000     55013.7800           0
+     370 B9   1    CLA  PX2  PX     0.000000     46422.2000           0
+     371 B9   1    CLA  DT2  DT     0.000000     49195.2000           0
+     372 B9   1    CLA  AK2  AK     0.000000     34620.7800           0
+     373 B9   1    CLA  LT2  LT     0.000000     55013.7800           0
+     374 B9   1    CLA  PX3  PX     0.000000     46422.2000           0
+     375 B9   1    CLA  DT3  DT     0.000000     49195.2000           0
+     376 B9   1    CLA  AK3  AK     0.000000     34620.7800           0
+     377 B9   1    CLA  LT3  LT     0.000000     55013.7800           0
+     378 C9   1    CLA  HB0  HB     0.000000     30478.0300           0
+     379 C9   1    CLA  PX1  PX     0.000000     46422.2000           0
+     380 C9   1    CLA  DT1  DT     0.000000     49195.2000           0
+     381 C9   1    CLA  AK1  AK     0.000000     34620.7800           0
+     382 C9   1    CLA  LT1  LT     0.000000     55013.7800           0
+     383 C9   1    CLA  PX2  PX     0.000000     46422.2000           0
+     384 C9   1    CLA  DT2  DT     0.000000     49195.2000           0
+     385 C9   1    CLA  AK2  AK     0.000000     34620.7800           0
+     386 C9   1    CLA  LT2  LT     0.000000     55013.7800           0
+     387 C9   1    CLA  PX3  PX     0.000000     46422.2000           0
+     388 C9   1    CLA  DT3  DT     0.000000     49195.2000           0
+     389 C9   1    CLA  AK3  AK     0.000000     34620.7800           0
+     390 C9   1    CLA  LT3  LT     0.000000     55013.7800           0
+     391 A10  1    CLA  HB0  HB     0.000000     30478.0300           0
+     392 A10  1    CLA  PX1  PX     0.000000     46422.2000           0
+     393 A10  1    CLA  DT1  DT     0.000000     49195.2000           0
+     394 A10  1    CLA  AK1  AK     0.000000     34620.7800           0
+     395 A10  1    CLA  LT1  LT     0.000000     55013.7800           0
+     396 A10  1    CLA  PX2  PX     0.000000     46422.2000           0
+     397 A10  1    CLA  DT2  DT     0.000000     49195.2000           0
+     398 A10  1    CLA  AK2  AK     0.000000     34620.7800           0
+     399 A10  1    CLA  LT2  LT     0.000000     55013.7800           0
+     400 A10  1    CLA  PX3  PX     0.000000     46422.2000           0
+     401 A10  1    CLA  DT3  DT     0.000000     49195.2000           0
+     402 A10  1    CLA  AK3  AK     0.000000     34620.7800           0
+     403 A10  1    CLA  LT3  LT     0.000000     55013.7800           0
+     404 B10  1    CLA  HB0  HB     0.000000     30478.0300           0
+     405 B10  1    CLA  PX1  PX     0.000000     46422.2000           0
+     406 B10  1    CLA  DT1  DT     0.000000     49195.2000           0
+     407 B10  1    CLA  AK1  AK     0.000000     34620.7800           0
+     408 B10  1    CLA  LT1  LT     0.000000     55013.7800           0
+     409 B10  1    CLA  PX2  PX     0.000000     46422.2000           0
+     410 B10  1    CLA  DT2  DT     0.000000     49195.2000           0
+     411 B10  1    CLA  AK2  AK     0.000000     34620.7800           0
+     412 B10  1    CLA  LT2  LT     0.000000     55013.7800           0
+     413 B10  1    CLA  PX3  PX     0.000000     46422.2000           0
+     414 B10  1    CLA  DT3  DT     0.000000     49195.2000           0
+     415 B10  1    CLA  AK3  AK     0.000000     34620.7800           0
+     416 B10  1    CLA  LT3  LT     0.000000     55013.7800           0
+     417 C10  1    CLA  HB0  HB     0.000000     30478.0300           0
+     418 C10  1    CLA  PX1  PX     0.000000     46422.2000           0
+     419 C10  1    CLA  DT1  DT     0.000000     49195.2000           0
+     420 C10  1    CLA  AK1  AK     0.000000     34620.7800           0
+     421 C10  1    CLA  LT1  LT     0.000000     55013.7800           0
+     422 C10  1    CLA  PX2  PX     0.000000     46422.2000           0
+     423 C10  1    CLA  DT2  DT     0.000000     49195.2000           0
+     424 C10  1    CLA  AK2  AK     0.000000     34620.7800           0
+     425 C10  1    CLA  LT2  LT     0.000000     55013.7800           0
+     426 C10  1    CLA  PX3  PX     0.000000     46422.2000           0
+     427 C10  1    CLA  DT3  DT     0.000000     49195.2000           0
+     428 C10  1    CLA  AK3  AK     0.000000     34620.7800           0
+     429 C10  1    CLA  LT3  LT     0.000000     55013.7800           0
+     430 A11  1    CLA  HB0  HB     0.000000     30478.0300           0
+     431 A11  1    CLA  PX1  PX     0.000000     46422.2000           0
+     432 A11  1    CLA  DT1  DT     0.000000     49195.2000           0
+     433 A11  1    CLA  AK1  AK     0.000000     34620.7800           0
+     434 A11  1    CLA  LT1  LT     0.000000     55013.7800           0
+     435 A11  1    CLA  PX2  PX     0.000000     46422.2000           0
+     436 A11  1    CLA  DT2  DT     0.000000     49195.2000           0
+     437 A11  1    CLA  AK2  AK     0.000000     34620.7800           0
+     438 A11  1    CLA  LT2  LT     0.000000     55013.7800           0
+     439 A11  1    CLA  PX3  PX     0.000000     46422.2000           0
+     440 A11  1    CLA  DT3  DT     0.000000     49195.2000           0
+     441 A11  1    CLA  AK3  AK     0.000000     34620.7800           0
+     442 A11  1    CLA  LT3  LT     0.000000     55013.7800           0
+     443 B11  1    CLA  HB0  HB     0.000000     30478.0300           0
+     444 B11  1    CLA  PX1  PX     0.000000     46422.2000           0
+     445 B11  1    CLA  DT1  DT     0.000000     49195.2000           0
+     446 B11  1    CLA  AK1  AK     0.000000     34620.7800           0
+     447 B11  1    CLA  LT1  LT     0.000000     55013.7800           0
+     448 B11  1    CLA  PX2  PX     0.000000     46422.2000           0
+     449 B11  1    CLA  DT2  DT     0.000000     49195.2000           0
+     450 B11  1    CLA  AK2  AK     0.000000     34620.7800           0
+     451 B11  1    CLA  LT2  LT     0.000000     55013.7800           0
+     452 B11  1    CLA  PX3  PX     0.000000     46422.2000           0
+     453 B11  1    CLA  DT3  DT     0.000000     49195.2000           0
+     454 B11  1    CLA  AK3  AK     0.000000     34620.7800           0
+     455 B11  1    CLA  LT3  LT     0.000000     55013.7800           0
+     456 C11  1    CLA  HB0  HB     0.000000     30478.0300           0
+     457 C11  1    CLA  PX1  PX     0.000000     46422.2000           0
+     458 C11  1    CLA  DT1  DT     0.000000     49195.2000           0
+     459 C11  1    CLA  AK1  AK     0.000000     34620.7800           0
+     460 C11  1    CLA  LT1  LT     0.000000     55013.7800           0
+     461 C11  1    CLA  PX2  PX     0.000000     46422.2000           0
+     462 C11  1    CLA  DT2  DT     0.000000     49195.2000           0
+     463 C11  1    CLA  AK2  AK     0.000000     34620.7800           0
+     464 C11  1    CLA  LT2  LT     0.000000     55013.7800           0
+     465 C11  1    CLA  PX3  PX     0.000000     46422.2000           0
+     466 C11  1    CLA  DT3  DT     0.000000     49195.2000           0
+     467 C11  1    CLA  AK3  AK     0.000000     34620.7800           0
+     468 C11  1    CLA  LT3  LT     0.000000     55013.7800           0
+
+     432 !NBOND: bonds
+       1       2       1       6       1      10       2       3
+       3       4       4       5       6       7       7       8
+       8       9      10      11      11      12      12      13
+      14      15      14      19      14      23      15      16
+      16      17      17      18      19      20      20      21
+      21      22      23      24      24      25      25      26
+      27      28      27      32      27      36      28      29
+      29      30      30      31      32      33      33      34
+      34      35      36      37      37      38      38      39
+      40      41      40      45      40      49      41      42
+      42      43      43      44      45      46      46      47
+      47      48      49      50      50      51      51      52
+      53      54      53      58      53      62      54      55
+      55      56      56      57      58      59      59      60
+      60      61      62      63      63      64      64      65
+      66      67      66      71      66      75      67      68
+      68      69      69      70      71      72      72      73
+      73      74      75      76      76      77      77      78
+      79      80      79      84      79      88      80      81
+      81      82      82      83      84      85      85      86
+      86      87      88      89      89      90      90      91
+      92      93      92      97      92     101      93      94
+      94      95      95      96      97      98      98      99
+      99     100     101     102     102     103     103     104
+     105     106     105     110     105     114     106     107
+     107     108     108     109     110     111     111     112
+     112     113     114     115     115     116     116     117
+     118     119     118     123     118     127     119     120
+     120     121     121     122     123     124     124     125
+     125     126     127     128     128     129     129     130
+     131     132     131     136     131     140     132     133
+     133     134     134     135     136     137     137     138
+     138     139     140     141     141     142     142     143
+     144     145     144     149     144     153     145     146
+     146     147     147     148     149     150     150     151
+     151     152     153     154     154     155     155     156
+     157     158     157     162     157     166     158     159
+     159     160     160     161     162     163     163     164
+     164     165     166     167     167     168     168     169
+     170     171     170     175     170     179     171     172
+     172     173     173     174     175     176     176     177
+     177     178     179     180     180     181     181     182
+     183     184     183     188     183     192     184     185
+     185     186     186     187     188     189     189     190
+     190     191     192     193     193     194     194     195
+     196     197     196     201     196     205     197     198
+     198     199     199     200     201     202     202     203
+     203     204     205     206     206     207     207     208
+     209     210     209     214     209     218     210     211
+     211     212     212     213     214     215     215     216
+     216     217     218     219     219     220     220     221
+     222     223     222     227     222     231     223     224
+     224     225     225     226     227     228     228     229
+     229     230     231     232     232     233     233     234
+     235     236     235     240     235     244     236     237
+     237     238     238     239     240     241     241     242
+     242     243     244     245     245     246     246     247
+     248     249     248     253     248     257     249     250
+     250     251     251     252     253     254     254     255
+     255     256     257     258     258     259     259     260
+     261     262     261     266     261     270     262     263
+     263     264     264     265     266     267     267     268
+     268     269     270     271     271     272     272     273
+     274     275     274     279     274     283     275     276
+     276     277     277     278     279     280     280     281
+     281     282     283     284     284     285     285     286
+     287     288     287     292     287     296     288     289
+     289     290     290     291     292     293     293     294
+     294     295     296     297     297     298     298     299
+     300     301     300     305     300     309     301     302
+     302     303     303     304     305     306     306     307
+     307     308     309     310     310     311     311     312
+     313     314     313     318     313     322     314     315
+     315     316     316     317     318     319     319     320
+     320     321     322     323     323     324     324     325
+     326     327     326     331     326     335     327     328
+     328     329     329     330     331     332     332     333
+     333     334     335     336     336     337     337     338
+     339     340     339     344     339     348     340     341
+     341     342     342     343     344     345     345     346
+     346     347     348     349     349     350     350     351
+     352     353     352     357     352     361     353     354
+     354     355     355     356     357     358     358     359
+     359     360     361     362     362     363     363     364
+     365     366     365     370     365     374     366     367
+     367     368     368     369     370     371     371     372
+     372     373     374     375     375     376     376     377
+     378     379     378     383     378     387     379     380
+     380     381     381     382     383     384     384     385
+     385     386     387     388     388     389     389     390
+     391     392     391     396     391     400     392     393
+     393     394     394     395     396     397     397     398
+     398     399     400     401     401     402     402     403
+     404     405     404     409     404     413     405     406
+     406     407     407     408     409     410     410     411
+     411     412     413     414     414     415     415     416
+     417     418     417     422     417     426     418     419
+     419     420     420     421     422     423     423     424
+     424     425     426     427     427     428     428     429
+     430     431     430     435     430     439     431     432
+     432     433     433     434     435     436     436     437
+     437     438     439     440     440     441     441     442
+     443     444     443     448     443     452     444     445
+     445     446     446     447     448     449     449     450
+     450     451     452     453     453     454     454     455
+     456     457     456     461     456     465     457     458
+     458     459     459     460     461     462     462     463
+     463     464     465     466     466     467     467     468
+
+     432 !NTHETA: angles
+       1      10      11       1       6       7       1       2       3
+       2       3       4       2       1      10       2       1       6
+       3       4       5       6       7       8       6       1      10
+       7       8       9      10      11      12      11      12      13
+      14      23      24      14      19      20      14      15      16
+      15      16      17      15      14      23      15      14      19
+      16      17      18      19      20      21      19      14      23
+      20      21      22      23      24      25      24      25      26
+      27      36      37      27      32      33      27      28      29
+      28      29      30      28      27      36      28      27      32
+      29      30      31      32      33      34      32      27      36
+      33      34      35      36      37      38      37      38      39
+      40      49      50      40      45      46      40      41      42
+      41      42      43      41      40      49      41      40      45
+      42      43      44      45      46      47      45      40      49
+      46      47      48      49      50      51      50      51      52
+      53      62      63      53      58      59      53      54      55
+      54      55      56      54      53      62      54      53      58
+      55      56      57      58      59      60      58      53      62
+      59      60      61      62      63      64      63      64      65
+      66      75      76      66      71      72      66      67      68
+      67      68      69      67      66      75      67      66      71
+      68      69      70      71      72      73      71      66      75
+      72      73      74      75      76      77      76      77      78
+      79      88      89      79      84      85      79      80      81
+      80      81      82      80      79      88      80      79      84
+      81      82      83      84      85      86      84      79      88
+      85      86      87      88      89      90      89      90      91
+      92     101     102      92      97      98      92      93      94
+      93      94      95      93      92     101      93      92      97
+      94      95      96      97      98      99      97      92     101
+      98      99     100     101     102     103     102     103     104
+     105     114     115     105     110     111     105     106     107
+     106     107     108     106     105     114     106     105     110
+     107     108     109     110     111     112     110     105     114
+     111     112     113     114     115     116     115     116     117
+     118     127     128     118     123     124     118     119     120
+     119     120     121     119     118     127     119     118     123
+     120     121     122     123     124     125     123     118     127
+     124     125     126     127     128     129     128     129     130
+     131     140     141     131     136     137     131     132     133
+     132     133     134     132     131     140     132     131     136
+     133     134     135     136     137     138     136     131     140
+     137     138     139     140     141     142     141     142     143
+     144     153     154     144     149     150     144     145     146
+     145     146     147     145     144     153     145     144     149
+     146     147     148     149     150     151     149     144     153
+     150     151     152     153     154     155     154     155     156
+     157     166     167     157     162     163     157     158     159
+     158     159     160     158     157     166     158     157     162
+     159     160     161     162     163     164     162     157     166
+     163     164     165     166     167     168     167     168     169
+     170     179     180     170     175     176     170     171     172
+     171     172     173     171     170     179     171     170     175
+     172     173     174     175     176     177     175     170     179
+     176     177     178     179     180     181     180     181     182
+     183     192     193     183     188     189     183     184     185
+     184     185     186     184     183     192     184     183     188
+     185     186     187     188     189     190     188     183     192
+     189     190     191     192     193     194     193     194     195
+     196     205     206     196     201     202     196     197     198
+     197     198     199     197     196     205     197     196     201
+     198     199     200     201     202     203     201     196     205
+     202     203     204     205     206     207     206     207     208
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+     210     211     212     210     209     218     210     209     214
+     211     212     213     214     215     216     214     209     218
+     215     216     217     218     219     220     219     220     221
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+     236     237     238     236     235     244     236     235     240
+     237     238     239     240     241     242     240     235     244
+     241     242     243     244     245     246     245     246     247
+     248     257     258     248     253     254     248     249     250
+     249     250     251     249     248     257     249     248     253
+     250     251     252     253     254     255     253     248     257
+     254     255     256     257     258     259     258     259     260
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+     262     263     264     262     261     270     262     261     266
+     263     264     265     266     267     268     266     261     270
+     267     268     269     270     271     272     271     272     273
+     274     283     284     274     279     280     274     275     276
+     275     276     277     275     274     283     275     274     279
+     276     277     278     279     280     281     279     274     283
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+     314     315     316     314     313     322     314     313     318
+     315     316     317     318     319     320     318     313     322
+     319     320     321     322     323     324     323     324     325
+     326     335     336     326     331     332     326     327     328
+     327     328     329     327     326     335     327     326     331
+     328     329     330     331     332     333     331     326     335
+     332     333     334     335     336     337     336     337     338
+     339     348     349     339     344     345     339     340     341
+     340     341     342     340     339     348     340     339     344
+     341     342     343     344     345     346     344     339     348
+     345     346     347     348     349     350     349     350     351
+     352     361     362     352     357     358     352     353     354
+     353     354     355     353     352     361     353     352     357
+     354     355     356     357     358     359     357     352     361
+     358     359     360     361     362     363     362     363     364
+     365     374     375     365     370     371     365     366     367
+     366     367     368     366     365     374     366     365     370
+     367     368     369     370     371     372     370     365     374
+     371     372     373     374     375     376     375     376     377
+     378     387     388     378     383     384     378     379     380
+     379     380     381     379     378     387     379     378     383
+     380     381     382     383     384     385     383     378     387
+     384     385     386     387     388     389     388     389     390
+     391     400     401     391     396     397     391     392     393
+     392     393     394     392     391     400     392     391     396
+     393     394     395     396     397     398     396     391     400
+     397     398     399     400     401     402     401     402     403
+     404     413     414     404     409     410     404     405     406
+     405     406     407     405     404     413     405     404     409
+     406     407     408     409     410     411     409     404     413
+     410     411     412     413     414     415     414     415     416
+     417     426     427     417     422     423     417     418     419
+     418     419     420     418     417     426     418     417     422
+     419     420     421     422     423     424     422     417     426
+     423     424     425     426     427     428     427     428     429
+     430     439     440     430     435     436     430     431     432
+     431     432     433     431     430     439     431     430     435
+     432     433     434     435     436     437     435     430     439
+     436     437     438     439     440     441     440     441     442
+     443     452     453     443     448     449     443     444     445
+     444     445     446     444     443     452     444     443     448
+     445     446     447     448     449     450     448     443     452
+     449     450     451     452     453     454     453     454     455
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+     457     458     459     457     456     465     457     456     461
+     458     459     460     461     462     463     461     456     465
+     462     463     464     465     466     467     466     467     468
+
+       0 !NPHI: dihedrals
+
+
+     468 !NIMPHI: impropers
+       1       2       3       4       1       6       7       8
+       1      10      11      12       2       6       1      10
+       2       1       6       7       2       1      10      11
+       2       3       4       5       6       1       2       3
+       6       1      10      11       6       7       8       9
+      10       1       2       3      10       1       6       7
+      10      11      12      13      14      15      16      17
+      14      19      20      21      14      23      24      25
+      15      19      14      23      15      14      19      20
+      15      14      23      24      15      16      17      18
+      19      14      15      16      19      14      23      24
+      19      20      21      22      23      14      15      16
+      23      14      19      20      23      24      25      26
+      27      28      29      30      27      32      33      34
+      27      36      37      38      28      32      27      36
+      28      27      32      33      28      27      36      37
+      28      29      30      31      32      27      28      29
+      32      27      36      37      32      33      34      35
+      36      27      28      29      36      27      32      33
+      36      37      38      39      40      41      42      43
+      40      45      46      47      40      49      50      51
+      41      45      40      49      41      40      45      46
+      41      40      49      50      41      42      43      44
+      45      40      41      42      45      40      49      50
+      45      46      47      48      49      40      41      42
+      49      40      45      46      49      50      51      52
+      53      54      55      56      53      58      59      60
+      53      62      63      64      54      58      53      62
+      54      53      58      59      54      53      62      63
+      54      55      56      57      58      53      54      55
+      58      53      62      63      58      59      60      61
+      62      53      54      55      62      53      58      59
+      62      63      64      65      66      67      68      69
+      66      71      72      73      66      75      76      77
+      67      71      66      75      67      66      71      72
+      67      66      75      76      67      68      69      70
+      71      66      67      68      71      66      75      76
+      71      72      73      74      75      66      67      68
+      75      66      71      72      75      76      77      78
+      79      80      81      82      79      84      85      86
+      79      88      89      90      80      84      79      88
+      80      79      84      85      80      79      88      89
+      80      81      82      83      84      79      80      81
+      84      79      88      89      84      85      86      87
+      88      79      80      81      88      79      84      85
+      88      89      90      91      92      93      94      95
+      92      97      98      99      92     101     102     103
+      93      97      92     101      93      92      97      98
+      93      92     101     102      93      94      95      96
+      97      92      93      94      97      92     101     102
+      97      98      99     100     101      92      93      94
+     101      92      97      98     101     102     103     104
+     105     106     107     108     105     110     111     112
+     105     114     115     116     106     110     105     114
+     106     105     110     111     106     105     114     115
+     106     107     108     109     110     105     106     107
+     110     105     114     115     110     111     112     113
+     114     105     106     107     114     105     110     111
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+     119     123     118     127     119     118     123     124
+     119     118     127     128     119     120     121     122
+     123     118     119     120     123     118     127     128
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+     127     118     123     124     127     128     129     130
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+     131     140     141     142     132     136     131     140
+     132     131     136     137     132     131     140     141
+     132     133     134     135     136     131     132     133
+     136     131     140     141     136     137     138     139
+     140     131     132     133     140     131     136     137
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+     144     149     150     151     144     153     154     155
+     145     149     144     153     145     144     149     150
+     145     144     153     154     145     146     147     148
+     149     144     145     146     149     144     153     154
+     149     150     151     152     153     144     145     146
+     153     144     149     150     153     154     155     156
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+     158     157     162     163     158     157     166     167
+     158     159     160     161     162     157     158     159
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+     166     157     158     159     166     157     162     163
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+     370     365     374     375     370     371     372     373
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+     379     378     387     388     379     380     381     382
+     383     378     379     380     383     378     387     388
+     383     384     385     386     387     378     379     380
+     387     378     383     384     387     388     389     390
+     391     392     393     394     391     396     397     398
+     391     400     401     402     392     396     391     400
+     392     391     396     397     392     391     400     401
+     392     393     394     395     396     391     392     393
+     396     391     400     401     396     397     398     399
+     400     391     392     393     400     391     396     397
+     400     401     402     403     404     405     406     407
+     404     409     410     411     404     413     414     415
+     405     409     404     413     405     404     409     410
+     405     404     413     414     405     406     407     408
+     409     404     405     406     409     404     413     414
+     409     410     411     412     413     404     405     406
+     413     404     409     410     413     414     415     416
+     417     418     419     420     417     422     423     424
+     417     426     427     428     418     422     417     426
+     418     417     422     423     418     417     426     427
+     418     419     420     421     422     417     418     419
+     422     417     426     427     422     423     424     425
+     426     417     418     419     426     417     422     423
+     426     427     428     429     430     431     432     433
+     430     435     436     437     430     439     440     441
+     431     435     430     439     431     430     435     436
+     431     430     439     440     431     432     433     434
+     435     430     431     432     435     430     439     440
+     435     436     437     438     439     430     431     432
+     439     430     435     436     439     440     441     442
+     443     444     445     446     443     448     449     450
+     443     452     453     454     444     448     443     452
+     444     443     448     449     444     443     452     453
+     444     445     446     447     448     443     444     445
+     448     443     452     453     448     449     450     451
+     452     443     444     445     452     443     448     449
+     452     453     454     455     456     457     458     459
+     456     461     462     463     456     465     466     467
+     457     461     456     465     457     456     461     462
+     457     456     465     466     457     458     459     460
+     461     456     457     458     461     456     465     466
+     461     462     463     464     465     456     457     458
+     465     456     461     462     465     466     467     468
+
+       0 !NDON: donors
+
+
+       0 !NACC: acceptors
+
+
+       0 !NNB
+
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0
+
+       1       0 !NGRP
+       0       0       0
+

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,90 @@
+# NAMD Config file - autogenerated by NAMDgui plugin
+# Author: Jan Saam,  saam at charite.de
+
+#set DIR			/lustre/beagle/fxv/CLATH/CG_MODEL/OPT/CAGE/PSWEEP
+
+set id                  FILEID
+# input
+coordinates             ../cg_clath_cage.pdb
+structure               ../cg_clath_cage.psf
+parameters              ../PAR/${id}.inp
+paratypecharmm          on
+
+# output
+#set output              cg_clath_cage.BLAB1_BLAB2
+outputname              ../OUT/$id
+dcdfile                 ../OUT/${id}.dcd
+xstFile                 ../OUT/${id}.xst
+dcdfreq                 1000
+xstFreq                 1000
+
+binaryoutput            yes
+binaryrestart           yes
+outputEnergies          1000
+restartfreq             1000
+
+fixedAtoms              off
+
+# Basic dynamics
+exclude                 scaled1-4
+1-4scaling              1
+COMmotion               no
+dielectric              1.0
+
+
+# Simulation space partitioning
+cutoff			630
+switching               on
+switchdist              629                 
+pairlistdist            640
+
+# Multiple timestepping
+firsttimestep           0
+timestep                1
+stepspercycle           20
+nonbondedFreq           1
+fullElectFrequency      1
+rigidBonds              all
+
+# Temperature control
+
+set temperature         310
+set tempini		0
+temperature             $temperature;  # initial temperature
+
+# Langevin Dynamics
+langevin                on;            # do langevin dynamics
+langevinDamping         0.5             # damping coefficient (gamma) of 1/ps
+langevinTemp            $temperature;   # bath temperature
+langevinHydrogen        no;             # don't couple langevin bath to hydrogens
+
+
+
+# Scripting
+
+# Simulated Annealing
+#reassignFreq 10000
+#reassignTemp 0
+#minimize 10000
+#for { set TEMP 0 } { $TEMP <= 310 } { incr TEMP 5 } {
+#  run 10000
+#  reassignTemp $TEMP
+#  langevinTemp $TEMP
+#}
+
+#run 2500000
+#
+#for { set TEMP 650 } { $TEMP >= 0 } { incr TEMP -5 } {
+#  reassignTemp $TEMP
+#  langevinTemp $TEMP
+#  run 10000
+#} 
+
+#reassignTemp $temperature
+#langevinTemp $temperature
+
+
+minimize            10000
+#reinitvels          $temperature
+#run 		    1000000 desired, 200000 min to get non-zero RMSDs
+run                 20000

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/* RMSD/* VMD/* CONF/* OUT/*


Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,79 @@
+* Charmm Parameter file
+* For 13 bead CG clathrin model
+* Handmade by FXV - 7-21-11
+* Initial guess (very rough)
+
+BONDS
+!
+
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb          b0
+!
+
+HB PX   0.5              85.5
+PX DT   0.018           135.2
+DT AK   0.045	        124.2
+AK LT   0.08	         94.1
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!
+!atom types     Ktheta    Theta0
+!
+PX HB PX	70.0		120.00
+DT PX HB	50.0		144.3
+AK DT PX	35.0		132.6
+LT AK DT	150.0		141.5
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types             Kchi    n   delta
+!
+X    X    X    X    0.0        1     0.0 ! No dihedrals
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types           Kpsi                   psi0
+!
+PX PX HB PX	200.00			0	161.17
+PX HB PX DT	 10.0			0	-30.4
+HB PX DT AK	 9.5			0	-16.1
+PX DT AK LT	 45.0			0	 26.1
+
+NONBONDED
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom  ignored    epsilon      Rmin/2
+!
+HB	0.000000	 HBEPS		43.075000
+PX	0.000000	 PXEPS		18.425000
+DT	0.000000	 DTEPS		10.455000
+AK	0.000000	 AKEPS		25.975000
+LT	0.000000	 LTEPS		36.905000
+
+
+END

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,74 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+# This code will run many short simulations in order to 
+# sweep the nonbonded parameter space
+
+# File names
+open (OFILE, ">", "rmsd_pd.dat");
+
+# Bead names
+my $b1name = "PX";
+my $b2name = "DT";
+
+# Bead ranges
+my $b1min=0.0;
+my $b1max=10.0;
+
+my $b2min=0.0;
+my $b2max=10.0;
+
+my $del=0.50;
+
+# Set large number to find RMSD min
+my $rmsdmin = 123456789.0;
+my $b1rmsdmin=0.0;
+my $b2rmsdmin=0.0;
+
+
+my $b1=$b1min;
+
+while ($b1<=$b1max) 
+{
+	my $b2=$b2min;
+
+	while ($b2<=$b2max)
+	{
+	
+
+
+		if (-s "RMSD/rmsd.$b1name${b1}_$b2name${b2}.dat")
+		{	
+			open(INPUT, "<", "RMSD/rmsd.$b1name${b1}_$b2name${b2}.dat");
+			my $_ = <INPUT>;
+
+			my @data = split(/ +/,$_);
+        		my $rmsd=$data[2]*1.0;
+			
+			# Find Minimum
+			if ($rmsd<$rmsdmin)
+			{
+				$rmsdmin=$rmsd;
+				$b1rmsdmin=$b1;
+				$b2rmsdmin=$b2;
+			}
+	
+			print OFILE "$b1 $b2 $rmsd\n";			
+			close(INPUT);
+		}		
+
+		$b2 = $b2+$del;
+	
+	}
+
+	print OFILE " \n";
+	$b1 = $b1+$del;
+
+}
+
+close(OFILE);
+
+print "Minimum Values\n";
+print "RMSD = $rmsdmin, eps_$b1name = $b1rmsdmin, eps_$b2name = $b2rmsdmin\n" ; 


Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,11 @@
+#! /bin/sh
+
+id=$1
+
+module load namd
+module load vmd
+
+  mpiexec      namd2 CONF/$id.conf  > OUT/$id.log 2>&1 
+# mpiexec -n 8 namd2 CONF/$id.conf  > OUT/$id.log 2>&1 
+
+vmd -dispdev text -e VMD/$id.tcl >> OUT/$id.log 2>&1


Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,44 @@
+type file;
+
+global string cwd = @arg("cwd",".");
+
+app (file blist) genConfigs (string max, string delta)
+{
+  gensweep cwd max delta stdout=@blist;
+}
+
+app (file rmsdout, file rmsd) rmsd (file i[], string id)
+{
+  rmsd id;
+}
+
+app (file plot_data) analyze (file[] rmsdfiles)
+{
+  analyze @filenames(rmsdfiles) stdout=@plot_data;
+}
+
+file pdb      <"cg_clath_cage.pdb">;
+file psf      <"cg_clath_cage.psf">;
+
+file rmsds[];
+
+string sweepMax=@arg("max","0.6"), sweepDelta=@arg("delta","0.5");
+
+string beadids[] = readData(genConfigs(sweepMax, sweepDelta));
+
+trace("Processing these bead IDs:", beadids);
+
+foreach beadid, i in beadids {
+  file conf   <single_file_mapper; file=@strcat("CONF/",beadid,".conf")>;
+  file inp    <single_file_mapper; file=@strcat("PAR/", beadid,".inp")>;
+  file vmdtcl <single_file_mapper; file=@strcat("VMD/", beadid,".tcl")>;
+
+  file log    <single_file_mapper; file=@strcat("OUT/", beadid,".log")>;
+  file dat    <single_file_mapper; file=@strcat("RMSD/",beadid,".dat")>;
+
+  (log,dat) = rmsd([conf,pdb,psf,inp,vmdtcl], beadid);
+  rmsds[i] = dat;
+}
+
+file plot_out <"OUT/plot_pd.txt">;
+plot_out = analyze(rmsds);

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,56 @@
+#====================================
+# THis script will measure the 
+# the average angles, bond lengths
+# and dihedral angles.
+#
+# -FXV Oct, 2011
+#===================================
+
+mol delete all
+
+# set atom selection
+set seltext "type HB AK" 
+
+# Set the initial frame
+set inifrm 200
+
+set psf cg_clath_cage.psf
+set pdb cg_clath_cage.pdb
+set dcd OUT/FILEID.dcd
+
+# Load input files
+mol load psf $psf
+# Load trajectory
+mol addfile $pdb type pdb
+mol addfile $dcd type dcd first $inifrm last -1 waitfor all
+
+# Get molecule information
+set mol [molinfo top]
+
+# Get the number of frames
+set nmfrm [molinfo $mol get numframes]
+puts "number of frames $nmfrm"
+
+# open rmsd file
+set frmsd [open RMSD/FILEID.dat w]
+
+# Select atoms
+set ref [atomselect top $seltext frame 0] 
+	
+# Loop over the number of frames
+for {set ifrm 0} {$ifrm <= $nmfrm} {incr ifrm} {
+	
+	set sel [atomselect top $seltext frame $ifrm]
+	
+	set irmsd [measure rmsd $ref $sel]
+	
+	lappend rmsdlist $irmsd
+
+
+}
+
+# Analysis
+puts $frmsd "B1 B2 [vecmean $rmsdlist]"
+
+exit
+

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,7 @@
+PATH=$PATH:$PWD
+
+# export SBATCH_RESERVATION=swift_test
+
+mkdir  -p CONF PAR VMD RMSD OUT
+
+swift -sites.file sites.xml -tc.file tc -config cf rmsd.swift -cwd=$PWD -max=${1:-0.0} -delta=${2:-0.5}


Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+mkdir -p saved/run000
+rundir=saved/run$(cd saved; /bin/ls -1 | tail -1 | sed -e 's/run//' | awk '{printf("%03d",$1+1)}')
+mkdir $rundir
+rmdir saved/run000
+
+echo Saving run in $rundir
+
+mv *.log *.rlog *.d *.kml _concurrent *.swiftx CONF PAR VMD RMSD OUT $rundir 2>/dev/null


Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,104 @@
+<config>
+
+  <pool handle="local">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="westmere">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">westmere</profile>
+    <profile namespace="globus" key="ppn">12</profile>
+    <profile namespace="globus" key="project">pi-gavoth</profile>
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <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">.03</profile>
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">true</profile>
+    <profile namespace="globus" key="jobtype">single</profile>
+    <profile namespace="globus" key="jobsPerNode">1</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="sandyb">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">sandyb</profile>
+    <profile namespace="globus" key="ppn">12</profile>
+    <profile namespace="globus" key="project">pi-gavoth</profile>
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <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">.03</profile>
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="jobtype">single</profile>
+    <profile namespace="globus" key="jobsPerNode">1</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+    <!-- <profile namespace="globus" key="slurm.qos">ht</profile> -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="bigmem">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">bigmem</profile>
+    <profile namespace="globus" key="ppn">16</profile>
+    <profile namespace="globus" key="project">pi-gavoth</profile>
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <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">.03</profile>
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:05:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="jobtype">single</profile>
+    <profile namespace="globus" key="jobsPerNode">1</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+    <!-- <profile namespace="globus" key="slurm.qos">ht</profile> -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+</config>

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,45 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+# Create NAMD input file for short simulations
+# to sweep the nonbonded parameter space
+#
+# ARGS: dir max delta  # FIXME: add bead names and epsilon
+
+chdir($ARGV[0]);
+
+# Bead names
+
+my $b1name = "PX";
+my $b2name = "DT";
+
+# Bead ranges
+
+my $b1min=0.0;
+my $b2min=0.0;
+
+my $b1max = $ARGV[1];
+my $b2max = $ARGV[1];
+my $del =   $ARGV[2];
+my $eps =   "-0.01";
+
+my $b1=$b1min;
+while ($b1<=$b1max) {
+  my $b2=$b2min;
+  while ($b2<=$b2max) {
+
+    my $s1=sprintf("%05.2f",$b1);
+    my $s2=sprintf("%05.2f",$b2);
+    my $fileid="${b1name}_${s1}_${b2name}_${s2}";
+
+    print("$fileid\n");
+    system("sed -e s/FILEID/${fileid}/g cg_clath_cage.temp.conf                 > CONF/$fileid.conf");
+    system("sed -e s/FILEID/${fileid}/g -e s/B1/$s1/ -e s/B2/$s2/ rmsd.temp.tcl > VMD/$fileid.tcl");
+    system("sed -e s/HBEPS/$eps/ -e s/PXEPS/-$s1/ -e s/DTEPS/-$s2/ -e s/AKEPS/$eps/ -e s/LTEPS/$eps/  par_cg_clath.temp.inp > PAR/$fileid.inp");
+
+    $b2 = $b2+$del;
+  }
+  $b1 = $b1+$del;
+}


Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,8 @@
+
+local     gensweep  sweep_pd.pl   null null null
+local     analyze   analyze_pd.pl null null null
+
+#bigmem   rmsd      rmsd.sh       null null null
+#sandyb   rmsd      rmsd.sh       null null null
+#trestles rmsd      rmsd.sh       null null null
+westmere  rmsd      rmsd.sh       null null null

Added: SwiftTutorials/CMTS_2013-06-17/setup.csh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/setup.csh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/setup.csh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,35 @@
+
+module load swift
+
+setenv SBATCH_RESERVATION swift
+
+set DIR=`dirname ${0}`
+cd $DIR
+set DIR=`pwd`
+
+echo Adding $DIR/bin to PATH:
+setenv PATH $DIR/bin:$PATH
+
+mkdir -p $HOME/.swift
+
+if ( -f $HOME/.swift/swift.properties ) then
+  echo Adding properties to end of $HOME/.swift/swift.properties
+else
+  echo creating $HOME/.swift/swift.properties
+endif
+
+cat >>$HOME/.swift/swift.properties <<END
+
+# Properties for Swift Tutorial
+
+status.mode=provider
+use.provider.staging=false
+use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+file.gc.enabled=false
+tcp.port.range=50000,51000
+END

Added: SwiftTutorials/CMTS_2013-06-17/setup.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/setup.sh	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/setup.sh	2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,50 @@
+
+echo -e "\nNOTE: This command must be run as \"source setup.sh\", not directly! \n"
+echo -e "Initializing Swift tutorial environment\n"
+
+module load swift
+
+# export SBATCH_RESERVATION=swift
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+echo -e "Adding $DIR/bin to PATH\n"
+
+PATH=$DIR/bin:$PATH
+
+# echo -e "PATH=$PATH\n"
+
+mkdir -p $HOME/.swift
+
+if [ -f $HOME/.swift/swift.properties ]; then
+  echo -e "Adding properties to end of $HOME/.swift/swift.properties\n"
+else
+  echo -e "creating $HOME/.swift/swift.properties\n"
+fi
+
+cat >>$HOME/.swift/swift.properties <<END
+
+#   Swift runtime properties for CMTS Cyber Tutorial 
+
+# Get sites and apps lists from these files in cwd:
+
+sites.file=sites.xml
+tc.file=apps
+
+# Data and status staging modes:
+
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+use.wrapper.staging=false
+status.mode=provider
+
+# For better debugging:
+
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+sitedir.keep=true
+file.gc.enabled=false
+file.gc.enabled=false
+
+END



From yadunandb at ci.uchicago.edu  Mon Jun 17 14:35:26 2013
From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 19:35:26 -0000
Subject: [Swift-commit] r6577 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part08
Message-ID: <20130617193525.6287B9CC43@svn.ci.uchicago.edu>

Author: yadunandb
Date: 2013-06-17 14:35:25 -0500 (Mon, 17 Jun 2013)
New Revision: 6577

Added:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p9.swift
Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README
Log:
Commiting part09



Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README	2013-06-17 19:21:41 UTC (rev 6576)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/README	2013-06-17 19:35:25 UTC (rev 6577)
@@ -1,14 +1,12 @@
 
-TOPIC: Example pipeline 
+TOPIC: Example pipeline with readData
 
-This example shows combining two app calls in a pipeline. There are two apps
-defined in this script: mysim4, and mysim4_filename. 
+This example shows combining two app calls in a pipeline. The mysim4 app from the
+previous example part08 is called twice here.
 
-mysim4 takes integer to determine the number of random numbers to generate.
-mysim4_filename reads a file to determine the number of random numbers to generate
+mysim4 takes an integer to determine the number of random numbers to generate.
+The random number generated by mysim4 is read from its output file and redirected 
+as an argument to itself to generate a random number of random numbers.
 
-In this example, we use mysim4 to generate a random number. The output of mysim4
-get passed as input to mysim4_filename.
-
 To run
 $ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p9.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p9.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part08/p9.swift	2013-06-17 19:35:25 UTC (rev 6577)
@@ -0,0 +1,32 @@
+type file;
+
+app (file o) mysim4 (int timesteps, int range_value, int count_value)
+{
+  random4 timesteps range_value count_value stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+  average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+int  nsim  = @toInt(@arg("nsim",  "10"));
+int  steps = @toInt(@arg("steps", "1"));
+int  range = @toInt(@arg("range", "100"));
+int  count = @toInt(@arg("count", "10"));
+
+foreach i in [0:nsim-1] {
+
+  file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+  simout   = mysim4(steps, range, 1);
+  int rand = readData(simout);
+
+  file simout2 <single_file_mapper; file=@strcat("output/sim_", i, ".tmp.out")>;
+  simout2  = mysim4(steps, range, rand);
+
+  sims[i] = simout2;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);



From yadunandb at ci.uchicago.edu  Mon Jun 17 14:37:12 2013
From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 19:37:12 -0000
Subject: [Swift-commit] r6578 - in
	SwiftTutorials/CMTS_2013-06-17/basic_swift: . part09
Message-ID: <20130617193711.5D53D9CC43@svn.ci.uchicago.edu>

Author: yadunandb
Date: 2013-06-17 14:37:11 -0500 (Mon, 17 Jun 2013)
New Revision: 6578

Added:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/apps
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/p9.swift
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/sites.xml
Log:

Committing Part09 example



Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README	2013-06-17 19:37:11 UTC (rev 6578)
@@ -0,0 +1,12 @@
+
+TOPIC: Example pipeline with readData
+
+This example shows combining two app calls in a pipeline. The mysim4 app from the
+previous example part08 is called twice here.
+
+mysim4 takes an integer to determine the number of random numbers to generate.
+The random number generated by mysim4 is read from its output file and redirected 
+as an argument to itself to generate a random number of random numbers.
+
+To run
+$ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/apps
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/apps	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/apps	2013-06-17 19:37:11 UTC (rev 6578)
@@ -0,0 +1,2 @@
+cmtsworkshop random4  random4.sh
+localhost    average  avg.sh

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/p9.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/p9.swift	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/p9.swift	2013-06-17 19:37:11 UTC (rev 6578)
@@ -0,0 +1,32 @@
+type file;
+
+app (file o) mysim4 (int timesteps, int range_value, int count_value)
+{
+  random4 timesteps range_value count_value stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+  average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+int  nsim  = @toInt(@arg("nsim",  "10"));
+int  steps = @toInt(@arg("steps", "1"));
+int  range = @toInt(@arg("range", "100"));
+int  count = @toInt(@arg("count", "10"));
+
+foreach i in [0:nsim-1] {
+
+  file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+  simout   = mysim4(steps, range, 1);
+  int rand = readData(simout);
+
+  file simout2 <single_file_mapper; file=@strcat("output/sim_", i, ".tmp.out")>;
+  simout2  = mysim4(steps, range, rand);
+
+  sims[i] = simout2;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);

Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/sites.xml	                        (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/sites.xml	2013-06-17 19:37:11 UTC (rev 6578)
@@ -0,0 +1,39 @@
+<config>
+
+  <pool handle="localhost">
+    <execution provider="local"/>
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+  </pool>
+
+  <pool handle="cmtsworkshop">
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <!-- Set partition and account here: -->
+    <profile namespace="globus" key="queue">cmtsworkshop</profile>
+    <profile namespace="globus" key="ppn">8</profile>
+    <profile namespace="globus" key="project">cmtsworkshop</profile>
+
+    <!-- Set number of jobs and nodes per job here: -->
+    <profile namespace="globus" key="slots">4</profile>
+    <profile namespace="globus" key="maxnodes">1</profile>
+    <profile namespace="globus" key="nodegranularity">1</profile>
+    <profile namespace="globus" key="jobsPerNode">8</profile> <!-- apps per node! -->
+    <profile namespace="karajan" key="jobThrottle">.31</profile> <!-- eg .31 -> 32 -->
+
+    <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+    <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+    <profile namespace="globus" key="maxtime">1800</profile>  <!-- in seconds! -->
+
+    <!-- Set data staging model and work dir here: -->
+    <filesystem provider="local"/>
+    <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+    <!-- Typically leave these constant: -->
+    <profile namespace="globus" key="slurm.exclusive">false</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+  </pool>
+
+</config>



From yadunandb at ci.uchicago.edu  Mon Jun 17 14:40:35 2013
From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 19:40:35 -0000
Subject: [Swift-commit] r6580 -
	SwiftTutorials/CMTS_2013-06-17/basic_swift/part09
Message-ID: <20130617194034.DADA59CC43@svn.ci.uchicago.edu>

Author: yadunandb
Date: 2013-06-17 14:40:34 -0500 (Mon, 17 Jun 2013)
New Revision: 6580

Modified:
   SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README
Log:
Updated README for part09



Modified: SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README	2013-06-17 19:37:38 UTC (rev 6579)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part09/README	2013-06-17 19:40:34 UTC (rev 6580)
@@ -5,8 +5,9 @@
 previous example part08 is called twice here.
 
 mysim4 takes an integer to determine the number of random numbers to generate.
-The random number generated by mysim4 is read from its output file and redirected 
-as an argument to itself to generate a random number of random numbers.
+Firt mysim4 is called with 1 to generate 1 random number. Then the random number 
+generated by mysim4 is read from its output file by the readData function and 
+redirected as an argument to mysim4 to generate a random number of random numbers.
 
 To run
-$ swift p8.swift -steps=10 -range=100 -count=6 -nsim=1
+$ swift p9.swift -steps=10 -range=100 -count=6 -nsim=1



From yadunandb at ci.uchicago.edu  Mon Jun 17 15:01:52 2013
From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu)
Date: Mon, 17 Jun 2013 20:01:52 -0000
Subject: [Swift-commit] r6583 - SwiftTutorials/CMTS_2013-06-17/namd_sweep
Message-ID: <20130617200151.B9F8B9CC43@svn.ci.uchicago.edu>

Author: yadunandb
Date: 2013-06-17 15:01:51 -0500 (Mon, 17 Jun 2013)
New Revision: 6583

Modified:
   SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
Log:

Updated README


Modified: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-17 19:55:12 UTC (rev 6582)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README	2013-06-17 20:01:51 UTC (rev 6583)
@@ -25,4 +25,5 @@
 
   swift rmsd.swift -cwd=$PWD -max=1.0 -delta=0.5  # 9 param sets (3 x 3)
 
-
+Output:
+  The output should be generated in the OUT/plot_pd.txt file.
\ No newline at end of file



From yadunandb at ci.uchicago.edu  Tue Jun 18 10:58:12 2013
From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu)
Date: Tue, 18 Jun 2013 15:58:12 -0000
Subject: [Swift-commit] r6586 - branches/release-0.94/tests/stress/internals
Message-ID: <20130618155812.44C989CC43@svn.ci.uchicago.edu>

Author: yadunandb
Date: 2013-06-18 10:58:12 -0500 (Tue, 18 Jun 2013)
New Revision: 6586

Added:
   branches/release-0.94/tests/stress/internals/swift.properties
   branches/release-0.94/tests/stress/internals/tc.template.data
Modified:
   branches/release-0.94/tests/stress/internals/x_recursion.timeout
Log:
Updated test scripts.


Added: branches/release-0.94/tests/stress/internals/swift.properties
===================================================================
--- branches/release-0.94/tests/stress/internals/swift.properties	                        (rev 0)
+++ branches/release-0.94/tests/stress/internals/swift.properties	2013-06-18 15:58:12 UTC (rev 6586)
@@ -0,0 +1,7 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=false
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false

Added: branches/release-0.94/tests/stress/internals/tc.template.data
===================================================================
--- branches/release-0.94/tests/stress/internals/tc.template.data	                        (rev 0)
+++ branches/release-0.94/tests/stress/internals/tc.template.data	2013-06-18 15:58:12 UTC (rev 6586)
@@ -0,0 +1,2 @@
+local bash /bin/bash null null null
+

Modified: branches/release-0.94/tests/stress/internals/x_recursion.timeout
===================================================================
--- branches/release-0.94/tests/stress/internals/x_recursion.timeout	2013-06-17 20:23:15 UTC (rev 6585)
+++ branches/release-0.94/tests/stress/internals/x_recursion.timeout	2013-06-18 15:58:12 UTC (rev 6586)
@@ -1 +1 @@
-99999
\ No newline at end of file
+300
\ No newline at end of file



From yadunandb at ci.uchicago.edu  Tue Jun 18 13:35:40 2013
From: yadunandb at ci.uchicago.edu (yadunandb at ci.uchicago.edu)
Date: Tue, 18 Jun 2013 18:35:40 -0000
Subject: [Swift-commit] r6587 -
	branches/release-0.94/tests/language-behaviour/IO
Message-ID: <20130618183539.6619B9CC9A@svn.ci.uchicago.edu>

Author: yadunandb
Date: 2013-06-18 13:35:39 -0500 (Tue, 18 Jun 2013)
New Revision: 6587

Added:
   branches/release-0.94/tests/language-behaviour/IO/readData3.out.expected
   branches/release-0.94/tests/language-behaviour/IO/readData3.swift
   branches/release-0.94/tests/language-behaviour/IO/title.txt
Log:

Adding test to confirm Bug: 1028



Added: branches/release-0.94/tests/language-behaviour/IO/readData3.out.expected
===================================================================
--- branches/release-0.94/tests/language-behaviour/IO/readData3.out.expected	                        (rev 0)
+++ branches/release-0.94/tests/language-behaviour/IO/readData3.out.expected	2013-06-18 18:35:39 UTC (rev 6587)
@@ -0,0 +1 @@
+9
\ No newline at end of file

Added: branches/release-0.94/tests/language-behaviour/IO/readData3.swift
===================================================================
--- branches/release-0.94/tests/language-behaviour/IO/readData3.swift	                        (rev 0)
+++ branches/release-0.94/tests/language-behaviour/IO/readData3.swift	2013-06-18 18:35:39 UTC (rev 6587)
@@ -0,0 +1,23 @@
+type file;
+
+/*
+   Test case added to confirm Bug 1028 - readData in a foreach loop fails to compile.
+   https://bugzilla.mcs.anl.gov/swift/show_bug.cgi?id=1028
+
+   This test is expected to fail to compile till bug is resolved.
+*/
+
+app (file o) mysim (int i)
+{
+  echo i stdout=@filename(o);
+}
+
+int nums[];
+foreach i in [0:9] {
+  file f <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+  f = mysim(i);
+  nums[i] = readData(f);
+}
+
+file result <"readData3.out">;
+result = mysim(nums[i]);
\ No newline at end of file

Added: branches/release-0.94/tests/language-behaviour/IO/title.txt
===================================================================
--- branches/release-0.94/tests/language-behaviour/IO/title.txt	                        (rev 0)
+++ branches/release-0.94/tests/language-behaviour/IO/title.txt	2013-06-18 18:35:39 UTC (rev 6587)
@@ -0,0 +1 @@
+Language Behavior tests : Subgroup local IO