From swift at ci.uchicago.edu  Sun Dec  2 00:20:04 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Sun,  2 Dec 2012 00:20:04 -0600 (CST)
Subject: [Swift-commit] cog r3525
Message-ID: <20121202062005.714DE8D00090@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3525 | davidkelly999 | 2012-12-02 00:18:55 -0600 (Sun, 02 Dec 2012) | 2 lines

Allow more user defined condor attributes

------------------------------------------------------------------------
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 3524)
+++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java	(working copy)
@@ -32,20 +32,18 @@
 		super(task, listener);
 	}
 
-	protected void writeAttr(String attrName, String arg, Writer wr)
-			throws IOException {
+	protected void writeAttr(String attrName, String arg, Writer wr) throws IOException {
 		Object value = getSpec().getAttribute(attrName);
 		if (value != null) {
 			wr.write(arg + String.valueOf(value) + '\n');
 		}
 	}
 
-	protected void writeScript(Writer wr, String exitcodefile, String stdout,
-			String stderr) throws IOException {
+	protected void writeScript(Writer wr, String exitcodefile, String stdout, String stderr) throws IOException {
 		boolean grid = false;
-		Task task = getTask();
 		JobSpecification spec = getSpec();
-		getSpec().unpackProviderAttributes();
+
+		// Handle some predefined jobTypes
 		String type = (String) spec.getAttribute("jobType");
 		if (logger.isDebugEnabled()) {
 			logger.debug("Job type: " + type);
@@ -58,27 +56,31 @@
 			String gridResource = (String) spec.getAttribute("gridResource");
 			wr.write("universe = grid\n");
 			wr.write("grid_resource = "+gridResource+"\n");
-
-// the below two lines are needed to cause the gridmonitor to be used
-// which is the point of all this...
+			// the below two lines are needed to cause the gridmonitor to be used
+			// which is the point of all this...
 			wr.write("stream_output = False\n");
 			wr.write("stream_error  = False\n");
-
 			wr.write("Transfer_Executable = false\n");
 		}
 		else {
-			wr.write("universe = vanilla\n");
+			if(spec.getAttribute("condor.universe") == null) {
+				wr.write("universe = vanilla\n");
+			}
 		}
+
 		if ("true".equals(spec.getAttribute("holdIsFailure"))) {
 			wr.write("periodic_remove = JobStatus == 5\n");
 		}
+		
 		writeAttr("count", "machine_count = ", wr);
+		wr.write("output = " + quote(stdout) + '\n');
+		wr.write("error = " + quote(stderr) + '\n');
+
 		if (spec.getStdInput() != null) {
 			wr.write("input = " + quote(spec.getStdInput()) + "\n");
 		}
-		wr.write("output = " + quote(stdout) + '\n');
-		wr.write("error = " + quote(stderr) + '\n');
-		Iterator i = spec.getEnvironmentVariableNames().iterator();
+
+		Iterator<String> i = spec.getEnvironmentVariableNames().iterator();
 		if (i.hasNext()) {
 			wr.write("environment = ");
 		}
@@ -99,7 +101,7 @@
 			}
 		}
 		wr.write("executable = " + quote(spec.getExecutable()) + "\n");
-		List args = spec.getArgumentsAsList();
+		List<String> args = spec.getArgumentsAsList();
 		if (args != null && args.size() > 0) {
 			wr.write("arguments = ");
 			i = args.iterator();
@@ -112,18 +114,15 @@
 		}
 		wr.write('\n');
 
-		String request_memory = (String) spec.getAttribute("request_memory");
-		if(request_memory != null) {
-			wr.write("request_memory = " + request_memory + '\n');
-		}
-		
-		String resources = (String) spec.getAttribute("condor.resource_list");
-		if (resources != null && resources.length() > 0) {
-			if (logger.isDebugEnabled())
-				logger.debug("condor.resource_list: " + resources);
-			wr.write(resources + '\n');
-		}
-		
+		// Handle all condor attributes specified by the user
+	    for(String a : spec.getAttributeNames()) {
+	    	if(a != null && a.startsWith("condor.")) {
+	    		String attributeName[] = a.split("condor.");
+	    		System.out.println(attributeName[1] + " = " + spec.getAttribute(a));
+	    		wr.write(attributeName[1] + " = " + spec.getAttribute(a) + '\n');
+	    	}
+	    }
+	    
 		wr.write("notification = Never\n");
 		wr.write("leave_in_queue = TRUE\n");
 		wr.write("queue\n");


From swift at ci.uchicago.edu  Sun Dec  2 00:45:04 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Sun,  2 Dec 2012 00:45:04 -0600 (CST)
Subject: [Swift-commit] cog r3526
Message-ID: <20121202064505.8DFF08D00090@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3526 | davidkelly999 | 2012-12-02 00:40:20 -0600 (Sun, 02 Dec 2012) | 2 lines

Remove debug statement

------------------------------------------------------------------------
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 3525)
+++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java	(working copy)
@@ -118,7 +118,6 @@
 	    for(String a : spec.getAttributeNames()) {
 	    	if(a != null && a.startsWith("condor.")) {
 	    		String attributeName[] = a.split("condor.");
-	    		System.out.println(attributeName[1] + " = " + spec.getAttribute(a));
 	    		wr.write(attributeName[1] + " = " + spec.getAttribute(a) + '\n');
 	    	}
 	    }


From swift at ci.uchicago.edu  Mon Dec  3 11:40:09 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Mon,  3 Dec 2012 11:40:09 -0600 (CST)
Subject: [Swift-commit] cog r3527
Message-ID: <20121203174010.481208D00090@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3527 | davidkelly999 | 2012-12-03 11:38:59 -0600 (Mon, 03 Dec 2012) | 2 lines

Some fixes to make condor more flexible

------------------------------------------------------------------------
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 3526)
+++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java	(working copy)
@@ -9,8 +9,12 @@
  */
 package org.globus.cog.abstraction.impl.scheduler.condor;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.Writer;
+import java.nio.channels.FileChannel;
 import java.util.Iterator;
 import java.util.List;
 
@@ -20,10 +24,12 @@
 import org.globus.cog.abstraction.impl.scheduler.common.AbstractProperties;
 import org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller;
 import org.globus.cog.abstraction.impl.scheduler.common.Job;
+import org.globus.cog.abstraction.impl.scheduler.common.ProcessException;
 import org.globus.cog.abstraction.impl.scheduler.common.ProcessListener;
 import org.globus.cog.abstraction.interfaces.FileLocation;
 import org.globus.cog.abstraction.interfaces.JobSpecification;
 import org.globus.cog.abstraction.interfaces.Task;
+import org.globus.gsi.gssapi.auth.AuthorizationException;
 
 public class CondorExecutor extends AbstractExecutor {
 	public static final Logger logger = Logger.getLogger(CondorExecutor.class);
@@ -32,20 +38,95 @@
 		super(task, listener);
 	}
 
-	protected void writeAttr(String attrName, String arg, Writer wr)
-			throws IOException {
+	protected void writeAttr(String attrName, String arg, Writer wr) throws IOException {
 		Object value = getSpec().getAttribute(attrName);
 		if (value != null) {
 			wr.write(arg + String.valueOf(value) + '\n');
 		}
 	}
 
-	protected void writeScript(Writer wr, String exitcodefile, String stdout,
-			String stderr) throws IOException {
+    public void start()
+    throws AuthorizationException, IOException, ProcessException {
+    	File scriptdir = new File(".");
+        script = File.createTempFile(getName(), ".submit", scriptdir);
+        if (!logger.isDebugEnabled()) {
+            script.deleteOnExit();
+        }
+        stdout = spec.getStdOutput() == null ? script.getAbsolutePath()
+                + ".stdout" : spec.getStdOutput();
+        stderr = spec.getStdError() == null ? script.getAbsolutePath()
+                + ".stderr" : spec.getStdError();
+        exitcode = script.getAbsolutePath() + ".exitcode";
+
+        if (logger.isDebugEnabled()) {
+            logger.debug("Writing " + getName() + " script to " + script);
+        }
+
+        String[] cmdline = buildCommandLine(scriptdir, script, exitcode,
+            stdout, stderr);
+
+        if (logger.isDebugEnabled()) {
+            logCommandLine(cmdline);
+        }
+        Process process = Runtime.getRuntime().exec(cmdline, null, null);
+
+        try {
+            process.getOutputStream().close();
+        }
+        catch (IOException e) {
+        }
+
+        try {
+            int code = process.waitFor();
+            if (code != 0) {
+                String errorText = getOutput(process.getInputStream())
+                        + getOutput(process.getErrorStream());
+                throw new ProcessException("Could not submit job ("
+                        + getProperties().getSubmitCommandName()
+                        + " reported an exit code of " + code + "). "
+                        + errorText);
+            }
+            if (logger.isDebugEnabled()) {
+                logger.debug(getProperties().getSubmitCommandName()
+                        + " done (exit code " + code + ")");
+            }
+        }
+        catch (InterruptedException e) {
+            if (logger.isDebugEnabled()) {
+                logger.debug("Interrupted exception while waiting for "
+                        + getProperties().getSubmitCommandName(), e);
+            }
+            if (listener != null) {
+                listener
+                    .processFailed("The submission process was interrupted");
+            }
+        }
+
+        String output = getOutput(process.getInputStream());
+        jobid = parseSubmitCommandOutput(output);
+        if (logger.isDebugEnabled()) {
+            logger.debug("Submitted job with id '" + jobid + "'");
+        }
+
+        if (jobid.length() == 0) {
+            String errorText = getOutput(process.getErrorStream());
+            if (listener != null)
+                listener.processFailed("Received empty jobid!\n" +
+                                       output + "\n" + errorText);
+        }
+
+        process.getInputStream().close();
+
+        getQueuePoller().addJob(
+            job = createJob(jobid, stdout, spec.getStdOutputLocation(), stderr,
+                spec.getStdErrorLocation(), exitcode, this));
+    }
+	
+	protected void writeScript(Writer wr, String exitcodefile, String stdout, String stderr) throws IOException {
 		boolean grid = false;
-		Task task = getTask();
 		JobSpecification spec = getSpec();
-		getSpec().unpackProviderAttributes();
+
+		// Handle some predefined jobTypes
 		String type = (String) spec.getAttribute("jobType");
 		if (logger.isDebugEnabled()) {
 			logger.debug("Job type: " + type);
@@ -58,27 +139,31 @@
 			String gridResource = (String) spec.getAttribute("gridResource");
 			wr.write("universe = grid\n");
 			wr.write("grid_resource = "+gridResource+"\n");
-
-// the below two lines are needed to cause the gridmonitor to be used
-// which is the point of all this...
+			// the below two lines are needed to cause the gridmonitor to be used
+			// which is the point of all this...
 			wr.write("stream_output = False\n");
 			wr.write("stream_error  = False\n");
-
 			wr.write("Transfer_Executable = false\n");
 		}
 		else {
-			wr.write("universe = vanilla\n");
+			if(spec.getAttribute("condor.universe") == null) {
+				wr.write("universe = vanilla\n");
+			}
 		}
+
 		if ("true".equals(spec.getAttribute("holdIsFailure"))) {
 			wr.write("periodic_remove = JobStatus == 5\n");
 		}
+		
 		writeAttr("count", "machine_count = ", wr);
+		wr.write("output = " + quote(stdout) + '\n');
+		wr.write("error = " + quote(stderr) + '\n');
+
 		if (spec.getStdInput() != null) {
 			wr.write("input = " + quote(spec.getStdInput()) + "\n");
 		}
-		wr.write("output = " + quote(stdout) + '\n');
-		wr.write("error = " + quote(stderr) + '\n');
-		Iterator i = spec.getEnvironmentVariableNames().iterator();
+
+		Iterator<String> i = spec.getEnvironmentVariableNames().iterator();
 		if (i.hasNext()) {
 			wr.write("environment = ");
 		}
@@ -98,8 +183,17 @@
 				wr.write("remote_initialdir = " + quote(spec.getDirectory()) + "\n");
 			}
 		}
+		
+        String basename[] = spec.getExecutable().split("/");		
+        FileChannel from = new FileInputStream(spec.getExecutable()).getChannel();
+        FileChannel to = new FileOutputStream(basename[basename.length-1]).getChannel();
+        to.transferFrom(from, 0, from.size());
+        from.close();
+        to.close();
+        
+		spec.getExecutable();
 		wr.write("executable = " + quote(spec.getExecutable()) + "\n");
-		List args = spec.getArgumentsAsList();
+		List<String> args = spec.getArgumentsAsList();
 		if (args != null && args.size() > 0) {
 			wr.write("arguments = ");
 			i = args.iterator();
@@ -110,20 +204,16 @@
 				}
 			}
 		}
-		wr.write('\n');
+ 		wr.write('\n');
 
-		String request_memory = (String) spec.getAttribute("request_memory");
-		if(request_memory != null) {
-			wr.write("request_memory = " + request_memory + '\n');
-		}
-		
-		String resources = (String) spec.getAttribute("condor.resource_list");
-		if (resources != null && resources.length() > 0) {
-			if (logger.isDebugEnabled())
-				logger.debug("condor.resource_list: " + resources);
-			wr.write(resources + '\n');
-		}
-		
+		// Handle all condor attributes specified by the user
+	    for(String a : spec.getAttributeNames()) {
+	    	if(a != null && a.startsWith("condor.")) {
+	    		String attributeName[] = a.split("condor.");
+	    		wr.write(attributeName[1] + " = " + spec.getAttribute(a) + '\n');
+	    	}
+	    }
+	    
 		wr.write("notification = Never\n");
 		wr.write("leave_in_queue = TRUE\n");
 		wr.write("queue\n");


From davidk at ci.uchicago.edu  Mon Dec  3 16:41:08 2012
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon,  3 Dec 2012 16:41:08 -0600 (CST)
Subject: [Swift-commit] r6096 - branches/release-0.94/libexec
Message-ID: <20121203224108.7405A9CCC2@svn.ci.uchicago.edu>

Author: davidk
Date: 2012-12-03 16:41:08 -0600 (Mon, 03 Dec 2012)
New Revision: 6096

Modified:
   branches/release-0.94/libexec/_swiftwrap
Log:
Fix for #887


Modified: branches/release-0.94/libexec/_swiftwrap
===================================================================
--- branches/release-0.94/libexec/_swiftwrap	2012-11-29 21:39:48 UTC (rev 6095)
+++ branches/release-0.94/libexec/_swiftwrap	2012-12-03 22:41:08 UTC (rev 6096)
@@ -1,3 +1,4 @@
+
 #!/bin/bash
 # this script must be invoked inside of bash, not plain sh
 # note that this script modifies $IFS
@@ -475,17 +476,33 @@
 	fail 254 "The executable $EXEC does not have the executable bit set"
 fi
 if [ "$KICKSTART" == "" ]; then
+
+    TIMEARGS=(-o swiftapp.resources -f APP_RESOURCES=real_time:%E,real_secs:%e,kernel_secs:%S,user_secs:%U,percent_cpu:%P,max_rss:%M,avg_rss:%t,avg_tot_vm:%K,avg_priv_data:%D,avg_priv_stack:%p,avg_shared_text:%X,page_size:%Z,major_pgfaults:%F,minor_pgfaults:%R,swaps:%W,invol_context_switches:%c,vol_waits%w,fs_reads:%I,fs_writes:%O,sock_recv:%r,sock_send:%s,signals:%k,exit_status:%x,command:%C)
+
+    if [ -x /usr/bin/time ]; then
+        TIMECMD="/usr/bin/time"
+    elif [ -x $HOME/swift.time ]; then
+        TIMECMD="$HOME/swift.time"
+    else
+        TIMECMD=""
+		TIMEARGS=""
+    fi
 	if [ "$STDIN" == "" ]; then
 		if [ "$SWIFT_GEN_SCRIPTS" != "" ]; then
 			genScripts
 		fi
-		"$EXEC" "${CMDARGS[@]}" 1>>"$STDOUT" 2>>"$STDERR"
+        "$TIMECMD" "${TIMEARGS[@]}" "$EXEC" "${CMDARGS[@]}" 1>>"$STDOUT" 2>>"$STDERR"
 	else
 		if [ "$SWIFT_GEN_SCRIPTS" != "" ]; then
 			genScripts
 		fi
-		"$EXEC" "${CMDARGS[@]}" 1>>"$STDOUT" 2>>"$STDERR" <"$STDIN"
+        "$TIMECMD" "${TIMEARGS[@]}" "$EXEC" "${CMDARGS[@]}" 1>>"$STDOUT" 2>>"$STDERR" <"$STDIN"
 	fi
+    TIME_EC=$?
+    if [ "_$TIMECMD" != _ ]; then
+		log "$(cat swiftapp.resources)"
+    fi
+    sh -c "exit $TIME_EC"
 	checkError $? "Application $EXEC failed with an exit code of $?"
 else
 	if [ ! -f "$KICKSTART" ]; then



From davidk at ci.uchicago.edu  Mon Dec  3 16:42:32 2012
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Mon,  3 Dec 2012 16:42:32 -0600 (CST)
Subject: [Swift-commit] r6097 - trunk/libexec
Message-ID: <20121203224232.C00E89CCC2@svn.ci.uchicago.edu>

Author: davidk
Date: 2012-12-03 16:42:32 -0600 (Mon, 03 Dec 2012)
New Revision: 6097

Modified:
   trunk/libexec/_swiftwrap
Log:
Fix for #887


Modified: trunk/libexec/_swiftwrap
===================================================================
--- trunk/libexec/_swiftwrap	2012-12-03 22:41:08 UTC (rev 6096)
+++ trunk/libexec/_swiftwrap	2012-12-03 22:42:32 UTC (rev 6097)
@@ -477,7 +477,7 @@
 fi
 if [ "$KICKSTART" == "" ]; then
 
-    TIMEARGS="-o swiftapp.resources -f APP_RESOURCES=real_time:%E,real_secs:%e,kernel_secs:%S,user_secs:%U,percent_cpu:%P,max_rss:%M,avg_rss:%t,avg_tot_vm:%K,avg_priv_data:%D,avg_priv_stack:%p,avg_shared_text:%X,page_size:%Z,major_pgfaults:%F,minor_pgfaults:%R,swaps:%W,invol_context_switches:%c,vol_waits%w,fs_reads:%I,fs_writes:%O,sock_recv:%r,sock_send:%s,signals:%k,exit_status:%x,command:%C"
+    TIMEARGS=(-o swiftapp.resources -f APP_RESOURCES=real_time:%E,real_secs:%e,kernel_secs:%S,user_secs:%U,percent_cpu:%P,max_rss:%M,avg_rss:%t,avg_tot_vm:%K,avg_priv_data:%D,avg_priv_stack:%p,avg_shared_text:%X,page_size:%Z,major_pgfaults:%F,minor_pgfaults:%R,swaps:%W,invol_context_switches:%c,vol_waits%w,fs_reads:%I,fs_writes:%O,sock_recv:%r,sock_send:%s,signals:%k,exit_status:%x,command:%C)
 
     if [ -x /usr/bin/time ]; then
         TIMECMD="/usr/bin/time"
@@ -491,16 +491,18 @@
 		if [ "$SWIFT_GEN_SCRIPTS" != "" ]; then
 			genScripts
 		fi
-		eval $TIMECMD $TIMEARGS "$EXEC" "${CMDARGS[@]}" 1>>"$STDOUT" 2>>"$STDERR"
+        "$TIMECMD" "${TIMEARGS[@]}" "$EXEC" "${CMDARGS[@]}" 1>>"$STDOUT" 2>>"$STDERR"
 	else
 		if [ "$SWIFT_GEN_SCRIPTS" != "" ]; then
 			genScripts
 		fi
-		eval $TIMECMD $TIMEARGS "$EXEC" "${CMDARGS[@]}" 1>>"$STDOUT" 2>>"$STDERR" <"$STDIN"
+        "$TIMECMD" "${TIMEARGS[@]}" "$EXEC" "${CMDARGS[@]}" 1>>"$STDOUT" 2>>"$STDERR" <"$STDIN"
 	fi
+    TIME_EC=$?
     if [ "_$TIMECMD" != _ ]; then
 		log "$(cat swiftapp.resources)"
     fi
+    sh -c "exit $TIME_EC"
 	checkError $? "Application $EXEC failed with an exit code of $?"
 else
 	if [ ! -f "$KICKSTART" ]; then



From swift at ci.uchicago.edu  Mon Dec  3 22:40:06 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Mon,  3 Dec 2012 22:40:06 -0600 (CST)
Subject: [Swift-commit] cog r3528
Message-ID: <20121204044006.4B0AC8D00087@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3528 | davidkelly999 | 2012-12-03 22:35:29 -0600 (Mon, 03 Dec 2012) | 2 lines

Fix compilation error

------------------------------------------------------------------------
Index: modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/common/AbstractExecutor.java
===================================================================
--- modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/common/AbstractExecutor.java	(revision 3527)
+++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/common/AbstractExecutor.java	(working copy)
@@ -47,12 +47,12 @@
         TRIGGERS['<'] = true;
     }
 
-    private File script;
-    private String stdout, stderr, exitcode, jobid;
-    private final JobSpecification spec;
-    private final Task task;
-    private final ProcessListener listener;
-    private Job job;
+    protected File script;
+    protected String stdout, stderr, exitcode, jobid;
+    protected final JobSpecification spec;
+    protected final Task task;
+    protected final ProcessListener listener;
+    protected Job job;
 
     protected AbstractExecutor(Task task, ProcessListener listener) {
         this.task = task;


From davidk at ci.uchicago.edu  Wed Dec  5 14:20:15 2012
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Wed,  5 Dec 2012 14:20:15 -0600 (CST)
Subject: [Swift-commit] r6098 - SwiftTutorials
Message-ID: <20121205202015.039B89D050@svn.ci.uchicago.edu>

Author: davidk
Date: 2012-12-05 14:20:14 -0600 (Wed, 05 Dec 2012)
New Revision: 6098

Added:
   SwiftTutorials/UofC_2012-11-27-fusion/
Log:
Creating fusion version of this tutorial




From davidk at ci.uchicago.edu  Tue Dec 11 11:43:36 2012
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 11 Dec 2012 11:43:36 -0600 (CST)
Subject: [Swift-commit] r6100 - in trunk/tests: language/working
	language-behaviour/IO
Message-ID: <20121211174336.18ECF9CCAA@svn.ci.uchicago.edu>

Author: davidk
Date: 2012-12-11 11:43:35 -0600 (Tue, 11 Dec 2012)
New Revision: 6100

Removed:
   trunk/tests/language-behaviour/IO/q7.swift
   trunk/tests/language/working/q7.swift
Log:
Removing two invalid tests from suite (bug #891)


Deleted: trunk/tests/language/working/q7.swift
===================================================================
--- trunk/tests/language/working/q7.swift	2012-12-05 20:21:35 UTC (rev 6099)
+++ trunk/tests/language/working/q7.swift	2012-12-11 17:43:35 UTC (rev 6100)
@@ -1,16 +0,0 @@
-type file {} 
-
-(file t) echo (string s) {   
-    app {
-        echo s stdout=@filename(t);
-    }
-}
-
-string outputNames[] = ["one", "two", "three"];
-
-file outputFiles[] <array_mapper;files=outputNames>;
-
-foreach f in outputFiles {
-    f = echo("hello");
-}
-

Deleted: trunk/tests/language-behaviour/IO/q7.swift
===================================================================
--- trunk/tests/language-behaviour/IO/q7.swift	2012-12-05 20:21:35 UTC (rev 6099)
+++ trunk/tests/language-behaviour/IO/q7.swift	2012-12-11 17:43:35 UTC (rev 6100)
@@ -1,14 +0,0 @@
-type file {} 
-
-app (file t) echo (string s) {   
-        echo s stdout=@filename(t);
-}
-
-string outputNames[]= ["one", "two", "three"];
-
-file outputFiles[] <array_mapper;files=outputNames>;
-
-foreach f in outputFiles {
-    f = echo("hello");
-}
-



From davidk at ci.uchicago.edu  Tue Dec 11 12:03:26 2012
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Tue, 11 Dec 2012 12:03:26 -0600 (CST)
Subject: [Swift-commit] r6101 - branches/release-0.94/libexec
Message-ID: <20121211180326.3CDC69CCAA@svn.ci.uchicago.edu>

Author: davidk
Date: 2012-12-11 12:03:25 -0600 (Tue, 11 Dec 2012)
New Revision: 6101

Modified:
   branches/release-0.94/libexec/release.txt
Log:
Update release name


Modified: branches/release-0.94/libexec/release.txt
===================================================================
--- branches/release-0.94/libexec/release.txt	2012-12-11 17:43:35 UTC (rev 6100)
+++ branches/release-0.94/libexec/release.txt	2012-12-11 18:03:25 UTC (rev 6101)
@@ -1 +1 @@
-trunk
+0.94RC2



From davidk at ci.uchicago.edu  Wed Dec 12 12:49:10 2012
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Wed, 12 Dec 2012 12:49:10 -0600 (CST)
Subject: [Swift-commit] r6102 - branches/release-0.94
Message-ID: <20121212184910.8B64C9CD0C@svn.ci.uchicago.edu>

Author: davidk
Date: 2012-12-12 12:49:10 -0600 (Wed, 12 Dec 2012)
New Revision: 6102

Modified:
   branches/release-0.94/build.xml
Log:
slurm-qsub-emulator needs an x bit


Modified: branches/release-0.94/build.xml
===================================================================
--- branches/release-0.94/build.xml	2012-12-11 18:03:25 UTC (rev 6101)
+++ branches/release-0.94/build.xml	2012-12-12 18:49:10 UTC (rev 6102)
@@ -115,6 +115,7 @@
                                 <include name="slurm-qsub"/>
   				<include name="slurm-qdel"/>
 				<include name="slurm-qstat"/>
+                                <include name="slurm-qsub-emulator"/>
 			</fileset>
 		</chmod>
 		<chmod perm="+x">



From swift at ci.uchicago.edu  Thu Dec 13 14:15:07 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Thu, 13 Dec 2012 14:15:07 -0600 (CST)
Subject: [Swift-commit] cog r3529
Message-ID: <20121213201507.7B6268D0009D@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3529 | hategan | 2012-12-13 14:12:59 -0600 (Thu, 13 Dec 2012) | 1 line

fixed block comparator
------------------------------------------------------------------------
Index: modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java
===================================================================
--- modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java	(revision 3528)
+++ modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java	(working copy)
@@ -437,7 +437,10 @@
                 public int compare(Block b1, Block b2) {
                     double s1 = b1.sizeLeft();
                     double s2 = b2.sizeLeft();
-                    if (s1 < s2) {
+                    if (s1 == s2) {
+                    	return 0;
+                    }
+                    else if (s1 < s2) {
                         return -1;
                     }
                     else {


From hategan at ci.uchicago.edu  Thu Dec 13 17:38:36 2012
From: hategan at ci.uchicago.edu (hategan at ci.uchicago.edu)
Date: Thu, 13 Dec 2012 17:38:36 -0600 (CST)
Subject: [Swift-commit] r6103 - trunk/resources
Message-ID: <20121213233836.308AB9CD0A@svn.ci.uchicago.edu>

Author: hategan
Date: 2012-12-13 17:38:36 -0600 (Thu, 13 Dec 2012)
New Revision: 6103

Modified:
   trunk/resources/swiftscript.g
Log:
escape "<", ">", and "&" in string literals when compiling

Modified: trunk/resources/swiftscript.g
===================================================================
--- trunk/resources/swiftscript.g	2012-12-12 18:49:10 UTC (rev 6102)
+++ trunk/resources/swiftscript.g	2012-12-13 23:38:36 UTC (rev 6103)
@@ -1147,7 +1147,7 @@
     | s:STRING_LITERAL
       {
         code=template("sConst");
-        code.setAttribute("value",quote(s.getText()));
+        code.setAttribute("value",quote(escape(s.getText())));
       }
     | t:"true"
       {



From hategan at ci.uchicago.edu  Thu Dec 13 17:38:53 2012
From: hategan at ci.uchicago.edu (hategan at ci.uchicago.edu)
Date: Thu, 13 Dec 2012 17:38:53 -0600 (CST)
Subject: [Swift-commit] r6104 - trunk/src/org/griphyn/vdl/engine
Message-ID: <20121213233853.ADE5F9CD0A@svn.ci.uchicago.edu>

Author: hategan
Date: 2012-12-13 17:38:53 -0600 (Thu, 13 Dec 2012)
New Revision: 6104

Modified:
   trunk/src/org/griphyn/vdl/engine/Karajan.java
Log:
escape "<", ">", and "&" in string literals when compiling

Modified: trunk/src/org/griphyn/vdl/engine/Karajan.java
===================================================================
--- trunk/src/org/griphyn/vdl/engine/Karajan.java	2012-12-13 23:38:36 UTC (rev 6103)
+++ trunk/src/org/griphyn/vdl/engine/Karajan.java	2012-12-13 23:38:53 UTC (rev 6104)
@@ -1629,7 +1629,7 @@
 		for (String key : stringInternMap.keySet()) {
 			String variableName = stringInternMap.get(key);
 			StringTemplate st = template("sConst");
-			st.setAttribute("innervalue",escapeQuotes(key));
+			st.setAttribute("innervalue",escapeQuotesAndMarkup(key));
 			StringTemplate vt = template("globalConstant");
 			vt.setAttribute("name",variableName);
 			vt.setAttribute("expr",st);
@@ -1661,6 +1661,30 @@
 		return in.replaceAll("\"", "&quot;");
 	}
 	
+	String escapeQuotesAndMarkup(String in) {
+	    StringBuilder sb = new StringBuilder();
+	    for (int i = 0; i < in.length(); i++) {
+	        char c = in.charAt(i);
+	        switch (c) {
+	            case '<':
+	                sb.append("&lt;");
+	                break;
+	            case '>':
+	                sb.append("&gt;");
+	                break;
+	            case '"':
+	                sb.append("&quot;");
+	                break;
+	            case '&':
+	                sb.append("&amp;");
+	                break;
+	            default:
+	                sb.append(c);
+	        }
+	    }
+        return sb.toString();
+    }
+	
 	public static String normalize(String type) {
 	    return org.griphyn.vdl.type.Types.normalize(type);
 	}



From wilde at ci.uchicago.edu  Mon Dec 17 14:43:23 2012
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Mon, 17 Dec 2012 14:43:23 -0600 (CST)
Subject: [Swift-commit] r6105 - SwiftApps/SciColSim
Message-ID: <20121217204323.0E44D9CCE6@svn.ci.uchicago.edu>

Author: wilde
Date: 2012-12-17 14:43:22 -0600 (Mon, 17 Dec 2012)
New Revision: 6105

Modified:
   SwiftApps/SciColSim/Makefile
   SwiftApps/SciColSim/gengraphs.sh
   SwiftApps/SciColSim/graphsim.cpp
   SwiftApps/SciColSim/testgraph.py
   SwiftApps/SciColSim/trimgraph.sh
Log:
Updates for graph testing.

Modified: SwiftApps/SciColSim/Makefile
===================================================================
--- SwiftApps/SciColSim/Makefile	2012-12-13 23:38:53 UTC (rev 6104)
+++ SwiftApps/SciColSim/Makefile	2012-12-17 20:43:22 UTC (rev 6105)
@@ -2,7 +2,7 @@
 
 ifeq ($(UNAME), Linux)
 
-all:	openmp-optimizer graphsim
+all:	openmp-optimizer graphsim openmptest
 
 openmp-optimizer: optimizer.cpp
 	g++ -DP_OPENMP -static -O -fopenmp -I boost_1_47_0 -o openmp-optimizer optimizer.cpp
@@ -10,6 +10,9 @@
 graphsim: graphsim.cpp
 	g++ -DP_OPENMP -static -pg -O -fopenmp -I boost_1_47_0 -o graphsim graphsim.cpp
 
+openmptest: openmptest.cpp
+	g++ -DP_OPENMP -static -O -fopenmp -o openmptest openmptest.cpp
+
 clean:
 	@rm -rvf openmp-optimizer
 
@@ -17,11 +20,17 @@
 
 ifeq ($(UNAME), Darwin)
 
-all:	openmp-optimizer dispatch-optimizer orig-optimizer
+all:	openmp-optimizer dispatch-optimizer orig-optimizer graphsim openmptest
 
 openmp-optimizer: optimizer.cpp
 	g++ -DP_OPENMP -fopenmp -I boost_1_47_0 -o openmp-optimizer optimizer.cpp
 
+graphsim: graphsim.cpp
+	g++ -DP_OPENMP -fopenmp -I boost_1_47_0 -g -o graphsim graphsim.cpp
+
+openmptest: openmptest.cpp
+	g++ -DP_OPENMP -fopenmp  -g -o openmptest openmptest.cpp
+
 dispatch-optimizer: optimizer.cpp
 	g++ -DP_DISPATCH -I boost_1_47_0 -o dispatch-optimizer optimizer.cpp
 

Modified: SwiftApps/SciColSim/gengraphs.sh
===================================================================
--- SwiftApps/SciColSim/gengraphs.sh	2012-12-13 23:38:53 UTC (rev 6104)
+++ SwiftApps/SciColSim/gengraphs.sh	2012-12-17 20:43:22 UTC (rev 6105)
@@ -2,7 +2,8 @@
 
 mkdir -p graph
 
-for s in $(seq 1000 1000 10000); do
+# for s in $(seq 1000 1000 10000); do
+for s in 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000; do
   ./trimgraph.sh $s 1.0 > graph/$s.100
   ./trimgraph.sh $s 0.1 > graph/$s.10
   ./trimgraph.sh  $s 0.5 > graph/$s.50

Modified: SwiftApps/SciColSim/graphsim.cpp
===================================================================
--- SwiftApps/SciColSim/graphsim.cpp	2012-12-13 23:38:53 UTC (rev 6104)
+++ SwiftApps/SciColSim/graphsim.cpp	2012-12-17 20:43:22 UTC (rev 6105)
@@ -800,56 +800,65 @@
 
 
     //=============================================================
-    void update_probabilities(void){
+  void update_probabilities(void){
 
 
-        //=========================
-		// Compute sampling probabilities
-		// first pass: \xi_i,j
-		for(int i=0; i<N_nodes-1; i++){
-			for( int j=i+1; j<N_nodes; j++){
+    //=========================
+    // Compute sampling probabilities
+    // first pass: \xi_i,j
+    int i, j;
+    //#pragma omp parallel for private (j)
+    //#pragma omp parallel for 
 
-				double bg = 0.;
+    //    #pragma omp parallel for default(none) shared( Prob, alpha_i, alpha_m, beta, k_max, gamma, delta, Rank, Dist) private(i,j)
+    #pragma omp parallel for private(i,j)
 
-				Prob[i][j] = alpha_i*log(min(Rank[i]+1.,Rank[j]+1.)) +
-                alpha_m*log(max(Rank[i]+1.,Rank[j]+1.));
+    for( i=0; i<N_nodes-1; i++){
+      for(  j=i+1; j<N_nodes; j++){
 
-                if (Dist[i][j] > 0.){
+	double bg = 0.;
 
-                    double k = Dist[i][j];
-                    if (k >= k_max){
-                        k = k_max-1;
-                    }
+	Prob[i][j] = alpha_i*log(min(Rank[i]+1.,Rank[j]+1.)) +
+	  alpha_m*log(max(Rank[i]+1.,Rank[j]+1.));
 
-                    bg = beta * log(k/k_max) + gamma * log(1. - k/k_max);
+	if (Dist[i][j] > 0.){
 
-                } else {
-                    bg = delta;
-                }
+	  double k = Dist[i][j];
+	  if (k >= k_max){
+	    k = k_max-1;
+	  }
 
-				Prob[i][j] = exp(Prob[i][j] + bg);
-			}
-		}
+	  bg = beta * log(k/k_max) + gamma * log(1. - k/k_max);
 
+	} else {
+	  bg = delta;
+	}
 
-		// second pass: sum
-		double Summa = 0.;
+	Prob[i][j] = exp(Prob[i][j] + bg);
+      }
+    }
 
-		for(int i=0; i<N_nodes-1; i++){
-			for( int j=i+1; j<N_nodes; j++){
-				Summa += Prob[i][j];
-			}
-		}
 
-		// third pass: normalize
-		for(int i=0; i<N_nodes-1; i++){
-			for( int j=i+1; j<N_nodes; j++){
-				Prob[i][j] /= Summa;
-			}
-		}
+    // second pass: sum
+    double Summa = 0.;
 
+    #pragma omp parallel
+    for(i=0; i<N_nodes-1; i++){
+      for(j=i+1; j<N_nodes; j++){
+	Summa += Prob[i][j];
+      }
     }
 
+    // third pass: normalize
+    #pragma omp parallel 
+    for( i=0; i<N_nodes-1; i++){
+      for(  j=i+1; j<N_nodes; j++){
+	Prob[i][j] /= Summa;
+      }
+    }
+
+  }
+
 	// Now we are ready for simulations
 	//==============================================
 	void update_world(){
@@ -859,10 +868,15 @@
 		// Given current universe compute shortest paths
 		//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+std::cout << "Before updates" << std::endl;
 		update_current_graph();
+std::cout << "after current" << std::endl;
 		update_ranks();
+std::cout << "after ranks" << std::endl;
 		update_distances();
+std::cout << "after distances" << std::endl;
 		update_probabilities();
+std::cout << "after probs" << std::endl;
 
 		//===============================
 		// sampling
@@ -876,12 +890,15 @@
 
 			while(publishable < N_steps){
 
+std::cout << "failed:1 before sample\n";
 		    	result = sample();
+std::cout << "failed:1 after sample\n";
 			    publishable += result;
 			    failed += (1-result);
 
 			}
 
+std::cout << "failed:1 before for\n";
 			for(int i=0; i<N_nodes-1; i++){
 				for( int j=i+1; j<N_nodes; j++){
 
@@ -889,9 +906,11 @@
 
 					if (Tried[i][j]>0. && Final[i][j]>0.){
 						novel+=1.;
+std::cout << "failed:1 novel: " << novel << std::endl;
 					}
 				}
 			}
+std::cout << "failed:1 after for\n";
 
 		}
 		//^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -901,6 +920,7 @@
 			int n_failed;
 			//, n_check = 0;
 
+std::cout << "failed:0 before for\n";
 			for(int i=0; i<N_nodes-1; i++){
 				for( int j=i+1; j<N_nodes; j++){
 					if (Final[i][j] == 0.){
@@ -918,12 +938,17 @@
 				//std::cout << std::endl;
 			}
 
+std::cout << "failed:0 after for\n";
 			n_failed = sample_failed_number(pfail);
+
+
+std::cout << "failed:0 before while\n";
 			while(publishable < N_steps){
 
 		    	result = sample();
 			    publishable += result;
 			}
+std::cout << "failed:0 after while\n";
 
 
 			current_loss += (n_failed + N_steps);
@@ -934,6 +959,8 @@
 
 					if (Tried[i][j]>0. && Final[i][j]>0.){
 						novel+=1.;
+std::cout << "failed:0 novel: " << novel << std::endl;
+
 					}
 				}
 			}
@@ -943,6 +970,7 @@
 
 
 		//^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+verbose_level = 2;
 		if (verbose_level == 2){
             std::cout << (current_repeat+1) << "  epoch=" << (current_epoch+1)
 
@@ -1887,7 +1915,7 @@
     double T_start=params2[0], T_end=params2[1], Target_rejection=params2[3], starting_jump=params2[4];
     int Annealing_repeats = (int) params2[2];
 
-    print_memory_status();
+    // print_memory_status();
 
 #ifdef P_DISPATCH
     dispatch_group_t group = dispatch_group_create();

Modified: SwiftApps/SciColSim/testgraph.py
===================================================================
--- SwiftApps/SciColSim/testgraph.py	2012-12-13 23:38:53 UTC (rev 6104)
+++ SwiftApps/SciColSim/testgraph.py	2012-12-17 20:43:22 UTC (rev 6105)
@@ -140,7 +140,7 @@
   optimizerRepeats = 1
   evolveReruns     = 1
   annealingSteps   = 1
-  NWorkers         = "1"
+  NWorkers         = "2"
   openmp           = "OMP_NUM_THREADS=" + NWorkers
   operation        = "m"  # n=normal, m=manual (runs 1 multi_loss call)
   seed             = "" # "123456"
@@ -159,8 +159,9 @@
 for target in range(startTarget,endTarget,incrTarget):
   for i in range(optimizerRepeats):
     args = "rm -f bestdb.txt; " + \
-           openmp + " " + app + " 0 0 0 0 0 " + str(target) + " 40000 20 " + str(evolveReruns) + \
-           " 2 1 2. 0.01 " + str(annealingSteps) + " 0.3 2.3 0 0 0 0 0 " + operation + " " + NWorkers + " " + seed + \
+           openmp + " " + "/usr/bin/time -l " + \
+                          app + " 0 0 0 0 0 " + str(target) + " 40000 20 " + str(evolveReruns) + \
+           " 2 2 2. 0.01 " + str(annealingSteps) + " 0.3 2.3 0 0 0 0 0 " + operation + " " + NWorkers + " " + seed + \
            " # >& out.T"+str(target)+".i"+str(i) + "; #mv bestdb.txt best.T" + str(target) + ".i" + str(i) 
     print("\n**** Calling optimizer: "+args+"\n")
     os.system(args);

Modified: SwiftApps/SciColSim/trimgraph.sh
===================================================================
--- SwiftApps/SciColSim/trimgraph.sh	2012-12-13 23:38:53 UTC (rev 6104)
+++ SwiftApps/SciColSim/trimgraph.sh	2012-12-17 20:43:22 UTC (rev 6105)
@@ -3,7 +3,7 @@
 vertices=${1:-100}
 fraction=${2:-1.0}
 
-tmp=$(mktemp)
+tmp=$(mktemp -t trimgraph)
 
 awk '
 NR == 1 { }



From wilde at ci.uchicago.edu  Mon Dec 17 16:17:26 2012
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Mon, 17 Dec 2012 16:17:26 -0600 (CST)
Subject: [Swift-commit] r6106 - SwiftApps/SciColSim
Message-ID: <20121217221726.3D15A9CCE6@svn.ci.uchicago.edu>

Author: wilde
Date: 2012-12-17 16:17:26 -0600 (Mon, 17 Dec 2012)
New Revision: 6106

Added:
   SwiftApps/SciColSim/openmptest.cpp
Log:
Add openmptest.cpp test program to verify concurrency levels.

Added: SwiftApps/SciColSim/openmptest.cpp
===================================================================
--- SwiftApps/SciColSim/openmptest.cpp	                        (rev 0)
+++ SwiftApps/SciColSim/openmptest.cpp	2012-12-17 22:17:26 UTC (rev 6106)
@@ -0,0 +1,103 @@
+#include <fstream>
+#include <iostream>
+#include <stdio.h>
+#include <time.h>
+#include <ctime>
+#include <algorithm>
+#include <string>
+
+#include <math.h>
+
+#include <stdio.h>
+#include <sys/param.h>
+#include <sys/time.h>
+#include <sys/types.h>
+#include "unistd.h"
+
+#include <fstream>
+#include <stdlib.h>
+
+//#define N 23000
+#define N 10000
+
+float Prob[N][N];
+float Rank[N];
+float Dist[N][N];
+
+float alpha_i = 1.0;
+float alpha_m = 1.0;
+float beta = 1.0;
+float gam = 1.0;
+float delta = 1.0;
+float k_max = 1.0;
+
+float min(float a, float b)
+{
+  if(a<b) return(a); else return(b);
+}
+
+float max(float a, float b)
+{
+  if(a>b) return(a); else return(b);
+}
+
+void update(void){
+
+    int i, j;
+    float Summa = 0.;
+
+printf("Loop 1\n");
+    //#pragma omp parallel for private (j)
+#pragma omp parallel for default(none) shared( Prob, alpha_i, alpha_m, beta, k_max, gam, delta, Rank, Dist) private(i,j)
+    for( i=0; i<N-1; i++){
+      for(  j=i+1; j<N; j++){
+
+	float bg = 0.;
+
+	Prob[i][j] = alpha_i*log(min(Rank[i]+1.,Rank[j]+1.)) +
+	  alpha_m*log(max(Rank[i]+1.,Rank[j]+1.));
+	if (Dist[i][j] > 0.){
+	  float k = Dist[i][j];
+	  if (k >= k_max){
+	    k = k_max-1;
+	  }
+	  bg = beta * log(k/k_max) + gam * log(1. - k/k_max);
+	} else {
+	  bg = delta;
+	}
+	Prob[i][j] = exp(Prob[i][j] + bg);
+      }
+    }
+
+printf("Loop 2\n");
+    #pragma omp parallel for private(i)
+    for(i=0; i<N-1; i++){
+      for(j=i+1; j<N; j++){
+	Summa += Prob[i][j];
+      }
+    }
+
+printf("Loop 3\n");
+    #pragma omp parallel for private(i)
+    for( i=0; i<N-1; i++){
+      for(  j=i+1; j<N; j++){
+	Prob[i][j] /= Summa;
+      }
+    }
+}
+
+main()
+{
+  int i, j;
+  for(i=0;i<N;i++) {
+    Rank[i] = 1.0;
+    for(j=0;j<N;j++) {
+      Prob[i][j] = Dist[i][j] = 1.0;
+    }
+  }
+
+  for(;;) {
+   printf("update\n");
+   update();	
+  }
+}



From wilde at ci.uchicago.edu  Mon Dec 17 18:15:14 2012
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Mon, 17 Dec 2012 18:15:14 -0600 (CST)
Subject: [Swift-commit] r6107 - SwiftApps/SciColSim
Message-ID: <20121218001514.C0E439D042@svn.ci.uchicago.edu>

Author: wilde
Date: 2012-12-17 18:15:14 -0600 (Mon, 17 Dec 2012)
New Revision: 6107

Added:
   SwiftApps/SciColSim/samplegraph.sh
Log:
add script to downsample the graph

Added: SwiftApps/SciColSim/samplegraph.sh
===================================================================
--- SwiftApps/SciColSim/samplegraph.sh	                        (rev 0)
+++ SwiftApps/SciColSim/samplegraph.sh	2012-12-18 00:15:14 UTC (rev 6107)
@@ -0,0 +1,52 @@
+#! /bin/sh
+
+fraction=${1:-1.0}
+
+tmp=$(mktemp -t samplegraph)
+
+awk '
+
+function crand()
+{
+    _cliff_seed = (100 * log(_cliff_seed)) % 1
+    if (_cliff_seed < 0)
+        _cliff_seed = - _cliff_seed
+    return _cliff_seed
+}
+     
+BEGIN { 
+  getmsec="perl -MTime::HiRes=gettimeofday -e \"print int(1000*gettimeofday()).qq(\\n);\""
+  getmsec | getline msec
+  close(getmsec)
+  _cliff_seed = (msec % 10000) / 10000
+ nv=0
+}
+
+NR == 1 { }
+
+(NR > 1) && (crand() < fraction) {
+  if ( $1 in vertices ) {
+     v1 = vertices[$1]
+  }
+  else {
+     vertices[$1] = v1 = nv++;
+  }
+  if ( $2 in vertices ) {
+     v2 = vertices[$2]
+  }
+  else {
+     vertices[$2] = v2 = nv++;
+  }
+  print v1, v2  
+}
+
+END {print nv}
+
+' fraction=$fraction < big_graph.v01.txt >$tmp
+
+edges=$(wc -l <$tmp)
+vertices=$(tail -1 $tmp)
+
+echo $vertices $edges
+sed -e '$d' <$tmp
+rm $tmp


Property changes on: SwiftApps/SciColSim/samplegraph.sh
___________________________________________________________________
Added: svn:executable
   + *



From lgadelha at ci.uchicago.edu  Wed Dec 19 07:58:29 2012
From: lgadelha at ci.uchicago.edu (lgadelha at ci.uchicago.edu)
Date: Wed, 19 Dec 2012 07:58:29 -0600 (CST)
Subject: [Swift-commit] r6108 - provenancedb
Message-ID: <20121219135831.0805D9CD0C@svn.ci.uchicago.edu>

Author: lgadelha
Date: 2012-12-19 07:57:43 -0600 (Wed, 19 Dec 2012)
New Revision: 6108

Modified:
   provenancedb/README.asciidoc
   provenancedb/info-to-runtime
   provenancedb/prov-init.sql
   provenancedb/prov-to-sql.sh
Log:
Update to provenance extraction scripts to match new format of runtime information in wrapper logs.


Modified: provenancedb/README.asciidoc
===================================================================
--- provenancedb/README.asciidoc	2012-12-18 00:15:14 UTC (rev 6107)
+++ provenancedb/README.asciidoc	2012-12-19 13:57:43 UTC (rev 6108)
@@ -188,10 +188,15 @@
 
 === Example: MODIS
 
-Run MODIS.
+Run MODIS:
 
 --------------------------------------
 swift modis.swift
+--------------------------------------
+
+After running MODIS, one can import provenenace information into the database using:
+
+--------------------------------------
 swift-prov-import-all-logs
 --------------------------------------
 
@@ -213,8 +218,8 @@
  modis.swift     | 5483          | 3339        | SUCCESS     | 2012-10-26 11:44:59.909-02 |   85.050
 --------------------------------------
 
+List the 
 
-
 --------------------------------------
 select * from ancestors('dataset:20121026-1146-jng6bir4:720000001604');
 

Modified: provenancedb/info-to-runtime
===================================================================
--- provenancedb/info-to-runtime	2012-12-18 00:15:14 UTC (rev 6107)
+++ provenancedb/info-to-runtime	2012-12-19 13:57:43 UTC (rev 6108)
@@ -10,7 +10,7 @@
     
     if [ "X$record" != "X" ] && [ -f $record ] ; then
 	
-	grep '^RUNTIME_INFO=' $record | sed "s/^RUNTIME_INFO=\(.*\)$/$globalid \1/"
+	grep '^APP_RESOURCES=' $record | sed "s/^APP_RESOURCES=\(.*\)$/$globalid \1/"
 	
     else
 	echo no wrapper log for $id >&2

Modified: provenancedb/prov-init.sql
===================================================================
--- provenancedb/prov-init.sql	2012-12-18 00:15:14 UTC (rev 6107)
+++ provenancedb/prov-init.sql	2012-12-19 13:57:43 UTC (rev 6108)
@@ -117,8 +117,31 @@
      start_time        numeric,
      duration          numeric,
      final_state       varchar(32),
-     site              varchar(256)
+     site              varchar(256),
+     real_secs	       numeric,
+     kernel_secs       numeric,
+     user_secs	       numeric,
+     percent_cpu       numeric,
+     max_rss	       numeric,
+     avg_rss	       numeric,
+     avg_tot_vm	       numeric,
+     avg_priv_data     numeric,
+     avg_priv_stack    numeric,
+     avg_shared_text   numeric,
+     page_size	       numeric,
+     major_pgfaults    numeric,
+     minor_pgfaults    numeric,
+     swaps	       numeric,
+     invol_context_switches	numeric,
+     vol_waits			numeric,
+     fs_reads			numeric,
+     fs_writes			numeric,
+     sock_recv			numeric,
+     sock_send			numeric,
+     signals			numeric,
+     exit_status		numeric
 );
+
 --     maxrss            numeric,
 --     walltime          numeric,
 --     systime           numeric,
@@ -291,7 +314,13 @@
 );
 
 create view provenance_graph_edge as 
-       select function_call_id as parent, dataset_id as child from dataset_out
-    union all
-       select dataset_id as parent, function_call_id as child from dataset_in;
+       	    select function_call_id as parent, dataset_id as child 
+       	    from dataset_out
+       union all
+       	    select dataset_id as parent, function_call_id as child 
+	    from dataset_in;
 	
+create view script_run_summary as 
+       select id,swift_version,cog_version,final_state,
+       	      start_time,duration,script_filename 
+       from script_run;
\ No newline at end of file

Modified: provenancedb/prov-to-sql.sh
===================================================================
--- provenancedb/prov-to-sql.sh	2012-12-18 00:15:14 UTC (rev 6107)
+++ provenancedb/prov-to-sql.sh	2012-12-19 13:57:43 UTC (rev 6108)
@@ -129,13 +129,31 @@
 echo "    - Wrapper log resource consumption info."
 if [ -f runtime.txt ]; then
     while read execute2_id runtime; do
-	timestamp=$(echo $runtime | awk -F "," '{print $1}' | awk -F ":" '{print $2}')
-	cpu_usage=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
-	max_phys_mem=$(echo $runtime | awk -F "," '{print $3}' | awk -F ":" '{print $2}')
-	max_virtual_mem=$(echo $runtime | awk -F "," '{print $4}' | awk -F ":" '{print $2}')
-	io_read_bytes=$(echo $runtime | awk -F "," '{print $5}' | awk -F ":" '{print $2}')
-	io_write_bytes=$(echo $runtime | awk -F "," '{print $6}' | awk -F ":" '{print $2}')
-	echo "INSERT INTO rt_info (app_exec_id, timestamp, cpu_usage, max_phys_mem, max_virt_mem, io_read, io_write) VALUES ('$execute2_id', $timestamp, $cpu_usage, $max_phys_mem, $max_virtual_mem, $io_read_bytes, $io_write_bytes);"  >> /tmp/$RUNID.sql
+	real_secs=$(echo $runtime | awk -F "," '{print $1}' | awk -F ":" '{print $2}')
+	kernel_secs=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	user_secs=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	percent_cpu=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	max_rss=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	avg_rss=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	avg_tot_vm=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	avg_priv_data=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	avg_priv_stack=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	avg_shared_text=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	page_size=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	major_pgfaults=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	minor_pgfaults=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	swaps=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	invol_context_switches=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	vol_waits=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	fs_reads=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	fs_writes=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	sock_recv=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	sock_send=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	signals=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	exit_status=$(echo $runtime | awk -F "," '{print $2}' | awk -F ":" '{print $2}')
+	
+	echo "UPDATE app_exec SET real_secs='$real_secs', kernel_secs='$kernel_secs', user_secs='$user_secs', percent_cpu='$percent_cpu', max_rss='$max_rss', avg_rss='$avg_rss', avg_tot_vm='$avg_tot_vm', avg_priv_data='$avg_priv_data', avg_priv_stack='$avg_priv_stack', avg_priv_stack='$avg_priv_stack', avg_shared_text='$avg_shared_text', page_size='$page_size', major_pgfaults='$major_pgfaults', minor_pgfaults='$minor_pgfaults', swaps='$swaps', invol_context_switches='$invol_context_switches', vol_waits='$vol_waits', fs_reads='$fs_reads', fs_writes='$fs_writes', sock_recv='$sock_recv', sock_send='$sock_send', signals='$signals', exit_status='$exit_status' WHERE app_exec_id='$execute2_id';"
+	#echo "INSERT INTO rt_info (app_exec_id, timestamp, cpu_usage, max_phys_mem, max_virt_mem, io_read, io_write) VALUES ('$execute2_id', $timestamp, $cpu_usage, $max_phys_mem, $max_virtual_mem, $io_read_bytes, $io_write_bytes);"  >> /tmp/$RUNID.sql
 
 #	for key in $(echo maxrss walltime systime usertime cpu fsin fsout timesswapped socketrecv socketsent majorpagefaults minorpagefaults contextswitchesinv contextswitchesvol); do
 #	    value=$(echo $runtime | awk -F "," '{print $1}' | awk -F ":" '{print $2}')



From lgadelha at ci.uchicago.edu  Wed Dec 19 08:06:35 2012
From: lgadelha at ci.uchicago.edu (lgadelha at ci.uchicago.edu)
Date: Wed, 19 Dec 2012 08:06:35 -0600 (CST)
Subject: [Swift-commit] r6109 - trunk/libexec
Message-ID: <20121219140635.DF9E49CD0C@svn.ci.uchicago.edu>

Author: lgadelha
Date: 2012-12-19 08:06:35 -0600 (Wed, 19 Dec 2012)
New Revision: 6109

Modified:
   trunk/libexec/_swiftwrap
Log:
- fixed missing delimiter 
- removed "command" since it is already in the wrapper log 
- removed "real_time" since it is the same as "real_secs", in a different format 


Modified: trunk/libexec/_swiftwrap
===================================================================
--- trunk/libexec/_swiftwrap	2012-12-19 13:57:43 UTC (rev 6108)
+++ trunk/libexec/_swiftwrap	2012-12-19 14:06:35 UTC (rev 6109)
@@ -477,7 +477,7 @@
 fi
 if [ "$KICKSTART" == "" ]; then
 
-    TIMEARGS=(-o swiftapp.resources -f APP_RESOURCES=real_time:%E,real_secs:%e,kernel_secs:%S,user_secs:%U,percent_cpu:%P,max_rss:%M,avg_rss:%t,avg_tot_vm:%K,avg_priv_data:%D,avg_priv_stack:%p,avg_shared_text:%X,page_size:%Z,major_pgfaults:%F,minor_pgfaults:%R,swaps:%W,invol_context_switches:%c,vol_waits%w,fs_reads:%I,fs_writes:%O,sock_recv:%r,sock_send:%s,signals:%k,exit_status:%x,command:%C)
+    TIMEARGS=(-o swiftapp.resources -f APP_RESOURCES=real_secs:%e,kernel_secs:%S,user_secs:%U,percent_cpu:%P,max_rss:%M,avg_rss:%t,avg_tot_vm:%K,avg_priv_data:%D,avg_priv_stack:%p,avg_shared_text:%X,page_size:%Z,major_pgfaults:%F,minor_pgfaults:%R,swaps:%W,invol_context_switches:%c,vol_waits:%w,fs_reads:%I,fs_writes:%O,sock_recv:%r,sock_send:%s,signals:%k,exit_status:%x)
 
     if [ -x /usr/bin/time ]; then
         TIMECMD="/usr/bin/time"



From swift at ci.uchicago.edu  Wed Dec 19 14:35:26 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Wed, 19 Dec 2012 14:35:26 -0600 (CST)
Subject: [Swift-commit] cog r3530
Message-ID: <20121219203526.CFE2F8D0009F@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3530 | davidkelly999 | 2012-12-19 14:31:15 -0600 (Wed, 19 Dec 2012) | 3 lines

Ability to run condor easily in environments with non-shared filesystems (using condor transfer mechanisms for the wrapper scripts and relative paths)
New "nonshared" jobtype

------------------------------------------------------------------------
Index: modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/QueuePoller.java
===================================================================
--- modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/QueuePoller.java	(revision 3529)
+++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/QueuePoller.java	(working copy)
@@ -18,7 +18,6 @@
 import org.globus.cog.abstraction.impl.scheduler.common.AbstractProperties;
 import org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller;
 import org.globus.cog.abstraction.impl.scheduler.common.Job;
-import org.globus.cog.abstraction.interfaces.JobSpecification;
 
 public class QueuePoller extends AbstractQueuePoller {
 	public static final Logger logger = Logger.getLogger(QueuePoller.class);
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 3529)
+++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/CondorExecutor.java	(working copy)
@@ -9,12 +9,8 @@
  */
 package org.globus.cog.abstraction.impl.scheduler.condor;
 
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.Writer;
-import java.nio.channels.FileChannel;
 import java.util.Iterator;
 import java.util.List;
 
@@ -24,12 +20,10 @@
 import org.globus.cog.abstraction.impl.scheduler.common.AbstractProperties;
 import org.globus.cog.abstraction.impl.scheduler.common.AbstractQueuePoller;
 import org.globus.cog.abstraction.impl.scheduler.common.Job;
-import org.globus.cog.abstraction.impl.scheduler.common.ProcessException;
 import org.globus.cog.abstraction.impl.scheduler.common.ProcessListener;
 import org.globus.cog.abstraction.interfaces.FileLocation;
 import org.globus.cog.abstraction.interfaces.JobSpecification;
 import org.globus.cog.abstraction.interfaces.Task;
-import org.globus.gsi.gssapi.auth.AuthorizationException;
 
 public class CondorExecutor extends AbstractExecutor {
 	public static final Logger logger = Logger.getLogger(CondorExecutor.class);
@@ -44,86 +38,10 @@
 			wr.write(arg + String.valueOf(value) + '\n');
 		}
 	}
-
-    public void start()
-    throws AuthorizationException, IOException, ProcessException {
-    	File scriptdir = new File(".");
-        script = File.createTempFile(getName(), ".submit", scriptdir);
-        if (!logger.isDebugEnabled()) {
-            script.deleteOnExit();
-        }
-        stdout = spec.getStdOutput() == null ? script.getAbsolutePath()
-                + ".stdout" : spec.getStdOutput();
-        stderr = spec.getStdError() == null ? script.getAbsolutePath()
-                + ".stderr" : spec.getStdError();
-        exitcode = script.getAbsolutePath() + ".exitcode";
-
-        if (logger.isDebugEnabled()) {
-            logger.debug("Writing " + getName() + " script to " + script);
-        }
-
-        String[] cmdline = buildCommandLine(scriptdir, script, exitcode,
-            stdout, stderr);
-
-        if (logger.isDebugEnabled()) {
-            logCommandLine(cmdline);
-        }
-        Process process = Runtime.getRuntime().exec(cmdline, null, null);
-
-        try {
-            process.getOutputStream().close();
-        }
-        catch (IOException e) {
-        }
-
-        try {
-            int code = process.waitFor();
-            if (code != 0) {
-                String errorText = getOutput(process.getInputStream())
-                        + getOutput(process.getErrorStream());
-                throw new ProcessException("Could not submit job ("
-                        + getProperties().getSubmitCommandName()
-                        + " reported an exit code of " + code + "). "
-                        + errorText);
-            }
-            if (logger.isDebugEnabled()) {
-                logger.debug(getProperties().getSubmitCommandName()
-                        + " done (exit code " + code + ")");
-            }
-        }
-        catch (InterruptedException e) {
-            if (logger.isDebugEnabled()) {
-                logger.debug("Interrupted exception while waiting for "
-                        + getProperties().getSubmitCommandName(), e);
-            }
-            if (listener != null) {
-                listener
-                    .processFailed("The submission process was interrupted");
-            }
-        }
-
-        String output = getOutput(process.getInputStream());
-        jobid = parseSubmitCommandOutput(output);
-        if (logger.isDebugEnabled()) {
-            logger.debug("Submitted job with id '" + jobid + "'");
-        }
-
-        if (jobid.length() == 0) {
-            String errorText = getOutput(process.getErrorStream());
-            if (listener != null)
-                listener.processFailed("Received empty jobid!\n" +
-                                       output + "\n" + errorText);
-        }
-
-        process.getInputStream().close();
-
-        getQueuePoller().addJob(
-            job = createJob(jobid, stdout, spec.getStdOutputLocation(), stderr,
-                spec.getStdErrorLocation(), exitcode, this));
-    }
 	
 	protected void writeScript(Writer wr, String exitcodefile, String stdout, String stderr) throws IOException {
 		boolean grid = false;
+		boolean nonshared = false;
 		JobSpecification spec = getSpec();
 
 		// Handle some predefined jobTypes
@@ -145,6 +63,13 @@
 			wr.write("stream_error  = False\n");
 			wr.write("Transfer_Executable = false\n");
 		}
+		else if("nonshared".equals(type)) {
+			nonshared = true;
+			wr.write("universe = vanilla\n");
+			wr.write("should_transfer_files = YES\n");
+			wr.write("when_to_transfer_output = ON_EXIT_OR_EVICT\n");
+			wr.write("Transfer_Executable = false\n");
+		}
 		else {
 			if(spec.getAttribute("condor.universe") == null) {
 				wr.write("universe = vanilla\n");
@@ -177,23 +102,26 @@
 		wr.write("\n");
 
 		if (spec.getDirectory() != null) {
-			if(!grid) {
-				wr.write("initialdir = " + quote(spec.getDirectory()) + "\n");
-			} else {
+			if(grid) {
 				wr.write("remote_initialdir = " + quote(spec.getDirectory()) + "\n");
 			}
+			else if(!nonshared) {
+				wr.write("initialdir = " + quote(spec.getDirectory()) + "\n");
+			}
 		}
-		
-        String basename[] = spec.getExecutable().split("/");		
-        FileChannel from = new FileInputStream(spec.getExecutable()).getChannel();
-        FileChannel to = new FileOutputStream(basename[basename.length-1]).getChannel();
-        to.transferFrom(from, 0, from.size());
-        from.close();
-        to.close();
         
 		spec.getExecutable();
 		wr.write("executable = " + quote(spec.getExecutable()) + "\n");
 		List<String> args = spec.getArgumentsAsList();
+		String wrapper = args.get(0);
+
+		// Use a relative path to the wrapper script
+		if(nonshared && args.size() > 1) {
+			String wrapperSplit[] = args.get(0).split("/");
+			String basename = wrapperSplit[wrapperSplit.length-1];
+			args.set(0, basename);
+		}
+		
 		if (args != null && args.size() > 0) {
 			wr.write("arguments = ");
 			i = args.iterator();
@@ -206,7 +134,14 @@
 		}
  		wr.write('\n');
 
-		// Handle all condor attributes specified by the user
+ 		// Transfer wrapper and remove full path name from executable arguments
+ 		if(nonshared) {
+ 			if(wrapper != null) {
+ 				wr.write("transfer_input_files = " + wrapper + '\n'); 				
+ 			}
+ 		}
+
+ 		// Handle all condor attributes specified by the user
 	    for(String a : spec.getAttributeNames()) {
 	    	if(a != null && a.startsWith("condor.")) {
 	    		String attributeName[] = a.split("condor.");
Index: modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/Properties.java
===================================================================
--- modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/Properties.java	(revision 3529)
+++ modules/provider-localscheduler/src/org/globus/cog/abstraction/impl/scheduler/condor/Properties.java	(working copy)
@@ -8,12 +8,10 @@
  * Created on Oct 20, 2005
  */
 package org.globus.cog.abstraction.impl.scheduler.condor;
-
-import org.apache.log4j.Logger;
 import org.globus.cog.abstraction.impl.scheduler.common.AbstractProperties;
 
 public class Properties extends AbstractProperties {
-	private static Logger logger = Logger.getLogger(Properties.class);
+	private static final long serialVersionUID = 1L;
 
 	public static final String PROPERTIES = "provider-condor.properties";
 	


From wilde at ci.uchicago.edu  Fri Dec 28 18:38:49 2012
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Fri, 28 Dec 2012 18:38:49 -0600 (CST)
Subject: [Swift-commit] r6111 - SwiftApps/SciColSim
Message-ID: <20121229003849.B30159CCF8@svn.ci.uchicago.edu>

Author: wilde
Date: 2012-12-28 18:38:49 -0600 (Fri, 28 Dec 2012)
New Revision: 6111

Added:
   SwiftApps/SciColSim/annealing.osg.swift
Log:
Save OSG-enabled version as a separate file for time being.

Added: SwiftApps/SciColSim/annealing.osg.swift
===================================================================
--- SwiftApps/SciColSim/annealing.osg.swift	                        (rev 0)
+++ SwiftApps/SciColSim/annealing.osg.swift	2012-12-29 00:38:49 UTC (rev 6111)
@@ -0,0 +1,460 @@
+import "math";
+import "colortext";
+
+/*
+ *TODO:
+ */
+
+type file;
+
+type Res
+{
+    float loss;
+    float sdev;
+    float tavg;
+    float tsdev;
+}
+
+global boolean FIX_VARIABLES = true;
+global int var_fixed[] = [0,0,0,0,0];
+global int Nworkers = @toint(@arg("nworkers","4"));
+global int rerunsPerApp= @toint(@arg("rerunsperapp", "100"));
+
+( float nx ) newx( float x, float dx )
+{
+    float r = (random());
+
+    if (r > 0.5)
+    {
+      nx = x + (random())*dx; //Java already returns a float between [0-1]
+    }
+    else
+    {
+        nx = x - (random())*dx;
+    }
+    // tracef("newx(%f,%f)=%f\n",x,dx,nx);
+}
+
+app (file outfile, file loss ) evolve_wget ( string args[], file graph )
+{
+   bash "-c" @strcat("wget http://www.ci.uchicago.edu/~davidk/SciColSim/evolve-wrapper.sh; ",
+                     "chmod +x ./evolve-wrapper.sh; ./evolve-wrapper.sh ", @loss, " ",
+                     args[0], " ", args[1], " ", args[2], " ", args[3], " ", args[4], " ", 
+                     args[5], " ", args[6], " ", args[7], " ", args[8], " ", args[9], " ", 
+                     args[10], " ", args[11], " ", args[12], " ", args[13], " ", args[14],
+                     " ", args[15], " ", args[16], " ", args[17], " ", args[18], " ", 
+                     args[19], " ", args[20], " ", args[21], " ", args[22], " ", args[23])
+   stdout=@outfile;
+}
+
+app (file outfile, file loss ) evolve_wget_short ( string args[], file graph )
+{
+   bash_short "-c" @strcat("wget http://www.ci.uchicago.edu/~davidk/SciColSim/evolve-wrapper.sh; ",
+                     "chmod +x ./evolve-wrapper.sh; ./evolve-wrapper.sh ", @loss, " ",
+                     args[0], " ", args[1], " ", args[2], " ", args[3], " ", args[4], " ", 
+                     args[5], " ", args[6], " ", args[7], " ", args[8], " ", args[9], " ", 
+                     args[10], " ", args[11], " ", args[12], " ", args[13], " ", args[14],
+                     " ", args[15], " ", args[16], " ", args[17], " ", args[18], " ", 
+                     args[19], " ", args[20], " ", args[21], " ", args[22], " ", args[23])
+   stdout=@outfile;
+}
+
+app (file outfile, file loss ) evolve_wget_long ( string args[], file graph )
+{
+   bash_long "-c" @strcat("wget http://www.ci.uchicago.edu/~davidk/SciColSim/evolve-wrapper.sh; ",
+                     "chmod +x ./evolve-wrapper.sh; ./evolve-wrapper.sh ", @loss, " ",
+                     args[0], " ", args[1], " ", args[2], " ", args[3], " ", args[4], " ", 
+                     args[5], " ", args[6], " ", args[7], " ", args[8], " ", args[9], " ", 
+                     args[10], " ", args[11], " ", args[12], " ", args[13], " ", args[14],
+                     " ", args[15], " ", args[16], " ", args[17], " ", args[18], " ", 
+                     args[19], " ", args[20], " ", args[21], " ", args[22], " ", args[23])
+   stdout=@outfile;
+}
+
+app  (file outfile, file loss ) evolve ( string args[], file graph )
+{
+    evolve @loss args stdout=@outfile;  // graph is passed implicitly
+}
+
+app ( file x ) sumloss( file loss[] )
+{
+    sumloss @filenames(loss) stdout=@x;
+}
+
+/*
+
+  Program structure:
+
+  main
+    optimizer_sweep() - formerly, python script
+      multi_annealing()
+        multi_loss()
+         evolve()
+       sumloss()
+*/
+
+( file bestfile, file maxfile ) multi_annealing ( string some_out_filename,
+                                                  float T_start,
+                                                  float T_end,
+                                                  float Target_rejection,
+                                                  int evolve_reruns,
+                                                  float starting_jump,
+                                                  float params0[],
+                                                  float target_innov,
+                                                  int annealing_cycles )
+{
+    int cycle      = 10;     // const
+    int NEVOPARAMS = 5;      // const - 5 params, alpha 1,m through delta, does not include target_innovation
+
+    float rejection[][];  // [i][j] where i is cycle and j is evolve-parameter (alpha_i, alpha_m, beta, gamma, delta)
+    float trejection[][];
+
+    float x[][], dx[][], curr_loss[], curr_sdev[];
+
+    Res mlres[][];
+
+    mlres[0][0] = multi_loss( T_start, T_end, annealing_cycles, Target_rejection, starting_jump, 0, 0, params0, target_innov, evolve_reruns ); // FIXME: serves for all evolve-params ???
+    tracef( "multi_annealing: AR: initial: %f +- %f\n", mlres[0][0].loss, mlres[0][0].sdev );
+
+    foreach j in [0:NEVOPARAMS-1]
+    {
+        x[0][j]         = params0[j];
+        dx[0][j]        = starting_jump;
+        rejection[0][j] = 0.0;
+        curr_loss[j]    = mlres[0][0].loss;
+        curr_sdev[j]    = mlres[0][0].sdev;
+    }
+
+    iterate iter_i   // number of annealing cycles
+    {
+        int i = iter_i + 1;  // i ranges [1:n] in the swift script so that [0] can be the initial condition
+
+        // set new temperature, rejection threshold, and dx values for this cycle
+        float temperature = T_start*exp( @tofloat( i-1 ) * ( jlog( T_end ) - jlog( T_start ) ) / @tofloat( annealing_cycles ) );
+
+        tracef( @strcat( "multi_annealing: AR: i=%i ....T = ", color( 3, "%f" ),"\n" ), i, temperature );
+
+        // On each new "major" cycle within the annealing_cycles (other than the first) set new rejection and dx values
+
+        if ( i %% cycle == 1 && i > 1 )
+        {
+            tracef( "multi_annealing: new cycle at i=%i\n", i );
+            tracef( color( Pink, "multi_annealing: AR: New cycle at %i: prev dx[0-4]=[%f %f %f %f %f]\n" ), i, dx[i-1][0], dx[i-1][1], dx[i-1][2], dx[i-1][3], dx[i-1][4] );
+            foreach k in [0:NEVOPARAMS-1]
+            {
+                float newrejection = rejection[i-1][k] / @tofloat( cycle );
+                if ( newrejection > 0.0 )
+                {
+                    dx[i][k] = dx[i-1][k] / ( newrejection / Target_rejection );
+                    // FIXME: re-enable: rejection[i][k]=0.0;
+                    trejection[i][k]=0.0;
+                }
+                else
+                {
+                    dx[i][k] = dx[i-1][k] * 2.0;
+                    // FIXME: re-enable: rejection[i][k]=rejection[i-1][k];
+                    trejection[i][k]=newrejection;
+                }
+                // FIXME: HANGS? : tracef(color(Red,"Recomputed rejection: i=%d k=%d dx[i][k]=%f\n"), i, k, dx[i][k]);
+            }
+            tracef( color( Blue, "multi_annealing: AR: New cycle at %i: dx[0-4]=[%f %f %f %f %f]\n" ), i, dx[i][0], dx[i][1], dx[i][2], dx[i][3], dx[i][4] );
+        }
+        else  // If not new cycle, set dx[i][*] from previous dx ([i-1]). rejection[i][j] is set later.
+        {
+            foreach k in [0:NEVOPARAMS-1]
+            {
+                dx[i][k] = dx[i-1][k];
+            }
+        }
+
+        iterate j   // Try a new value for each non-fixed param; then write results and accept or reject
+        {
+            int curr = ( i * NEVOPARAMS ) + j;
+            int prev = curr-1;
+
+            if ( /* (!FIX_VARIABLES) || */ ( var_fixed[j] == 0 ) ) {  // Adjustable vars
+                // fixed=1,1,0,0,0: FIXME: FIX_VARIABLES flag has faulty logic but OK when TRUE
+                float try_x[];
+                foreach k in [0:NEVOPARAMS-1] // Select the evolve params to try
+                {
+                    if ( k < j )
+                    {
+                        try_x[k] = x[i][k]; // already set x[i][k]
+                    }
+                    else
+                    {
+                        if ( k == j )
+                        {
+                            try_x[k] = newx(x[i-1][j], dx[i-1][j]); // permute x[i-1][j]
+                        }
+                        else // k > j
+                        {
+                            try_x[k] = x[i-1][k]; // use x[i-1][k] (from prior cycle)
+                        }
+                    }
+                }
+                tracef( @strcat( "multi_annealing: AR: ", color( 10,"%f" ), " ", color( 9,"%i" ),"\n" ), try_x[j], j );
+
+                mlres[i][j] = multi_loss( T_start, T_end, annealing_cycles, Target_rejection, starting_jump, i, j, try_x, target_innov, evolve_reruns ); // do the N evolve()'s, N=evolve_rerusn
+
+                tracef( "multi_annealing: AR: %f +- %f\n", mlres[i][j].loss, mlres[i][j].sdev );
+                // Beyond this point, x[] and dx[] are being set for this i,j
+
+                float ALOT = 100000000000.0; // 100,000,000,000. = 10^11
+
+                if ( mlres[i][j].loss < ALOT )
+                {
+                    fprintf( some_out_filename, "N, %fs, %i, %i, %f, %f, |, %i, %f, [, %f, %f, %f, %f, %f, ], %f\n",
+                             mlres[i][j].tavg, i-1, j, dx[i][j], rejection[i][j], @toint(target_innov), mlres[i][j].loss, try_x[0], try_x[1], try_x[2], try_x[3], try_x[4], mlres[i][j].sdev );  // Note i-1 field: print that way to match with C++ output
+
+                    // fprintf( "max_dist_swift.txt", color( Red,"multi_annealing: AF: max_dist.txt - tbd\n" ) ); // FIXME: max_dist is global set in evolve()
+                }
+                else // does this ever occur? if so did we want to still do the ratio computation above???
+                {
+                    fprintf( some_out_filename, "A, %fs, %i, %i, %f, %f, |, %i, %f, [, %f, %f, %f, %f, %f, ], %f\n",
+                             mlres[i][j].tavg, i-1, j, dx[i][j], rejection[i][j], @toint(target_innov), mlres[i][j].loss, try_x[0], try_x[1], try_x[2], try_x[3], try_x[4], mlres[i][j].sdev );  // Note i-1 field: print that way to match with C++ output
+
+                    //tracef( "multi_annealing: Loss %f > ALOT at [i][j] = [%d][%d]\n", mlres[i][j].loss, i ,j );
+                }
+
+                float ratio = min( 1.0, exp( -( mlres[i][j].loss - curr_loss[prev] ) / temperature ) );
+                float r     = (random()); //Java already returns a random float between [0.0-1.0]
+
+                tracef("multi_annealing: AR: %f vs %f\n", r, ratio);
+
+                if (r > ratio) // Reject new parameter
+                {
+                    x[i][j]         = x[i-1][j];
+                    if ( i %% cycle == 1 && i > 1 )
+                    {
+                      rejection[i][j] = trejection[i][j] + 1.0;    // FIXME: triple-check this!
+                    }
+                    else
+                    {
+                      rejection[i][j] = rejection[i-1][j] + 1.0;  // FIXME: AR: Is this correct? incr rejection?
+                    }
+                    curr_loss[curr] = curr_loss[prev];
+                    curr_sdev[curr] = curr_sdev[prev];
+                    // FIXME: AR: the following prints seem to replicate values in the .cpp version - please clarify.
+                    tracef( "multi_annealing: AR: %i,%i %i Did not accept: %f (%i)\n", i, j, i, try_x[j], j );
+                    tracef( "multi_annealing: AR: %f %f %f %f %f\n", try_x[0],try_x[1],try_x[2],try_x[3],try_x[4] );
+                }
+                else // Accept new parameter
+                {
+                    tracef( "multi_annealing: Accepting try_x[j], i=%i j=%i\n",i,j );
+
+                    x[i][j]         = try_x[j];
+                    if ( i %% cycle == 1 && i > 1 )
+                    {
+                      rejection[i][j] = trejection[i][j];    // FIXME: triple-check this!
+                    }
+                    else
+                    {
+                      rejection[i][j] = rejection[i-1][j];  // FIXME: AR: Is this correct? no incr of rejection?
+                    }
+                    curr_loss[curr] = mlres[i][j].loss;
+                    curr_sdev[curr] = mlres[i][j].sdev;
+
+                    tracef( "multi_annealing: Accepting try_x[j], i=%i j=%i try_x[j]=%f\n", i, j, try_x[j] );
+                    float rj[];
+                    foreach k in [0:NEVOPARAMS-1]
+                    {
+                        if (k <= j)
+                        {
+                            rj[k] = rejection[i][k]; // Was either set from previous j or just set for this j
+                        }
+                        else
+                        {
+                            rj[k] = rejection[i-1][k]; // Not yet set, use previous
+                        }
+                    }
+                    tracef(@strcat("multi_annealing: AR: [%i][%i] ", color(8,"Rejection counts: "),
+                                   color(1,"%f"), " ", color(7,"%f"), " ", color(5,"%f"), " ", color(9,"%f"), " ", color(6,"%f"), "\n\n"),
+                           i, j, rj[0], rj[1], rj[2], rj[3], rj[4]);
+                    tracef(@strcat("multi_annealing: AR: %i ", color(8,"***** Did accept! "),
+                                   color(1,"%f"), " ", color(7,"%f"), " ", color(5,"%f"), " ", color(9,"%f"), " ", color(6,"%f"), "\n\n"),
+                           i, try_x[0], try_x[1], try_x[2], try_x[3], try_x[4]);
+                }
+            }
+            else // Fixed Vars
+            {
+                x[i][j]         = x[i-1][j];
+                rejection[i][j] = rejection[i-1][j];
+                curr_loss[curr] = curr_loss[prev];
+                curr_sdev[curr] = curr_sdev[prev];
+                // dx[i][j] not set for fixed vars
+            }
+        } until( j == (NEVOPARAMS-1) );
+    } until( iter_i == (annealing_cycles-1) );
+}
+
+(Res r) multi_loss( float t_start, float t_end, int annealing_steps, float t_rejection, float starting_jump, int ci, int cj, float x[], float target_innov, int evolve_reruns )
+{
+    tracef("%q\n", x);
+    file rfile[];
+    file ofile[]; // FIXME: to obtain timings and otehr stats
+
+    tracef( "multi_loss: entered: ci=%i cj=%i target_innov=%f evolve_reruns=%i x=%q\n",ci, cj, target_innov,evolve_reruns,x );
+
+    int appCalls = @toint(@tofloat(evolve_reruns) / @tofloat(rerunsPerApp));  // FIXME: handle fractional issues and rounding etc. For now must divide evenly
+
+    tracef("multi_loss appCalls=%i\n", appCalls);
+
+    foreach i in [1:appCalls]
+    {  // repeats of the evolove() - same as n_reruns
+        file outfile; // FIXME: map and save in future
+        string args[] = [ // FIXME: move this to a setargs() function
+            //    alpha_i           alpha_m        beta           gamma          delta          target_innov
+                 @strcat(x[0]),  @strcat(x[1]), @strcat(x[2]), @strcat(x[3]), @strcat(x[4]), @strcat(target_innov),
+
+            //     n_epochs n_steps   evolve_reruns           range
+            //    "40000",   "20",  @strcat(evolve_reruns),    "2",
+                  "40000",   "20",  @strcat(rerunsPerApp),     "2",
+
+            //    verbose_level
+                    "1",
+
+            //    T_start             T_end          Annealing_steps         Target_rejection         Starting_jump
+                 @strcat(t_start), @strcat(t_end), @strcat(annealing_steps), @strcat(t_rejection), @strcat(starting_jump),
+
+            //    FREEZE: alpha_i alpha_m beta gamma delta
+                            "0",    "0",  "0",  "0",  "0",
+
+            //   operation-code:(m,a)    Nworkers           seed
+                      "m",            @strcat(Nworkers), @arg("seed", "0" ) ];
+
+        file graph <"movie_graph.txt">;
+
+        if(@arg("wget") == "true") {
+
+           // Separate long runs from short runs when longruns option is set
+           if(@arg("longruns") == "true") {
+              float mean = @tofloat(@arg("minrange")) + @tofloat(@arg("maxrange")) / 2.0;
+              if(target_innov <= mean) {
+                 ( outfile, rfile[i] ) = evolve_wget_short( args, graph );
+              } 
+              else {
+                 ( outfile, rfile[i] ) = evolve_wget_long( args, graph );
+              }
+           }
+
+          ( outfile, rfile[i] ) = evolve_wget( args, graph );
+        }
+         
+        else {
+           ( outfile, rfile[i] ) = evolve( args, graph );
+        }
+
+        tracef("multi_loss: i=%i calling evolve, args=%q\n", i, args);
+        // tracef("multi_loss: after evolve: i=%i %k %k\n", i, outfile, rfile[i]);
+    }
+    file sumfile = sumloss(rfile);
+    r            = readData(sumfile);
+
+    tracef("multi_loss: returning: ci=%i cj=%i r.loss=%f r.sdev=%f\n",ci,cj,r.loss,r.sdev);
+    // file statfile = sumstats(ofile);  FIXME: to obtain timings and otehr stats
+    // s = readStat(statsfile);          FIXME: to obtain timings and otehr stats
+}
+
+optimizer_sweep() // Implements logic of python driver script
+{
+
+    int minrange = @toint(@arg("minrange", "58"));
+    int maxrange = @toint(@arg("maxrange", "59"));
+    int rangeinc = @toint(@arg("rangeinc", "50"));
+
+    // FIXME: add provision for random priming and random param values when x[i] == -100 (see optimizer.cpp main())
+
+    int nreps = @toint(@arg("nreps", "1"));
+
+//    file bestfile <single_file_mapper; file=@strcat("output/T",target,".R",rep,".best_opt_some")>;
+//    file maxfile <single_file_mapper; file=@strcat("output/T",target,".R",rep,".max_dist")>;
+
+    foreach target_innov in [minrange:maxrange:rangeinc]
+    {
+        foreach rep in [1:nreps]
+        {
+            string some_out_filename = @strcat( "best.T", @strcat(target_innov), ".R", @strcat(rep), ".txt" );
+            file outfile;  // <single_file_mapper; file=@strcat("output/T",target_innov,".R",rep,".out")>;
+            file lossfile; // <single_file_mapper; file=@strcat("output/T",target_innov,".R",rep,".loss_data")>;
+
+            ( outfile,lossfile ) = multi_annealing(
+                                                    some_out_filename,
+						                            @tofloat(@arg("tstart", "2.0")),
+                                                    @tofloat(@arg("tend", "0.01")),
+                                                    @tofloat(@arg("trejection", "0.3")),
+                                                    @toint(@arg("evoreruns", "100")),
+                                                    @tofloat(@arg("startingjump", "2.3")),
+                                                    [@tofloat(@arg("alphai", "0.0")), @tofloat(@arg("alpham", "0.0")), @tofloat(@arg("beta", "4.0")), @tofloat(@arg("gamma", "50.0")), @tofloat(@arg("delta", "-1.0"))],
+                                                    @tofloat(target_innov),
+                                                    @toint(@arg("annealingcycles", "50")) );
+        }
+    }
+}
+
+main()
+{
+    optimizer_sweep();
+}
+
+main();
+
+/*
+
+  Program structure:
+
+  main
+  optimizer_sweep()
+  multi_annealing()
+  multi_loss()
+  evolve()
+  sumloss()
+
+  Example parameter sets:
+
+  for target in range(58,59,50):
+  for i in range(1):
+  args="./toptimizer 0 0 4 50 -1 "+target+" 40000 20 75    2 1 2. 0.01 2 0.3 2.3 1 1 1 0 0 m // > out.T"+str(target)+".i"+str(i)
+  os.system(args);
+
+  string fastargs1[] = [
+  "0", "0", "4", "50", "-1", @strcat(target),
+  "40000", "20", "1000", "2",
+  "1",
+  "2.", "0.01", "100", "0.3", "2.3",
+  "1", "1", "0", "0", "0"];
+  string fastargs2[] = [
+  "0", "0", "4", "50", "-1", @strcat(target),
+  "40000", "20", "1000", "2",
+  "1",
+  "2.", "0.01",  "5", "0.3", "2.3",
+  "1", "1", "0", "0", "0", "m"];
+  string fastargs3[] = [
+  "0", "0", "4", "50", "-1", @strcat(target),
+  "40000", "20", @strcat(repeats), "2",
+  "1",
+  "2.", "0.01",  "2", "0.3", "2.3",
+  "1", "1", "0", "0", "0", "m"];
+*/
+
+(string args[]) setargs()
+{
+    // string longargs[] = @strcat("0 0 4 50 -1 ",target," 40000 20 1000 2 1 2. 0.01 100 0.3 2.3 1 1 0 0 0 m");
+
+    //  [alpha_i alpha_m beta gamma delta target_innov
+    //  [n_epochs n_steps n_reruns] [range]
+    //  [verbose_level]
+    //  [T_start T_end Annealing_steps Target_rejection Starting_jump]
+    //  [FREEZE_alpha_i FREEZE_alpha_m FREEZE_beta FREEZE_gamma FREEZE_delta] [operation-code:(m,a) Nworkers]
+}
+
+////////////////// HOLD JUNK
+
+//                    tracef(@strcat("multi_annealing: AR: %i ", color(8,"Rejection counts: "),
+//                                   color( /* 2 */ 1," %f"), "\n\n"),
+//                                   i, rejection[i][j] ); // , rejection[i][1], rejection[i][2], rejection[i][3], rejection[i][4]);
+// FIXME: determine correct rejection[] values to avoid hanging:
+//                    tracef(@strcat("multi_annealing: AR: %i ", color(8,"Rejection counts: "),
+//                                   color( /* 2 */ 1," %f"), color(7," %f"), color(5," %f"), color(9," %f"), color(6," %f"), "\n\n"),
+//                                   rejection[i][0], rejection[i][1], rejection[i][2], rejection[i][3], rejection[i][4]);
+// END FIXME



From wilde at ci.uchicago.edu  Sun Dec 30 13:53:22 2012
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 30 Dec 2012 13:53:22 -0600 (CST)
Subject: [Swift-commit] r6112 - in SwiftApps/SciColSim: . conf
Message-ID: <20121230195323.0141C9CCC0@svn.ci.uchicago.edu>

Author: wilde
Date: 2012-12-30 13:53:21 -0600 (Sun, 30 Dec 2012)
New Revision: 6112

Added:
   SwiftApps/SciColSim/evolve-wrapper.sh
Modified:
   SwiftApps/SciColSim/Makefile
   SwiftApps/SciColSim/README
   SwiftApps/SciColSim/TODO
   SwiftApps/SciColSim/annealing.swift
   SwiftApps/SciColSim/conf/local.cf
   SwiftApps/SciColSim/conf/local.xml
   SwiftApps/SciColSim/gengraphs.sh
   SwiftApps/SciColSim/optimizer.cpp
   SwiftApps/SciColSim/sumloss.sh
   SwiftApps/SciColSim/swiftopt.sh
   SwiftApps/SciColSim/testopt.py
Log:
Add dynamic loss-limits and fix std-dev code in optimizer.cpp. Revert swift script to pre-osg version; retain separate osg version. Adjust combine scripts for floating point errors in combining multiple graph-sim (optimizer.cpp) runs.

Modified: SwiftApps/SciColSim/Makefile
===================================================================
--- SwiftApps/SciColSim/Makefile	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/Makefile	2012-12-30 19:53:21 UTC (rev 6112)
@@ -6,6 +6,7 @@
 
 openmp-optimizer: optimizer.cpp
 	g++ -DP_OPENMP -static -O -fopenmp -I boost_1_47_0 -o openmp-optimizer optimizer.cpp
+#	g++ -static -O -I boost_1_47_0 -o openmp-optimizer optimizer.cpp
 
 #t: t.cpp
 #	g++ -DP_OPENMP -static -O -fopenmp -I boost_1_47_0 -o t t.cpp

Modified: SwiftApps/SciColSim/README
===================================================================
--- SwiftApps/SciColSim/README	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/README	2012-12-30 19:53:21 UTC (rev 6112)
@@ -246,7 +246,7 @@
 	-trejection=<float>
 
 	-evoreruns=<int>
-	   How many times to re-run the evolve.sh app
+	   How many times to re-run the evolve.sh app  // MW: # times to rerun evolve() not evolve.sh ???
 
 	-startingjump=<float>
 	    Controls the dx and/or rejection variable
@@ -314,7 +314,7 @@
 #        1 multi_loss to initialize
 # c)     100 Annealing_cycles (serial)
 # d)        5 repeats (1 per param, serial) of multi_loss:
-# e)          1000 to 10000 annealing_repeats (parallel) == multi_loss
+# e)          1000 to 10000 annealing_repeats (parallel) == multi_loss  
 # f)            evolve()
 
 Plots

Modified: SwiftApps/SciColSim/TODO
===================================================================
--- SwiftApps/SciColSim/TODO	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/TODO	2012-12-30 19:53:21 UTC (rev 6112)
@@ -1,11 +1,12 @@
 
+
 --- Questions and Open Issues ---
 
 When sampling the graph, we compress the node ids. Is this OK?
 
 Same 40K epoch count?  Is this really feasible?
 
-What values for otehr loop parameters?
+What values for other loop parameters?
 
 What sampling?
 
@@ -21,13 +22,53 @@
 
 Graph partitioning? => for greater total parallelism?
 
+*** NEW 12/25/2012:
 
+Code does 1 multi_loss to initialize : what if this returns "ALOT" ?
 
+Should one "alot" among the 1,000 to 10,000 reruns cause the whole batch to be ignored? (because just one causes the entire average to be greater than any possible minimum).
+
+
+
 x = done, - = in progress
 
-
 --- Top Prios ---
 
+For Andrey's Dec 2012 campaign:
+
+[ ]  generate test graph set
+[ ]  make graph file an optimizer parameter
+[ ]  check state of random number gens for both reprodicbility and diversity
+[ ]  count number of max_loss exceeded cases for sanity check
+[ ]  add timer to max_loss exit criter; track seeds that cause max_loss timer or value exceeding for repro testing.
+[ ]  constrain NUniverses to just those needed for the multiple threaded reruns
+[ ]  add a time check to ensure the dynamic limiter is kicking in to limit time
+[ ]  adjust rerunsPerApp to a dynamic value based on a scaling test
+[ ]  run good scaling tests to see if limiter is working
+[ ]  run actual annealing runs
+[ ]  improve output to validate the annealings and graphsims
+[ ]  do bug runs
+[ ]  get theresources for above: Beagle, Cloud, etc
+
+
+--- Older notes from graph studies with David:
+
+
+- Runtime, ram, science results (single floating pointer number called loss) for each param
+- Params = nodes, edges, and ti
+- As edges/nodes increase, time increases
+- 1000 osg jobs between 10 seconds and 24 hours
+- Example: iterate over ti in units of 100, graph sizes should be 
+- Automate, return eof when timed out, set max run time
+- Ability to see gprof output
+- Once with control structure he needs, then one run with large size to show hockey stick
+- Generate a table, then generate a graph
+- Email uc3 and midway account information
+
+
+
+From Jon's work:
+
 [x] Get code in shape for Andrey to do a comparison run between fast .py and .swift runs on his Mac.
 
 [-] Get initial tests run on Beagle at scale

Modified: SwiftApps/SciColSim/annealing.swift
===================================================================
--- SwiftApps/SciColSim/annealing.swift	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/annealing.swift	2012-12-30 19:53:21 UTC (rev 6112)
@@ -35,42 +35,6 @@
     // tracef("newx(%f,%f)=%f\n",x,dx,nx);
 }
 
-app (file outfile, file loss ) evolve_wget ( string args[], file graph )
-{
-   bash "-c" @strcat("wget http://www.ci.uchicago.edu/~davidk/SciColSim/evolve-wrapper.sh; ",
-                     "chmod +x ./evolve-wrapper.sh; ./evolve-wrapper.sh ", @loss, " ",
-                     args[0], " ", args[1], " ", args[2], " ", args[3], " ", args[4], " ", 
-                     args[5], " ", args[6], " ", args[7], " ", args[8], " ", args[9], " ", 
-                     args[10], " ", args[11], " ", args[12], " ", args[13], " ", args[14],
-                     " ", args[15], " ", args[16], " ", args[17], " ", args[18], " ", 
-                     args[19], " ", args[20], " ", args[21], " ", args[22], " ", args[23])
-   stdout=@outfile;
-}
-
-app (file outfile, file loss ) evolve_wget_short ( string args[], file graph )
-{
-   bash_short "-c" @strcat("wget http://www.ci.uchicago.edu/~davidk/SciColSim/evolve-wrapper.sh; ",
-                     "chmod +x ./evolve-wrapper.sh; ./evolve-wrapper.sh ", @loss, " ",
-                     args[0], " ", args[1], " ", args[2], " ", args[3], " ", args[4], " ", 
-                     args[5], " ", args[6], " ", args[7], " ", args[8], " ", args[9], " ", 
-                     args[10], " ", args[11], " ", args[12], " ", args[13], " ", args[14],
-                     " ", args[15], " ", args[16], " ", args[17], " ", args[18], " ", 
-                     args[19], " ", args[20], " ", args[21], " ", args[22], " ", args[23])
-   stdout=@outfile;
-}
-
-app (file outfile, file loss ) evolve_wget_long ( string args[], file graph )
-{
-   bash_long "-c" @strcat("wget http://www.ci.uchicago.edu/~davidk/SciColSim/evolve-wrapper.sh; ",
-                     "chmod +x ./evolve-wrapper.sh; ./evolve-wrapper.sh ", @loss, " ",
-                     args[0], " ", args[1], " ", args[2], " ", args[3], " ", args[4], " ", 
-                     args[5], " ", args[6], " ", args[7], " ", args[8], " ", args[9], " ", 
-                     args[10], " ", args[11], " ", args[12], " ", args[13], " ", args[14],
-                     " ", args[15], " ", args[16], " ", args[17], " ", args[18], " ", 
-                     args[19], " ", args[20], " ", args[21], " ", args[22], " ", args[23])
-   stdout=@outfile;
-}
-
 app  (file outfile, file loss ) evolve ( string args[], file graph )
 {
     evolve @loss args stdout=@outfile;  // graph is passed implicitly
@@ -86,315 +50,266 @@
   Program structure:
 
   main
-  optimizer_sweep() - formerly, python script
-  multi_annealing()
-  multi_loss()
-  evolve()
-  sumloss()
+    optimizer_sweep() - formerly, python script
+      multi_annealing()
+        multi_loss()
+         evolve()
+       sumloss()
 */
 
-( file bestfile, file maxfile ) multi_annealing ( string some_out_filename,
-                                                  float T_start,
-                                                  float T_end,
-                                                  float Target_rejection,
-                                                  int evolve_reruns,
-                                                  float starting_jump,
-                                                  float params0[],
-                                                  float target_innov,
-                                                  int annealing_cycles )
+(file bestfile, file maxfile) multi_annealing (string some_out_filename,
+                                               float T_start,
+                                               float T_end,
+                                               float Target_rejection,
+                                               int evolve_reruns,
+                                               float starting_jump,
+                                               float params0[],
+                                               float target_innov,
+                                               int annealing_cycles)
 {
-    int cycle      = 10;     // const
-    int NEVOPARAMS = 5;      // const - 5 params, alpha 1,m through delta, does not include target_innovation
+  int cycle      = 10;     // const
+  int NEVOPARAMS = 5;      // const - 5 params, alpha 1,m through delta, does not include target_innovation
 
-    float rejection[][];  // [i][j] where i is cycle and j is evolve-parameter (alpha_i, alpha_m, beta, gamma, delta)
-    float trejection[][];
+  float rejection[][];  // [i][j] where i is cycle and j is evolve-parameter (alpha_i, alpha_m, beta, gamma, delta)
+  float trejection[][];
 
-    float x[][], dx[][], curr_loss[], curr_sdev[];
+  float x[][], dx[][], curr_loss[], curr_sdev[];
 
-    Res mlres[][];
+  Res mlres[][];
 
-    mlres[0][0] = multi_loss( T_start, T_end, annealing_cycles, Target_rejection, starting_jump, 0, 0, params0, target_innov, evolve_reruns ); // FIXME: serves for all evolve-params ???
-    tracef( "multi_annealing: AR: initial: %f +- %f\n", mlres[0][0].loss, mlres[0][0].sdev );
+  mlres[0][0] = multi_loss(T_start, T_end, annealing_cycles, Target_rejection,
+                          starting_jump, 0, 0, params0, target_innov, evolve_reruns ); // FIXME: serves for all evolve-params ???
+  tracef( "multi_annealing: AR: initial: %f +- %f\n", mlres[0][0].loss, mlres[0][0].sdev );
 
-    foreach j in [0:NEVOPARAMS-1]
-    {
-        x[0][j]         = params0[j];
-        dx[0][j]        = starting_jump;
-        rejection[0][j] = 0.0;
-        curr_loss[j]    = mlres[0][0].loss;
-        curr_sdev[j]    = mlres[0][0].sdev;
-    }
+  foreach j in [0:NEVOPARAMS-1] {
+    x[0][j]         = params0[j];
+    dx[0][j]        = starting_jump;
+    rejection[0][j] = 0.0;
+    curr_loss[j]    = mlres[0][0].loss;
+    curr_sdev[j]    = mlres[0][0].sdev;
+  }
 
-    iterate iter_i   // number of annealing cycles
-    {
-        int i = iter_i + 1;  // i ranges [1:n] in the swift script so that [0] can be the initial condition
+  iterate iter_i {  // number of annealing cycles
+    int i = iter_i + 1;  // i ranges [1:n] in the swift script so that [0] can be the initial condition
 
-        // set new temperature, rejection threshold, and dx values for this cycle
-        float temperature = T_start*exp( @tofloat( i-1 ) * ( jlog( T_end ) - jlog( T_start ) ) / @tofloat( annealing_cycles ) );
+    // set new temperature, rejection threshold, and dx values for this cycle
+    float temperature = T_start*exp( @tofloat( i-1 ) * ( jlog( T_end ) - jlog( T_start ) ) / @tofloat( annealing_cycles ) );
 
-        tracef( @strcat( "multi_annealing: AR: i=%i ....T = ", color( 3, "%f" ),"\n" ), i, temperature );
+    tracef( @strcat( "multi_annealing: AR: i=%i ....T = ", color( 3, "%f" ),"\n" ), i, temperature );
 
-        // On each new "major" cycle within the annealing_cycles (other than the first) set new rejection and dx values
+    // On each new "major" cycle within the annealing_cycles (other than the first) set new rejection and dx values
 
-        if ( i %% cycle == 1 && i > 1 )
-        {
-            tracef( "multi_annealing: new cycle at i=%i\n", i );
-            tracef( color( Pink, "multi_annealing: AR: New cycle at %i: prev dx[0-4]=[%f %f %f %f %f]\n" ), i, dx[i-1][0], dx[i-1][1], dx[i-1][2], dx[i-1][3], dx[i-1][4] );
-            foreach k in [0:NEVOPARAMS-1]
-            {
-                float newrejection = rejection[i-1][k] / @tofloat( cycle );
-                if ( newrejection > 0.0 )
-                {
-                    dx[i][k] = dx[i-1][k] / ( newrejection / Target_rejection );
-                    // FIXME: re-enable: rejection[i][k]=0.0;
-                    trejection[i][k]=0.0;
-                }
-                else
-                {
-                    dx[i][k] = dx[i-1][k] * 2.0;
-                    // FIXME: re-enable: rejection[i][k]=rejection[i-1][k];
+    if (i %% cycle == 1 && i > 1) {
+      tracef( "multi_annealing: new cycle at i=%i\n", i );
+      tracef( color( Pink, "multi_annealing: AR: New cycle at %i: prev dx[0-4]=[%f %f %f %f %f]\n" ),
+                     i, dx[i-1][0], dx[i-1][1], dx[i-1][2], dx[i-1][3], dx[i-1][4] );
+      foreach k in [0:NEVOPARAMS-1] {
+        float newrejection = rejection[i-1][k] / @tofloat( cycle );
+        if (newrejection > 0.0) {
+          dx[i][k] = dx[i-1][k] / ( newrejection / Target_rejection );
+          // FIXME: re-enable: rejection[i][k]=0.0;
+          trejection[i][k]=0.0;
+        }
+        else {
+          dx[i][k] = dx[i-1][k] * 2.0;
+          // FIXME: re-enable: rejection[i][k]=rejection[i-1][k];
                     trejection[i][k]=newrejection;
-                }
+        }
                 // FIXME: HANGS? : tracef(color(Red,"Recomputed rejection: i=%d k=%d dx[i][k]=%f\n"), i, k, dx[i][k]);
+      }
+      tracef( color( Blue, "multi_annealing: AR: New cycle at %i: dx[0-4]=[%f %f %f %f %f]\n" ),
+                             i, dx[i][0], dx[i][1], dx[i][2], dx[i][3], dx[i][4] );
+    }
+    else { // If not new cycle, set dx[i][*] from previous dx ([i-1]). rejection[i][j] is set later.
+      foreach k in [0:NEVOPARAMS-1] {
+        dx[i][k] = dx[i-1][k];
+      }
+    }
+    iterate j {  // Try a new value for each non-fixed param; then write results and accept or reject
+      int curr = ( i * NEVOPARAMS ) + j;
+      int prev = curr-1;
+
+      if ( /* (!FIX_VARIABLES) || */ ( var_fixed[j] == 0 ) ) {  // Adjustable vars
+           // fixed=1,1,0,0,0: FIXME: FIX_VARIABLES flag has faulty logic but OK when TRUE
+        float try_x[];
+        foreach k in [0:NEVOPARAMS-1] { // Select the evolve params to try
+          if (k < j) {
+            try_x[k] = x[i][k]; // already set x[i][k]
+          }
+          else {
+            if (k == j) {
+              try_x[k] = newx(x[i-1][j], dx[i-1][j]); // permute x[i-1][j]
             }
-            tracef( color( Blue, "multi_annealing: AR: New cycle at %i: dx[0-4]=[%f %f %f %f %f]\n" ), i, dx[i][0], dx[i][1], dx[i][2], dx[i][3], dx[i][4] );
-        }
-        else  // If not new cycle, set dx[i][*] from previous dx ([i-1]). rejection[i][j] is set later.
-        {
-            foreach k in [0:NEVOPARAMS-1]
-            {
-                dx[i][k] = dx[i-1][k];
+            else { // k > j
+              try_x[k] = x[i-1][k]; // use x[i-1][k] (from prior cycle)
             }
+          }
         }
+        tracef( @strcat( "multi_annealing: AR: ", color( 10,"%f" ), " ", color( 9,"%i" ),"\n" ), try_x[j], j );
+        mlres[i][j] = multi_loss( T_start, T_end, annealing_cycles, Target_rejection, starting_jump,
+                                  i, j, try_x, target_innov, evolve_reruns ); // do the N evolve()'s, N=evolve_rerusn
+        tracef( "multi_annealing: AR: %f +- %f\n", mlres[i][j].loss, mlres[i][j].sdev );
+        // Beyond this point, x[] and dx[] are being set for this i,j
+        float ALOT = 100000000000.0; // 100,000,000,000. = 10^11
+        if (mlres[i][j].loss < ALOT) {
+          fprintf( some_out_filename, "N, %fs, %i, %i, %f, %f, |, %i, %f, [, %f, %f, %f, %f, %f, ], %f\n",
+                  mlres[i][j].tavg, i-1, j, dx[i][j], rejection[i][j], @toint(target_innov), mlres[i][j].loss,
+                  try_x[0], try_x[1], try_x[2], try_x[3], try_x[4], mlres[i][j].sdev );
+                  // Note i-1 field: print that way to match with C++ output
 
-        iterate j   // Try a new value for each non-fixed param; then write results and accept or reject
-        {
-            int curr = ( i * NEVOPARAMS ) + j;
-            int prev = curr-1;
-
-            if ( /* (!FIX_VARIABLES) || */ ( var_fixed[j] == 0 ) ) {  // Adjustable vars
-                // fixed=1,1,0,0,0: FIXME: FIX_VARIABLES flag has faulty logic but OK when TRUE
-                float try_x[];
-                foreach k in [0:NEVOPARAMS-1] // Select the evolve params to try
-                {
-                    if ( k < j )
-                    {
-                        try_x[k] = x[i][k]; // already set x[i][k]
-                    }
-                    else
-                    {
-                        if ( k == j )
-                        {
-                            try_x[k] = newx(x[i-1][j], dx[i-1][j]); // permute x[i-1][j]
-                        }
-                        else // k > j
-                        {
-                            try_x[k] = x[i-1][k]; // use x[i-1][k] (from prior cycle)
-                        }
-                    }
-                }
-                tracef( @strcat( "multi_annealing: AR: ", color( 10,"%f" ), " ", color( 9,"%i" ),"\n" ), try_x[j], j );
-
-                mlres[i][j] = multi_loss( T_start, T_end, annealing_cycles, Target_rejection, starting_jump, i, j, try_x, target_innov, evolve_reruns ); // do the N evolve()'s, N=evolve_rerusn
-
-                tracef( "multi_annealing: AR: %f +- %f\n", mlres[i][j].loss, mlres[i][j].sdev );
-                // Beyond this point, x[] and dx[] are being set for this i,j
-
-                float ALOT = 100000000000.0; // 100,000,000,000. = 10^11
-
-                if ( mlres[i][j].loss < ALOT )
-                {
-                    fprintf( some_out_filename, "N, %fs, %i, %i, %f, %f, |, %i, %f, [, %f, %f, %f, %f, %f, ], %f\n",
-                             mlres[i][j].tavg, i-1, j, dx[i][j], rejection[i][j], @toint(target_innov), mlres[i][j].loss, try_x[0], try_x[1], try_x[2], try_x[3], try_x[4], mlres[i][j].sdev );  // Note i-1 field: print that way to match with C++ output
-
-                    // fprintf( "max_dist_swift.txt", color( Red,"multi_annealing: AF: max_dist.txt - tbd\n" ) ); // FIXME: max_dist is global set in evolve()
-                }
-                else // does this ever occur? if so did we want to still do the ratio computation above???
-                {
-                    fprintf( some_out_filename, "A, %fs, %i, %i, %f, %f, |, %i, %f, [, %f, %f, %f, %f, %f, ], %f\n",
-                             mlres[i][j].tavg, i-1, j, dx[i][j], rejection[i][j], @toint(target_innov), mlres[i][j].loss, try_x[0], try_x[1], try_x[2], try_x[3], try_x[4], mlres[i][j].sdev );  // Note i-1 field: print that way to match with C++ output
-
-                    //tracef( "multi_annealing: Loss %f > ALOT at [i][j] = [%d][%d]\n", mlres[i][j].loss, i ,j );
-                }
-
-                float ratio = min( 1.0, exp( -( mlres[i][j].loss - curr_loss[prev] ) / temperature ) );
-                float r     = (random()); //Java already returns a random float between [0.0-1.0]
-
-                tracef("multi_annealing: AR: %f vs %f\n", r, ratio);
-
-                if (r > ratio) // Reject new parameter
-                {
-                    x[i][j]         = x[i-1][j];
-                    if ( i %% cycle == 1 && i > 1 )
-                    {
-                      rejection[i][j] = trejection[i][j] + 1.0;    // FIXME: triple-check this!
-                    }
-                    else
-                    {
-                      rejection[i][j] = rejection[i-1][j] + 1.0;  // FIXME: AR: Is this correct? incr rejection?
-                    }
-                    curr_loss[curr] = curr_loss[prev];
-                    curr_sdev[curr] = curr_sdev[prev];
-                    // FIXME: AR: the following prints seem to replicate values in the .cpp version - please clarify.
-                    tracef( "multi_annealing: AR: %i,%i %i Did not accept: %f (%i)\n", i, j, i, try_x[j], j );
-                    tracef( "multi_annealing: AR: %f %f %f %f %f\n", try_x[0],try_x[1],try_x[2],try_x[3],try_x[4] );
-                }
-                else // Accept new parameter
-                {
-                    tracef( "multi_annealing: Accepting try_x[j], i=%i j=%i\n",i,j );
-
-                    x[i][j]         = try_x[j];
-                    if ( i %% cycle == 1 && i > 1 )
-                    {
-                      rejection[i][j] = trejection[i][j];    // FIXME: triple-check this!
-                    }
-                    else
-                    {
-                      rejection[i][j] = rejection[i-1][j];  // FIXME: AR: Is this correct? no incr of rejection?
-                    }
-                    curr_loss[curr] = mlres[i][j].loss;
-                    curr_sdev[curr] = mlres[i][j].sdev;
-
-                    tracef( "multi_annealing: Accepting try_x[j], i=%i j=%i try_x[j]=%f\n", i, j, try_x[j] );
-                    float rj[];
-                    foreach k in [0:NEVOPARAMS-1]
-                    {
-                        if (k <= j)
-                        {
-                            rj[k] = rejection[i][k]; // Was either set from previous j or just set for this j
-                        }
-                        else
-                        {
-                            rj[k] = rejection[i-1][k]; // Not yet set, use previous
-                        }
-                    }
-                    tracef(@strcat("multi_annealing: AR: [%i][%i] ", color(8,"Rejection counts: "),
-                                   color(1,"%f"), " ", color(7,"%f"), " ", color(5,"%f"), " ", color(9,"%f"), " ", color(6,"%f"), "\n\n"),
-                           i, j, rj[0], rj[1], rj[2], rj[3], rj[4]);
-                    tracef(@strcat("multi_annealing: AR: %i ", color(8,"***** Did accept! "),
-                                   color(1,"%f"), " ", color(7,"%f"), " ", color(5,"%f"), " ", color(9,"%f"), " ", color(6,"%f"), "\n\n"),
-                           i, try_x[0], try_x[1], try_x[2], try_x[3], try_x[4]);
-                }
+                  // fprintf( "max_dist_swift.txt", color( Red,"multi_annealing: AF: max_dist.txt - tbd\n" ) );
+                  // FIXME: max_dist is global set in evolve()
+        }
+        else { // does this ever occur? if so did we want to still do the ratio computation above???
+          fprintf( some_out_filename, "A, %fs, %i, %i, %f, %f, |, %i, %f, [, %f, %f, %f, %f, %f, ], %f\n",
+                   mlres[i][j].tavg, i-1, j, dx[i][j], rejection[i][j], @toint(target_innov), mlres[i][j].loss,
+                   try_x[0], try_x[1], try_x[2], try_x[3], try_x[4], mlres[i][j].sdev );
+                   // Note i-1 field: print that way to match with C++ output
+          //tracef( "multi_annealing: Loss %f > ALOT at [i][j] = [%d][%d]\n", mlres[i][j].loss, i ,j );
+        }
+        float ratio = min( 1.0, exp( -( mlres[i][j].loss - curr_loss[prev] ) / temperature ) );
+        float r = (random()); //Java already returns a random float between [0.0-1.0]
+        tracef("multi_annealing: AR: %f vs %f\n", r, ratio);
+        if (r > ratio) { // Reject new parameter
+          x[i][j] = x[i-1][j];
+          if (i %% cycle == 1 && i > 1) {
+            rejection[i][j] = trejection[i][j] + 1.0;    // FIXME: triple-check this!
+          }
+          else {
+            rejection[i][j] = rejection[i-1][j] + 1.0;  // FIXME: AR: Is this correct? incr rejection?
+          }
+          curr_loss[curr] = curr_loss[prev];
+          curr_sdev[curr] = curr_sdev[prev];
+          // FIXME: AR: the following prints seem to replicate values in the .cpp version - please clarify.
+          tracef( "multi_annealing: AR: %i,%i %i Did not accept: %f (%i)\n", i, j, i, try_x[j], j );
+          tracef( "multi_annealing: AR: %f %f %f %f %f\n", try_x[0],try_x[1],try_x[2],try_x[3],try_x[4] );
+        }
+        else { // Accept new parameter
+          tracef( "multi_annealing: Accepting try_x[j], i=%i j=%i\n",i,j );
+          x[i][j] = try_x[j];
+          if (i %% cycle == 1 && i > 1) {
+            rejection[i][j] = trejection[i][j];    // FIXME: triple-check this!
+          }
+          else {
+            rejection[i][j] = rejection[i-1][j];  // FIXME: AR: Is this correct? no incr of rejection?
+          }
+          curr_loss[curr] = mlres[i][j].loss;
+          curr_sdev[curr] = mlres[i][j].sdev;
+          tracef( "multi_annealing: Accepting try_x[j], i=%i j=%i try_x[j]=%f\n", i, j, try_x[j] );
+          float rj[];
+          foreach k in [0:NEVOPARAMS-1] {
+            if (k <= j) {
+              rj[k] = rejection[i][k]; // Was either set from previous j or just set for this j
             }
-            else // Fixed Vars
-            {
-                x[i][j]         = x[i-1][j];
-                rejection[i][j] = rejection[i-1][j];
-                curr_loss[curr] = curr_loss[prev];
-                curr_sdev[curr] = curr_sdev[prev];
-                // dx[i][j] not set for fixed vars
+            else {
+              rj[k] = rejection[i-1][k]; // Not yet set, use previous
             }
-        } until( j == (NEVOPARAMS-1) );
+          }
+          tracef(@strcat("multi_annealing: AR: [%i][%i] ", color(8,"Rejection counts: "),
+                         color(1,"%f"), " ", color(7,"%f"), " ", color(5,"%f"), " ", color(9,"%f"), " ", color(6,"%f"), "\n\n"),
+                         i, j, rj[0], rj[1], rj[2], rj[3], rj[4]);
+          tracef(@strcat("multi_annealing: AR: %i ", color(8,"***** Did accept! "),
+                         color(1,"%f"), " ", color(7,"%f"), " ", color(5,"%f"), " ", color(9,"%f"), " ", color(6,"%f"), "\n\n"),
+                         i, try_x[0], try_x[1], try_x[2], try_x[3], try_x[4]);
+          }
+        }
+        else {// Fixed Vars
+          x[i][j] = x[i-1][j];
+          rejection[i][j] = rejection[i-1][j];
+          curr_loss[curr] = curr_loss[prev];
+          curr_sdev[curr] = curr_sdev[prev];
+          // dx[i][j] not set for fixed vars
+        }
+      } until( j == (NEVOPARAMS-1) );
     } until( iter_i == (annealing_cycles-1) );
 }
 
-(Res r) multi_loss( float t_start, float t_end, int annealing_steps, float t_rejection, float starting_jump, int ci, int cj, float x[], float target_innov, int evolve_reruns )
+(Res r) multi_loss(float t_start, float t_end, int annealing_steps, float t_rejection, float starting_jump,
+                   int ci, int cj, float x[], float target_innov, int evolve_reruns)
 {
-    tracef("%q\n", x);
-    file rfile[];
-    file ofile[]; // FIXME: to obtain timings and otehr stats
+  tracef("%q\n", x);
+  file rfile[];
+  file ofile[]; // FIXME: to obtain timings and otehr stats
 
-    tracef( "multi_loss: entered: ci=%i cj=%i target_innov=%f evolve_reruns=%i x=%q\n",ci, cj, target_innov,evolve_reruns,x );
+  tracef( "multi_loss: entered: ci=%i cj=%i target_innov=%f evolve_reruns=%i x=%q\n",ci, cj, target_innov,evolve_reruns,x );
 
-    int appCalls = @toint(@tofloat(evolve_reruns) / @tofloat(rerunsPerApp));  // FIXME: handle fractional issues and rounding etc. For now must divide evenly
+  int appCalls = @toint(@tofloat(evolve_reruns)/@tofloat(rerunsPerApp)); // FIXME: handle fractional issues and rounding etc.
+                                                                         // For now must divide evenly
+  tracef("multi_loss appCalls=%i\n", appCalls);
 
-    tracef("multi_loss appCalls=%i\n", appCalls);
-
-    foreach i in [1:appCalls]
-    {  // repeats of the evolove() - same as n_reruns
-        file outfile; // FIXME: map and save in future
-        string args[] = [ // FIXME: move this to a setargs() function
+  foreach i in [1:appCalls] { // repeats of the evolove() - same as n_reruns
+    file outfile; // FIXME: map and save in future
+    string args[] = [ // FIXME: move this to a setargs() function
             //    alpha_i           alpha_m        beta           gamma          delta          target_innov
                  @strcat(x[0]),  @strcat(x[1]), @strcat(x[2]), @strcat(x[3]), @strcat(x[4]), @strcat(target_innov),
-
             //     n_epochs n_steps   evolve_reruns           range
             //    "40000",   "20",  @strcat(evolve_reruns),    "2",
                   "40000",   "20",  @strcat(rerunsPerApp),     "2",
-
             //    verbose_level
                     "1",
-
-            //    T_start             T_end          Annealing_steps         Target_rejection         Starting_jump
-                 @strcat(t_start), @strcat(t_end), @strcat(annealing_steps), @strcat(t_rejection), @strcat(starting_jump),
-
+            //    T_start           T_end           Annealing_steps           Target_rejection      Starting_jump
+                  @strcat(t_start), @strcat(t_end), @strcat(annealing_steps), @strcat(t_rejection), @strcat(starting_jump),
             //    FREEZE: alpha_i alpha_m beta gamma delta
-                            "0",    "0",  "0",  "0",  "0",
+                          "0",    "0",    "0", "0",  "0",
+            //    operation-code:(m,a)  Nworkers           seed
+                  "m",                  @strcat(Nworkers), @arg("seed", "0" ) ];
 
-            //   operation-code:(m,a)    Nworkers           seed
-                      "m",            @strcat(Nworkers), @arg("seed", "0" ) ];
+    file graph <"movie_graph.txt">;
 
-        file graph <"movie_graph.txt">;
+    (outfile, rfile[i]) = evolve(args, graph);
+    tracef("multi_loss: i=%i calling evolve, args=%q\n", i, args);
+    // tracef("multi_loss: after evolve: i=%i %k %k\n", i, outfile, rfile[i]);
+  }
+  file sumfile = sumloss(rfile);
+  r = readData(sumfile);
 
-        if(@arg("wget") == "true") {
-
-           // Separate long runs from short runs when longruns option is set
-           if(@arg("longruns") == "true") {
-              float mean = @tofloat(@arg("minrange")) + @tofloat(@arg("maxrange")) / 2.0;
-              if(target_innov <= mean) {
-                 ( outfile, rfile[i] ) = evolve_wget_short( args, graph );
-              } 
-              else {
-                 ( outfile, rfile[i] ) = evolve_wget_long( args, graph );
-              }
-           }
-
-          ( outfile, rfile[i] ) = evolve_wget( args, graph );
-        }
-         
-        else {
-           ( outfile, rfile[i] ) = evolve( args, graph );
-        }
-
-        tracef("multi_loss: i=%i calling evolve, args=%q\n", i, args);
-        // tracef("multi_loss: after evolve: i=%i %k %k\n", i, outfile, rfile[i]);
-    }
-    file sumfile = sumloss(rfile);
-    r            = readData(sumfile);
-
-    tracef("multi_loss: returning: ci=%i cj=%i r.loss=%f r.sdev=%f\n",ci,cj,r.loss,r.sdev);
-    // file statfile = sumstats(ofile);  FIXME: to obtain timings and otehr stats
-    // s = readStat(statsfile);          FIXME: to obtain timings and otehr stats
+  tracef("multi_loss: returning: ci=%i cj=%i r.loss=%f r.sdev=%f\n",ci,cj,r.loss,r.sdev);
+  // file statfile = sumstats(ofile);  FIXME: to obtain timings and other stats
+  // s = readStat(statsfile);          FIXME: to obtain timings and other stats
 }
 
 optimizer_sweep() // Implements logic of python driver script
 {
 
-    int minrange = @toint(@arg("minrange", "58"));
-    int maxrange = @toint(@arg("maxrange", "59"));
-    int rangeinc = @toint(@arg("rangeinc", "50"));
+  int minrange = @toint(@arg("minrange", "58"));
+  int maxrange = @toint(@arg("maxrange", "59"));
+  int rangeinc = @toint(@arg("rangeinc", "50"));
 
-    // FIXME: add provision for random priming and random param values when x[i] == -100 (see optimizer.cpp main())
+  // FIXME: add provision for random priming and random param values when x[i] == -100 (see optimizer.cpp main())
 
-    int nreps = @toint(@arg("nreps", "1"));
+  int nreps = @toint(@arg("nreps", "1"));
 
-//    file bestfile <single_file_mapper; file=@strcat("output/T",target,".R",rep,".best_opt_some")>;
-//    file maxfile <single_file_mapper; file=@strcat("output/T",target,".R",rep,".max_dist")>;
+//file bestfile <single_file_mapper; file=@strcat("output/T",target,".R",rep,".best_opt_some")>;
+//file maxfile <single_file_mapper; file=@strcat("output/T",target,".R",rep,".max_dist")>;
 
-    foreach target_innov in [minrange:maxrange:rangeinc]
-    {
-        foreach rep in [1:nreps]
-        {
-            string some_out_filename = @strcat( "best.T", @strcat(target_innov), ".R", @strcat(rep), ".txt" );
-            file outfile;  // <single_file_mapper; file=@strcat("output/T",target_innov,".R",rep,".out")>;
-            file lossfile; // <single_file_mapper; file=@strcat("output/T",target_innov,".R",rep,".loss_data")>;
+  foreach target_innov in [minrange:maxrange:rangeinc] {
+    foreach rep in [1:nreps] {
 
-            ( outfile,lossfile ) = multi_annealing(
-                                                    some_out_filename,
-						                            @tofloat(@arg("tstart", "2.0")),
-                                                    @tofloat(@arg("tend", "0.01")),
-                                                    @tofloat(@arg("trejection", "0.3")),
-                                                    @toint(@arg("evoreruns", "100")),
-                                                    @tofloat(@arg("startingjump", "2.3")),
-                                                    [@tofloat(@arg("alphai", "0.0")), @tofloat(@arg("alpham", "0.0")), @tofloat(@arg("beta", "4.0")), @tofloat(@arg("gamma", "50.0")), @tofloat(@arg("delta", "-1.0"))],
-                                                    @tofloat(target_innov),
-                                                    @toint(@arg("annealingcycles", "50")) );
-        }
+      string some_out_filename = @strcat( "best.T", @strcat(target_innov), ".R", @strcat(rep), ".txt" );
+      file outfile;  // <single_file_mapper; file=@strcat("output/T",target_innov,".R",rep,".out")>;
+      file lossfile; // <single_file_mapper; file=@strcat("output/T",target_innov,".R",rep,".loss_data")>;
+
+      (outfile,lossfile) = multi_annealing(some_out_filename,
+		                           @tofloat(@arg("tstart", "2.0")),
+                                           @tofloat(@arg("tend", "0.01")),
+                                           @tofloat(@arg("trejection", "0.3")),
+                                           @toint(@arg("evoreruns", "100")),
+                                           @tofloat(@arg("startingjump", "2.3")),
+                                           [ @tofloat(@arg("alphai", "0.0")),
+                                             @tofloat(@arg("alpham", "0.0")),
+                                             @tofloat(@arg("beta", "4.0")),
+                                             @tofloat(@arg("gamma", "50.0")),
+                                             @tofloat(@arg("delta", "-1.0"))
+                                           ],
+                                           @tofloat(target_innov),
+                                           @toint(@arg("annealingcycles", "50")) );
     }
+  }
 }
 
 main()
 {
-    optimizer_sweep();
+  optimizer_sweep();
 }
 
 main();

Modified: SwiftApps/SciColSim/conf/local.cf
===================================================================
--- SwiftApps/SciColSim/conf/local.cf	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/conf/local.cf	2012-12-30 19:53:21 UTC (rev 6112)
@@ -4,6 +4,7 @@
 lazy.errors=true
 status.mode=provider
 use.provider.staging=false
+use.wrapper.staging=false
 provider.staging.pin.swiftfiles=false
 
 #app sumloss=$PWD/../sumloss.sh

Modified: SwiftApps/SciColSim/conf/local.xml
===================================================================
--- SwiftApps/SciColSim/conf/local.xml	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/conf/local.xml	2012-12-30 19:53:21 UTC (rev 6112)
@@ -1,7 +1,7 @@
 <config>
   <pool handle="local" >
     <execution provider="local" url="none" />
-    <profile namespace="karajan" key="jobThrottle">_JOB_THROTTLE_</profile>
+    <profile namespace="karajan" key="jobThrottle">.03</profile>
     <profile namespace="karajan" key="initialScore">10000</profile>
     <filesystem provider="local"/>
     <workdirectory>_WORK_/local</workdirectory>

Added: SwiftApps/SciColSim/evolve-wrapper.sh
===================================================================
--- SwiftApps/SciColSim/evolve-wrapper.sh	                        (rev 0)
+++ SwiftApps/SciColSim/evolve-wrapper.sh	2012-12-30 19:53:21 UTC (rev 6112)
@@ -0,0 +1,42 @@
+#!/bin/bash -x
+
+crash()
+{
+    MSG=$1
+    echo ${MSG}  >&2
+    exit 1
+}
+
+launchDirectory=$PWD
+echo Viewing first input
+echo Arguments are $@
+
+# Verify WN_TMP is defined
+if [ -z "$OSG_WN_TMP" ]; then
+   crash "OSG_WN_TMP is undefined"
+fi
+
+# Verify engage subdirectory of OSG_WN_TMP
+mkdir -p $OSG_WN_TMP/engage
+if [ ! -d "$OSG_WN_TMP/engage" ]; then
+   crash "OSG_WN_TMP/engage does not exist"
+fi
+
+tmpDirectory=`mktemp -d $OSG_WN_TMP/engage/SciColSim.XXXXXX`
+cd $tmpDirectory
+
+# Retrieve software
+wget http://www.ci.uchicago.edu/~davidk/SciColSim/evolve.sh 
+chmod +x evolve.sh
+wget http://www.ci.uchicago.edu/~davidk/SciColSim/openmp-optimizer 
+chmod +x openmp-optimizer
+wget http://www.ci.uchicago.edu/~davidk/SciColSim/movie_graph.txt
+
+# Run evolve
+mkdir -p $( dirname $1)
+./evolve.sh "$@"
+cp $1 $launchDirectory/$( dirname $1 )
+
+# Finish
+cd $launchDirectory
+rm -rf $tmpDirectory

Modified: SwiftApps/SciColSim/gengraphs.sh
===================================================================
--- SwiftApps/SciColSim/gengraphs.sh	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/gengraphs.sh	2012-12-30 19:53:21 UTC (rev 6112)
@@ -2,21 +2,8 @@
 
 mkdir -p graph
 
-# for s in $(seq 1000 1000 10000); do
-for s in 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000; do
-  ./trimgraph.sh $s 1.0 > graph/$s.100
-  ./trimgraph.sh $s 0.1 > graph/$s.10
-  ./trimgraph.sh  $s 0.5 > graph/$s.50
+for p in .001 .002 .003 .004 .005 .006 .007 .008 .009 .010; do
+  for ((i=0;i<10;i++)); do
+    ./samplegraph.sh $p > g/bg${p}.${i}
+  done
 done
-
-# Runtime, ram, science results (single floating pointer number called loss) for each param
-# Params = nodes, edges, and ti
-# As edges/nodes increase, time increases
-# 1000 osg jobs between 10 seconds and 24 hours
-# Example: iterate over ti in units of 100, graph sizes should be 
-# Automate, return eof when timed out, set max run time
-# Ability to see gprof output
-# Once with control structure he needs, then one run with large size to show hockey stick
-# Generate a table, then generate a graph
-# Email uc3 and midway account information
-

Modified: SwiftApps/SciColSim/optimizer.cpp
===================================================================
--- SwiftApps/SciColSim/optimizer.cpp	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/optimizer.cpp	2012-12-30 19:53:21 UTC (rev 6112)
@@ -11,7 +11,7 @@
 #define MAXNworkers 24
 int Nworkers=MAXNworkers;
 
-#define NUniverse 240
+#define NUniverse 24
 
 // Add operation code to enable existing code to be used at lower level from Swift scripts:
 
@@ -71,8 +71,6 @@
 
 #define FIX_VARIABLES 1
 
-#define MAX_LOSS 160
-
 using namespace boost;
 using namespace std;
 using namespace boost::numeric::ublas;
@@ -98,6 +96,7 @@
 typedef graph_traits < graph_t >::vertex_descriptor vertex_descriptor;
 typedef graph_traits < graph_t >::edge_descriptor edge_descriptor;
 
+double max_loss = -1.0; // intialized to "unset"; set by first Universe constructor to run.
 
 //================================================
 string strDouble(double number)
@@ -262,8 +261,8 @@
 
 	int current_epoch;
 	double current_loss;
-	int current_repeat;
-    double current_novelty;
+  int current_repeat;
+  double current_novelty;
 
 	int mode_identify_failed;
     int verbose_level; // 0 is silent, higher is more
@@ -300,7 +299,22 @@
 
         base_generator_type gene(42u);
         generator = gene;
-        generator.seed(static_cast<unsigned int>(std::time(0)));
+//        generator.seed(static_cast<unsigned int>(std::time(0)));
+
+
+    if ( initSeed != 0.0 ) {
+        generator.seed(static_cast<unsigned int>(initSeed));
+      }
+    else {
+        timeval t;
+        gettimeofday(&t, NULL);
+        generator.seed(static_cast<unsigned int>(t.tv_usec));
+      }
+
+
+
+
+
         boost::uniform_real<> uni_d(0,1);
         uni_dist = uni_d;
 
@@ -490,8 +504,7 @@
 				}
 			}
 		}
-
-
+		if(max_loss <= 0.0) set_max_loss(N_nodes, M_edges, TargetNovelty);
     }
 
 
@@ -992,6 +1005,7 @@
     void evolve_to_target_and_save(int istart, int iend, double* storage, int* counters){
 
         double ALOT=100000000000.;
+
         double ratio = 0.0;
         int check = 0;
 
@@ -1001,82 +1015,25 @@
 
             for(int i=0; i< N_epochs &&  current_novelty < TargetNovelty; i++){
 
-                if(ratio < max_loss_value((int)TargetNovelty)){
+                if(ratio < max_loss){
                     update_world();
                 }
                 else{
-                    check = 1;
+		  cout << "k=" << k << " i=" << i << " ratio=" << ratio << " max_loss=" << max_loss << endl;
                     break;
                 }
                 ratio = current_loss/current_novelty;
             }
-            if( check ){
-                storage[k]=ALOT;
-            }
-            else{
+            if( ratio < max_loss )
                 storage[k]=current_loss/current_novelty;
-            }
+            else
+                storage[k]=ALOT;
             counters[k]=1;
-
             reset_world();
         }
-
     }
 
     //==============================================
-    double Omax_loss_value(int tn){
-
-        if( tn == 58 )           return 128.286;
-        else if( tn == 108 )     return 131.866;
-        else if( tn == 158 )     return 135.551;
-        else if( tn == 208 )     return 139.694;
-        else if( tn == 258 )     return 144.163;
-        else if( tn == 308 )     return 148.967;
-        else if( tn == 358 )     return 154.201;
-        else if( tn == 408 )     return 159.962;
-        else if( tn == 458 )     return 166.441;
-        else if( tn == 508 )     return 173.655;
-        else if( tn == 558 )     return 181.921;
-        else if( tn == 608 )     return 191.246;
-        else if( tn == 658 )     return 202.150;
-        else if( tn == 708 )     return 215.197;
-        else if( tn == 758 )     return 202.150;  // Verify with Andrey. Same as TargetNovelty of 658
-        else if( tn == 808 )     return 251.698;
-        else if( tn == 858 )     return 279.201;
-        else if( tn == 908 )     return 320.112;
-        else if( tn == 958 )     return 394.774;
-        else if( tn == 1008 )    return 1052.38;  // Huge number here. Why?
-        else                      return 10000.;   /* Pray that this does not occur. Ask Andrey what to do */
-    }
-    double max_loss_value(int tn){
-
-      switch(tn) {
-        case 58:      return 128.286;
-        case 108:     return 131.866;
-        case 158:     return 135.551;
-        case 208:     return 139.694;
-        case 258:     return 144.163;
-        case 308:     return 148.967;
-        case 358:     return 154.201;
-        case 408:     return 159.962;
-        case 458:     return 166.441;
-        case 508:     return 173.655;
-        case 558:     return 181.921;
-        case 608:     return 191.246;
-        case 658:     return 202.150;
-        case 708:     return 215.197;
-        case 758:     return 202.150;  // Verify with Andrey. Same as TargetNovelty of 658
-        case 808:     return 251.698;
-        case 858:     return 279.201;
-        case 908:     return 320.112;
-        case 958:     return 394.774;
-        case 1008:    return 1052.38;  // Huge number here. Why?
-        default:      return 10000.;   /* Pray that this does not occur. Ask Andrey what to do */
-      }
-    }
-
-
-    //==============================================
     int get_reruns(void){
         return N_repeats;
     }
@@ -1185,140 +1142,53 @@
         return 0;
     }
 
-#ifdef notdef
-    //=================================================================
-    void try_annealing(double starting_jump, int iterations,
-                       double temp_start, double temp_end, double target_rejection){
+//--------
 
-        double dx[5]={0.,0.,0.,0.,0};
-        double x[5]={0.,0.,0.,0.,0};
-        double rejection[5]={0., 0., 0., 0., 0.};
-        double curr_x, curr_err, x_tmp;
-        double temperature;
-        double ratio, r;
-        int cycle=10;
-        boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
+void set_max_loss(long long v, long long e, long long t) {
 
-        // set up parameter for annealing
+  cout << "set_max_loss v=" << v << " e=" << e << " t=" << t << " max_loss=" << max_loss << endl;
 
-        x[0]=alpha_i;
-        x[1]=alpha_m;
-        x[2]=beta;
-        x[3]=gamma;
-        x[4]=delta;
+  // Based on formulas from random_analytical.pdf
 
-        for(int i=0;i<5;i++){
-            dx[i] = starting_jump;
-        }
+  double sum, ERLt, VarRLt;
 
-        // establish the current value
+  // (9): E[RLt] = (1/t) * SUM(i=0 to T of: (V*(V-1) / (2 * (E-i))
 
-        //..........................................
-        evolve_to_target();
-        std::cout << CumulativeRelativeLoss << " +- " << CRLsquare << std::endl;
+  sum = 0;
+  for(int i=0;i<t;i++) {
+    sum += ((double)(v*(v-1))) / ((double)(2*(e-i)));
+  }
+  ERLt = (1.0/(double) t) * sum;
 
-        curr_x   = CumulativeRelativeLoss;
-        curr_err = CRLsquare;
-        CumulativeRelativeLoss = 0;
-        CRLsquare = 0;
-        //...........................................
+  // (12): Var[RLt] = 1 / (T**2) * SUM( i=0 to T of: ((V*(V-1))/2) - E + 1 ) / ((E-i)**2)
 
-        // optimization cycle
-        for(int i=0; i<iterations; i++){
-
-            temperature = temp_start*exp( i*(log(temp_end)-log(temp_start))/(double)iterations);
-            std::cout  << std::endl << "....T = " << wrap_double(temperature,3) << std::endl << std::endl;
-
-            if (i % cycle == 0 && i > 0){
-
-                for (int k=0; k<5; k++){
-
-                    rejection[k]/=(double)cycle;
-                    if (rejection[k] > 0){
-                        dx[k] = dx[k]/(rejection[k]/target_rejection);
-                        rejection[k]=0.;
-                    }
-                    else{
-                        dx[k]*=2.;
-                    }
-                    std::cout  << dx[k] << " ";
-                }
-                std::cout  << std::endl;
-            }
-
-
-            for (int j=0; j<5; j++){
-
-                // get new value of x[j]
-                x_tmp = get_new_x(x[j],dx[j]);
-
-
-
-                //.............................................
-                set_parameter(x_tmp, j);
-
-
-                evolve_to_target();
-
-                std::cout  << std::endl << "......... " << std::endl;
-                std::cout << "Trying... " << CumulativeRelativeLoss << " +- " << CRLsquare << std::endl;
-
-                ratio = min(1.,exp(-(CumulativeRelativeLoss-curr_x)/temperature));
-                r = uni();
-                std::cout << r << " vs " << ratio << std::endl;
-
-                if (r > ratio){
-
-                    std::cout << string_wrap(id, 4) <<" "<< (i+1) << ","<< (j)
-                    <<" "<< (i+1) << " Did not accept "
-                    << x_tmp << "(" << j << ")" << std::endl;
-                    std::cout << alpha_i << " "<< alpha_m << " "
-                    << beta << " " << gamma << " "
-                    << delta << " " << std::endl;
-                    set_parameter(x[j], j);
-                    CumulativeRelativeLoss = 0;
-                    CRLsquare = 0;
-
-                    rejection[j]+=1.;
-                }
-
-                else {
-
-                    curr_x   = CumulativeRelativeLoss;
-                    curr_err = CRLsquare;
-                    x[j] = x_tmp;
-                    CumulativeRelativeLoss = 0;
-                    CRLsquare = 0;
-                    std::cout << (i+1) << string_wrap((string) " Rejection counts: ", 8)
-                    << wrap_double(rejection[0],2)
-                    << " "<< wrap_double(rejection[1], 7) << " "
-                    << wrap_double(rejection[2],5) << " " << wrap_double(rejection[2],9) << " "
-                    << wrap_double(rejection[4],6) << " "
-                    << std::endl << std::endl;
-
-                    std::cout << string_wrap(id, 4) <<" "<< (i+1) <<","<< (j)
-                    <<" "
-                    << string_wrap((string) "***** Did accept! ", 3)
-                    << wrap_double(alpha_i,2)
-                    << " "<< wrap_double(alpha_m, 7) << " "
-                    << wrap_double(beta,5) << " "
-                    << wrap_double(gamma,9) << " "
-                    << wrap_double(delta,6) << " "
-                    << std::endl << std::endl;
-
-                }
-                //........................................................
-
-            }
-
-        }
-
+  sum = 0;
+  for(int i=0;i<t;i++) {
+    sum +=  
+      ( (((double)(v*(v-1)))/ 2.0) - (double)e + (double)i )
+      /  
+      (double)((e-i)*(e-i))
+      ;
+    if ( (double)((e-i)*(e-i)) == 0.0 ) {
+      printf( "set_max_loss: while doing variance: zero denom: %d %d\n", e, i);
+      exit(1);
     }
+  }
+  int tmp = t*t;
+  VarRLt = (1.0/(double)((t) * t)) * sum;
+  if (VarRLt < 0.0) {
+    printf( "set_max_loss: while doing variance: VarRLT %d < 0\n", VarRLt);
+    exit(1);
+  }
 
-#endif
+  // (9) + 3sigma = E[RLt] + 3 * SQRT(Var)
 
-};
+  max_loss = ERLt + (3.0 * sqrt(VarRLt));
+  printf("set_max_loss: %12d %12.3f %12.8e %12.3f\n", t, ERLt, VarRLt, max_loss);
+}
 
+}; // End of class Universe
+
 //============================================================
 
 #ifdef P_DISPATCH
@@ -1385,14 +1255,30 @@
      }
 #endif
 
+/*
     for (int i=0; i<N; i++){
         Loss+=Results[i]/(double)N;
         LossSquare+=Results[i]*Results[i]/(double)N;
     }
 
     double two_std = ((LossSquare - Loss*Loss)/(double)N);
+    double two_std_dev = 2.*sqrt(two_std);
+*/
 
-    two_std = 2.*sqrt(two_std);
+    double sumsqdel;
+    Loss = 0.0, sumsqdel = 0.0;
+    for (int i=0; i<N; i++) {
+      Loss+=Results[i];
+    }
+    Loss /= (double)N;
+    for (int i=0; i<N; i++) {
+      double delta = Results[i] - Loss;
+      sumsqdel += delta*delta;
+    }
+    double variance = sumsqdel / double(N);
+    double two_std = 2.0 * sqrt(variance);
+
+    cout << "multi_loss: Loss=" << Loss << " sumsqdel=" << sumsqdel << " variance=" << variance << " two_std=" << two_std << endl;
     std::pair<double,double> Res;
     Res.first=Loss;
     Res.second=two_std;

Modified: SwiftApps/SciColSim/sumloss.sh
===================================================================
--- SwiftApps/SciColSim/sumloss.sh	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/sumloss.sh	2012-12-30 19:53:21 UTC (rev 6112)
@@ -34,6 +34,7 @@
 
   x = (loss_sq - (loss*loss))/n
   y = (tavg_sq - ( tavg*tavg))/tn
+  if(x<0.0) x=0.0;
   sdev = 2.0 * sqrt(x)
   tsdev = 2.0 * sqrt(y)
 

Modified: SwiftApps/SciColSim/swiftopt.sh
===================================================================
--- SwiftApps/SciColSim/swiftopt.sh	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/swiftopt.sh	2012-12-30 19:53:21 UTC (rev 6112)
@@ -11,7 +11,7 @@
 
 # Function to run Swift
 runswift() {
-   SWIFT_HEAP_MAX=$ram SWIFT_LIB=.. $swift >> swift.out 2>&1 -tc.file tc.data -sites.file $1 -config cf annealing.swift -e33="$escapecode" \
+   SWIFT_HEAP_MAX=$ram SWIFT_LIB=.. swift >> swift.out 2>&1 -tc.file tc.data -sites.file $1 -config cf annealing.swift -e33="$escapecode" \
                                             \
    -minrange=$min_target_innovation         \
    -maxrange=$max_target_innovation         \
@@ -78,7 +78,7 @@
 cp params/$paramfile $rundir/paramfile
 sed -e '/^[[:space:]]*\(#.*\)*$/d' -e 's/#.*//' -e 's/  */=/' -e 's/^/export /' <params/$paramfile >$rundir/params.annealing
 source $rundir/params.annealing
-swift=../swift/bin/swift # relative to runNNN/ dirs
+#swift=../swift/bin/swift # relative to runNNN/ dirs
 echo Optimization $rundir: site=$execsite paramfile=$paramfile
 
 # Report an error if configuration files are missing
@@ -129,13 +129,14 @@
 # Run gensites
 if [ ! "$USE_SCS" == 1 ]; then
    cp ../conf/$execsite.cf cf
-   SWIFT_HOME=../swift/bin ../swift/bin/gensites -p ../conf/$execsite.cf ../conf/$execsite.xml > $execsite.xml
+   # SWIFT_HOME=../swift/bin ../swift/bin/gensites -p ../conf/$execsite.cf ../conf/$execsite.xml > $execsite.xml
+   gensites -p ../conf/$execsite.cf ../conf/$execsite.xml > $execsite.xml
 fi
 
 echo "Run dir=$rundir" >> ABOUT
 echo "Work dir=$WORK" >> ABOUT
 echo "Total jobs=$total_jobs" >> ABOUT
-echo "Run Command: SWIFT_HEAP_MAX=$ram SWIFT_LIB=.. $swift >> swift.out 2>&1 -tc.file tc.data -sites.file $execsite.xml -config cf annealing.swift -minrange=$min_target_innovation -maxrange=$max_target_innovation-rangeinc=$target_innovation_increment -nreps=$annealing_repeats -annealingcycles=$annealing_cycles -evoreruns=$evolve_reruns -alphai=$alpha_i -alpham=$alpha_m -beta=$beta -gamma=$gamma -delta=$delta -nworkers=$nworkers -rerunsperapp=$reruns_per_opt_invocation -e33="$escapecode"" >> ABOUT
+echo "Run Command: SWIFT_HEAP_MAX=$ram SWIFT_LIB=.. swift >> swift.out 2>&1 -tc.file tc.data -sites.file $execsite.xml -config cf annealing.swift -minrange=$min_target_innovation -maxrange=$max_target_innovation-rangeinc=$target_innovation_increment -nreps=$annealing_repeats -annealingcycles=$annealing_cycles -evoreruns=$evolve_reruns -alphai=$alpha_i -alpham=$alpha_m -beta=$beta -gamma=$gamma -delta=$delta -nworkers=$nworkers -rerunsperapp=$reruns_per_opt_invocation -e33="$escapecode"" >> ABOUT
 
 if [ _$dryrun != _ ]; then
   exit 0

Modified: SwiftApps/SciColSim/testopt.py
===================================================================
--- SwiftApps/SciColSim/testopt.py	2012-12-29 00:38:49 UTC (rev 6111)
+++ SwiftApps/SciColSim/testopt.py	2012-12-30 19:53:21 UTC (rev 6112)
@@ -11,8 +11,7 @@
 
 #paramset="default"
 paramset="mw2"
-#paramset="VERYFASTTEST"
-#paramset="VERYFASTTEST"
+verboseLevel = "1"
 
 print("Running with parameter set " + paramset + "\n\n");
 
@@ -112,21 +111,25 @@
   openmp           = "OMP_NUM_THREADS=" + NWorkers
   operation        = "n"  # n=normal, m=manual (runs 1 multi_loss call)
   seed             = "1234567"
-  app              = "./openmp-optimizer";
+  app              = "./openmp-optimizer"
 
 elif paramset == "mw2":  # Timing TEST PARAMETERS by Mike
   
   startTarget      = 58
-  endTarget        = 209
+  endTarget        = 59
   incrTarget       = 50
   optimizerRepeats = 1
   evolveReruns     = 240
+  evolveReruns     = 8
   annealingSteps   = 1
-  NWorkers         = "8"
+  NWorkers         = "1"
   openmp           = "OMP_NUM_THREADS=" + NWorkers
+  openmp           = ""
+
   operation        = "m"  # n=normal, m=manual (runs 1 multi_loss call)
   seed             = "123456"
-  app              = "./openmp-optimizer";
+  app              = "./openmp-optimizer"
+  verboseLevel     = "1"
 
 # Ensure we dont pass new parameters to original optimizer versions
 # (but they would be ignored)
@@ -142,7 +145,7 @@
   for i in range(optimizerRepeats):
     args = "rm -f bestdb.txt; " + \
            openmp + " " + app + " 0 0 0 0 0 " + str(target) + " 40000 20 " + str(evolveReruns) + \
-           " 2 1 2. 0.01 " + str(annealingSteps) + " 0.3 2.3 0 0 0 0 0 " + operation + " " + NWorkers + " " + seed + \
+           " 2 " + verboseLevel + " 2. 0.01 " + str(annealingSteps) + " 0.3 2.3 0 0 0 0 0 " + operation + " " + NWorkers + " " + seed + \
            " >& out.T"+str(target)+".i"+str(i) + "; #mv bestdb.txt best.T" + str(target) + ".i" + str(i) 
     print("\n**** Calling optimizer: "+args+"\n")
     os.system(args);



From wilde at ci.uchicago.edu  Sun Dec 30 13:55:18 2012
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 30 Dec 2012 13:55:18 -0600 (CST)
Subject: [Swift-commit] r6113 - in SwiftApps/SciColSim: conf params
Message-ID: <20121230195518.DF20E9CCC0@svn.ci.uchicago.edu>

Author: wilde
Date: 2012-12-30 13:55:18 -0600 (Sun, 30 Dec 2012)
New Revision: 6113

Added:
   SwiftApps/SciColSim/conf/midway01.cf
   SwiftApps/SciColSim/conf/midway01.xml
   SwiftApps/SciColSim/params/ARtest03
Log:
add new configs and params.

Added: SwiftApps/SciColSim/conf/midway01.cf
===================================================================
--- SwiftApps/SciColSim/conf/midway01.cf	                        (rev 0)
+++ SwiftApps/SciColSim/conf/midway01.cf	2012-12-30 19:55:18 UTC (rev 6113)
@@ -0,0 +1,11 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=false
+status.mode=provider
+use.provider.staging=false
+use.wrapper.staging=false
+provider.staging.pin.swiftfiles=false
+
+#app local sumloss=$PWD/../sumloss.sh
+#app midway01 evolve=$PWD/../evolve.sh

Added: SwiftApps/SciColSim/conf/midway01.xml
===================================================================
--- SwiftApps/SciColSim/conf/midway01.xml	                        (rev 0)
+++ SwiftApps/SciColSim/conf/midway01.xml	2012-12-30 19:55:18 UTC (rev 6113)
@@ -0,0 +1,64 @@
+<config>
+
+  <pool handle="local" >
+    <execution provider="local" url="none" />
+    <profile namespace="karajan" key="jobThrottle">0.09</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+    <filesystem provider="local"/>
+    <workdirectory>_WORK_/local</workdirectory>
+  </pool>
+
+  <pool handle="midway01">
+
+    <execution provider="coaster" jobmanager="local:slurm"/>
+
+    <profile namespace="env" key="SWIFT_GEN_SCRIPTS">KEEP</profile>
+
+    <profile namespace="globus" key="jobsPerNode">16</profile>
+    <profile namespace="globus" key="ppn">16</profile>
+    <profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
+    <profile namespace="globus" key="workerLoggingDirectory">_WORK_/workers</profile>
+    <profile namespace="globus" key="lowOverAllocation">100</profile>
+    <profile namespace="globus" key="highOverAllocation">100</profile>
+    <profile namespace="globus" key="maxTime">1800</profile>
+    <profile namespace="globus" key="maxWallTime">00:05:00</profile>
+    <profile namespace="globus" key="slots">20</profile>
+    <profile namespace="globus" key="nodeGranularity">1</profile>
+    <profile namespace="globus" key="maxNodes">1</profile>
+    <profile namespace="globus" key="queue">sandyb</profile>
+
+    <profile namespace="karajan" key="jobThrottle">4.00</profile>
+    <profile namespace="karajan" key="initialScore">10000</profile>
+
+    <filesystem provider="local"/>
+    <workdirectory>_WORK_/beagle</workdirectory>
+
+  </pool>
+
+</config>
+
+<!-- 
+
+<pool handle="sandyb">
+
+  <execution provider="coaster" jobmanager="local:slurm" url="localhost:2"/>
+
+  <profile namespace="globus" key="jobsPerNode">12</profile>
+  <profile namespace="globus" key="ppn">12</profile>
+  <profile namespace="globus" key="slots">10</profile>
+  <profile namespace="globus" key="maxnodes">1</profile>
+  <profile namespace="globus" key="nodegranularity">1</profile>
+  <profile namespace="globus" key="queue">sandyb</profile>
+
+  <profile namespace="karajan" key="jobThrottle">3.99</profile>
+  <profile namespace="karajan" key="initialScore">10000</profile>
+
+  <profile namespace="globus" key="highOverAllocation">100</profile>
+  <profile namespace="globus" key="lowOverAllocation">100</profile>
+  <profile namespace="globus" key="maxtime">2000</profile>
+  <profile namespace="globus" key="maxwalltime">00:04:00</profile>
+
+  <filesystem provider="local" url="none" />
+  <workdirectory>/project/joshuaelliott/narr/swiftwork/</workdirectory>
+
+-->
\ No newline at end of file

Added: SwiftApps/SciColSim/params/ARtest03
===================================================================
--- SwiftApps/SciColSim/params/ARtest03	                        (rev 0)
+++ SwiftApps/SciColSim/params/ARtest03	2012-12-30 19:55:18 UTC (rev 6113)
@@ -0,0 +1,18 @@
+
+min_target_innovation        58     # starting target innovation value to try
+max_target_innovation        59     # stops before this target innovation value
+target_innovation_increment  50     # increment target innovation by this amount 
+
+annealing_repeats            1      # times to repeate the entire optimization process for each target_innovation
+annealing_cycles             10     # times to perform the simulated annealing loop for all non-fixed parameters
+
+evolve_reruns                32   # times to perform evolve_to_target_and_save() (objective function - is batched)
+nworkers                     16    # number of parallel threads (cores) to use per invocation of C++ optimizer
+reruns_per_opt_invocation    16     # reruns_per_opt_invocation mod nworkers must == 0 !!! <=== NOTE WELL !!!
+
+alpha_i                      0.0     # 5 evolve() parameters: must be decimal values !!!
+alpha_m                      0.0     # alpha_i and alpha_m are fixed for now
+beta                         0.0     # rest are varied by the optimization process
+gamma                        0.0
+delta                        0.0 
+ 



From swift at ci.uchicago.edu  Sun Dec 30 21:20:06 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Sun, 30 Dec 2012 21:20:06 -0600 (CST)
Subject: [Swift-commit] cog r3531
Message-ID: <20121231032006.DDC8B8D00081@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3531 | hategan | 2012-12-30 21:17:41 -0600 (Sun, 30 Dec 2012) | 1 line

added flag to disable idle block cleanup
------------------------------------------------------------------------
Index: modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java
===================================================================
--- modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java	(revision 3530)
+++ modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java	(working copy)
@@ -361,6 +361,12 @@
      *
      */
     protected void removeIdleBlocks() {
+    
+    	if (settings.getDisableIdleBlockCleanup()) {
+    		System.out.println("Idle block cleanup disabled");
+    		return;
+    	}
+    
         ArrayList<Block> sorted;
 
         synchronized (blocks) {
Index: modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/Settings.java
===================================================================
--- modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/Settings.java	(revision 3530)
+++ modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/Settings.java	(working copy)
@@ -50,7 +50,7 @@
                        "ppn", "ldLibraryPath", "workerCopies",
                        "directory", "useHashBang",
                        "providerAttributes", "parallelism", "pe",
-                       "coresPerNode"};
+                       "coresPerNode", "disableIdleBlockCleanup" };
 
     /**
      * The maximum number of blocks that can be active at one time
@@ -156,6 +156,8 @@
      * A pass-through setting for SGE, parallel environment
     */
     private String pe;
+    
+    private boolean disableIdleBlockCleanup = false;
 
     public Settings() {
         hook = new Hook();
@@ -564,6 +566,14 @@
     public void setUseHashBang(String uhb) {
         this.useHashBang = uhb;
     }
+    
+    public void setDisableIdleBlockCleanup(boolean disableIdleBlockCleanup) {
+    	this.disableIdleBlockCleanup = disableIdleBlockCleanup;
+    }
+    
+    public boolean getDisableIdleBlockCleanup() {
+    	return disableIdleBlockCleanup;
+    }
 
     public void set(String name, String value)
         throws IllegalArgumentException {


From swift at ci.uchicago.edu  Sun Dec 30 22:10:04 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Sun, 30 Dec 2012 22:10:04 -0600 (CST)
Subject: [Swift-commit] cog r3532
Message-ID: <20121231041005.9D4608D00081@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3532 | hategan | 2012-12-30 22:07:18 -0600 (Sun, 30 Dec 2012) | 1 line

removed debugging message
------------------------------------------------------------------------
Index: modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java
===================================================================
--- modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java	(revision 3531)
+++ modules/provider-coaster/src/org/globus/cog/abstraction/coaster/service/job/manager/BlockQueueProcessor.java	(working copy)
@@ -363,7 +363,6 @@
     protected void removeIdleBlocks() {
     
     	if (settings.getDisableIdleBlockCleanup()) {
-    		System.out.println("Idle block cleanup disabled");
     		return;
     	}
     


From swift at ci.uchicago.edu  Mon Dec 31 18:50:06 2012
From: swift at ci.uchicago.edu (swift at ci.uchicago.edu)
Date: Mon, 31 Dec 2012 18:50:06 -0600 (CST)
Subject: [Swift-commit] cog r3534
Message-ID: <20130101005006.D6BAA8D00081@bridled.ci.uchicago.edu>

------------------------------------------------------------------------
r3534 | hategan | 2012-12-31 18:46:00 -0600 (Mon, 31 Dec 2012) | 1 line

removed dependency on gt4 provider
------------------------------------------------------------------------
Index: modules/abstraction/dependencies.xml
===================================================================
--- modules/abstraction/dependencies.xml	(revision 3533)
+++ modules/abstraction/dependencies.xml	(working copy)
@@ -10,10 +10,6 @@
 	  <!--<ant antfile="${main.buildfile}" target="dep">
 		<property name="module" value="provider-gt2ft"/>
 	  </ant>-->
-	  
-	  <ant antfile="${main.buildfile}" target="dep">
-		<property name="module" value="provider-gt4_0_0"/>
-	  </ant>
 	  <!--<ant antfile="${main.buildfile}" target="dep">
 		<property name="module" value="provider-condor"/>
 	  </ant>-->


From wilde at ci.uchicago.edu  Sat Dec 22 22:33:23 2012
From: wilde at ci.uchicago.edu (wilde at ci.uchicago.edu)
Date: Sun, 23 Dec 2012 04:33:23 -0000
Subject: [Swift-commit] r6110 - SwiftApps/SciColSim
Message-ID: <20121223043322.747039CD0C@svn.ci.uchicago.edu>

Author: wilde
Date: 2012-12-22 22:33:21 -0600 (Sat, 22 Dec 2012)
New Revision: 6110

Added:
   SwiftApps/SciColSim/maxloss.cpp
   SwiftApps/SciColSim/maxloss.py
   SwiftApps/SciColSim/maxloss_ar.py
Modified:
   SwiftApps/SciColSim/Makefile
   SwiftApps/SciColSim/TODO
   SwiftApps/SciColSim/graphsim.cpp
   SwiftApps/SciColSim/samplegraph.sh
   SwiftApps/SciColSim/testgraph.py
Log:
Development snapshot. Test programs for dynamic max-loss; fine-grained OpenMP of graphsim; revised graph sampler.

Modified: SwiftApps/SciColSim/Makefile
===================================================================
--- SwiftApps/SciColSim/Makefile	2012-12-19 14:06:35 UTC (rev 6109)
+++ SwiftApps/SciColSim/Makefile	2012-12-23 04:33:21 UTC (rev 6110)
@@ -7,8 +7,11 @@
 openmp-optimizer: optimizer.cpp
 	g++ -DP_OPENMP -static -O -fopenmp -I boost_1_47_0 -o openmp-optimizer optimizer.cpp
 
+#t: t.cpp
+#	g++ -DP_OPENMP -static -O -fopenmp -I boost_1_47_0 -o t t.cpp
+
 graphsim: graphsim.cpp
-	g++ -DP_OPENMP -static -pg -O -fopenmp -I boost_1_47_0 -o graphsim graphsim.cpp
+	g++ -DP_OPENMP -static -pg -O2 -fopenmp -I boost_1_47_0 -o graphsim graphsim.cpp
 
 openmptest: openmptest.cpp
 	g++ -DP_OPENMP -static -O -fopenmp -o openmptest openmptest.cpp

Modified: SwiftApps/SciColSim/TODO
===================================================================
--- SwiftApps/SciColSim/TODO	2012-12-19 14:06:35 UTC (rev 6109)
+++ SwiftApps/SciColSim/TODO	2012-12-23 04:33:21 UTC (rev 6110)
@@ -1,6 +1,28 @@
 
+--- Questions and Open Issues ---
 
+When sampling the graph, we compress the node ids. Is this OK?
 
+Same 40K epoch count?  Is this really feasible?
+
+What values for otehr loop parameters?
+
+What sampling?
+
+Limits?
+-- placed correctly?
+-- size
+-- anomalous value for tn 758
+-- adjust all for new graph?
+
+What is range of TI to sweep over?
+
+Algorithmic improvements?
+
+Graph partitioning? => for greater total parallelism?
+
+
+
 x = done, - = in progress
 
 

Modified: SwiftApps/SciColSim/graphsim.cpp
===================================================================
--- SwiftApps/SciColSim/graphsim.cpp	2012-12-19 14:06:35 UTC (rev 6109)
+++ SwiftApps/SciColSim/graphsim.cpp	2012-12-23 04:33:21 UTC (rev 6110)
@@ -6,8 +6,6 @@
 //  Copyright 2011 University of Chicago. All rights reserved.
 //
 
-// Select OpenMP or Grand Central Dispatch for multithreading:
-
 #define MAXNworkers 1
 int Nworkers=MAXNworkers;
 
@@ -34,13 +32,8 @@
 #include <sys/types.h>
 #include "unistd.h"
 
-#ifdef P_DISPATCH
-#include <dispatch/dispatch.h>
-#endif
-
 #include <fstream>
 
-
 #include <stdlib.h>
 #include <boost/numeric/ublas/io.hpp>
 #include <boost/graph/graph_traits.hpp>
@@ -88,157 +81,122 @@
 typedef boost::graph_traits<Graph>::vertex_descriptor vertex_descriptor;
 
 namespace std {
-	using ::time;
+  using ::time;
 }
 
 static int var_fixed[5] = {1, 0, 1, 1, 0};
 
 typedef boost::minstd_rand base_generator_type;
 typedef adjacency_list < listS, vecS, directedS,
-no_property, property < edge_weight_t, int > > graph_t;
+			 no_property, property < edge_weight_t, int > > graph_t;
 typedef graph_traits < graph_t >::vertex_descriptor vertex_descriptor;
 typedef graph_traits < graph_t >::edge_descriptor edge_descriptor;
 
 
-//================================================
 string strDouble(double number)
 {
-    stringstream ss;//create a stringstream
-    ss << number;//add number to the stream
-    return ss.str();//return a string with the contents of the stream
+  stringstream ss;//create a stringstream
+  ss << number;//add number to the stream
+  return ss.str();//return a string with the contents of the stream
 }
 
-//================================================
-
 double gaussian(double sigma)
 {
-    double GaussNum = 0.0;
-    int NumInSum = 10;
-    for(int i = 0; i < NumInSum; i++)
-    {
-        GaussNum += ((double)rand()/(double)RAND_MAX - 0.5);
-    }
-    GaussNum = GaussNum*sqrt((double)12/(double)NumInSum);
-
-
-    return GaussNum;
-
+  double GaussNum = 0.0;
+  int NumInSum = 10;
+  for(int i = 0; i < NumInSum; i++)
+  {
+    GaussNum += ((double)rand()/(double)RAND_MAX - 0.5);
+  }
+  GaussNum = GaussNum*sqrt((double)12/(double)NumInSum);
+  return GaussNum;
 }
 
-
-
-//=================================================
 double diffclock(clock_t clock1,clock_t clock2)
 {
-	double diffticks=clock1-clock2;
-	double diffms=(diffticks)/CLOCKS_PER_SEC;
-	return diffms;
+  double diffticks=clock1-clock2;
+  double diffms=(diffticks)/CLOCKS_PER_SEC;
+  return diffms;
 }
 
-//================================================
-//================================================================
 double get_new_x(double x, double dx){
+  double new_x;
+  // boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
+  double r = rand()/(double)(pow(2.,31)-1.);
 
-    double new_x;
-    // boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
-    double r = rand()/(double)(pow(2.,31)-1.);
-
-    if (r > 0.5){
-        new_x = x + rand()*dx/(double)(pow(2.,31)-1.);
-    } else {
-        new_x = x - rand()*dx/(double)(pow(2.,31)-1.);
-    }
-
-    return new_x;
-
+  if (r > 0.5){
+    new_x = x + rand()*dx/(double)(pow(2.,31)-1.);
+  } else {
+    new_x = x - rand()*dx/(double)(pow(2.,31)-1.);
+  }
+  return new_x;
 }
 
-
-//===============================================
 string string_wrap(string ins, int mode){
-
-    std::ostringstream s;
-
-    switch(mode){
-        case 0:
-            s << "\033[1;29m" << ins << "\033[0m";
-            break;
-        case 1:
-            s << "\033[1;34m" << ins << "\033[0m";
-            break;
-        case 2:
-            s << "\033[1;44m" << ins << "\033[0m";
-            break;
-        case 3:
-            s << "\033[1;35m" << ins << "\033[0m";
-            break;
-        case 4:
-            s << "\033[1;33;44m" << ins << "\033[0m";
-            break;
-        case 5:
-            s << "\033[1;47;34m" << ins << "\033[0m";
-            break;
-        case 6:
-            s << "\033[1;1;31m" << ins << "\033[0m";
-            break;
-        case 7:
-            s << "\033[1;1;33m" << ins << "\033[0m";
-            break;
-        case 8:
-            s << "\033[1;1;43;34m" << ins << "\033[0m";
-            break;
-        case 9:
-            s << "\033[1;1;37m" << ins << "\033[0m";
-            break;
-        case 10:
-            s << "\033[1;30;47m" << ins << "\033[0m";
-            break;
-        default:
-            s << ins;
-    }
-
-    return s.str();
+  std::ostringstream s;
+  switch(mode){
+  case 0:
+    s << "\033[1;29m" << ins << "\033[0m";
+    break;
+  case 1:
+    s << "\033[1;34m" << ins << "\033[0m";
+    break;
+  case 2:
+    s << "\033[1;44m" << ins << "\033[0m";
+    break;
+  case 3:
+    s << "\033[1;35m" << ins << "\033[0m";
+    break;
+  case 4:
+    s << "\033[1;33;44m" << ins << "\033[0m";
+    break;
+  case 5:
+    s << "\033[1;47;34m" << ins << "\033[0m";
+    break;
+  case 6:
+    s << "\033[1;1;31m" << ins << "\033[0m";
+    break;
+  case 7:
+    s << "\033[1;1;33m" << ins << "\033[0m";
+    break;
+  case 8:
+    s << "\033[1;1;43;34m" << ins << "\033[0m";
+    break;
+  case 9:
+    s << "\033[1;1;37m" << ins << "\033[0m";
+    break;
+  case 10:
+    s << "\033[1;30;47m" << ins << "\033[0m";
+    break;
+  default:
+    s << ins;
+  }
+  return s.str();
 }
 
-
-//===============================================
 string wrap_double(double val, int mode){
-
-    std::ostringstream s;
-    s << string_wrap(strDouble(val),mode);
-
-    return s.str();
+  std::ostringstream s;
+  s << string_wrap(strDouble(val),mode);
+  return s.str();
 }
 
-
-
-//===============================================
 const
 string i2string(int i){
-
-    std::ostringstream s;
-    s << "worker"
+  std::ostringstream s;
+  s << "worker"
     << lexical_cast<std::string>(i);
-
-    return s.str();
-
+  return s.str();
 }
 
-//===============================================
 char* i2char(int i){
-
-    std::ostringstream s;
-    s << "worker"
+  std::ostringstream s;
+  s << "worker"
     << lexical_cast<std::string>(i);
-
-    char* a=new char[s.str().size()+1];
-    memcpy(a,s.str().c_str(), s.str().size());
-
-    return a;
+  char* a=new char[s.str().size()+1];
+  memcpy(a,s.str().c_str(), s.str().size());
+  return a;
 }
 
-//================================================
-
 typedef struct {
   unsigned long size,resident,share,text,lib,data,dt;
 } statm_t;
@@ -253,13 +211,12 @@
     perror(statm_path);
     exit(99);
   }
-
   if(7 != fscanf(f,"%ld %ld %ld %ld %ld %ld %ld",
 		 &sp->size,&sp->resident,&sp->share,&sp->text,&sp->lib,&sp->data,&sp->dt))
-    {
-      perror(statm_path);
-      exit(99);
-    }
+  {
+    perror(statm_path);
+    exit(99);
+  }
   fclose(f);
 }
 
@@ -277,529 +234,522 @@
 	 MB(size), MB(resident), MB(share), MB(text), MB(lib), MB(data), MB(dt) );
 }
 
+timeval startTime, endTime;
+double elapsedTime;
+char timenow[100];
+
+char *now()
+{
+  timeval endTime;
+  double elapsedTime;
+
+  gettimeofday(&endTime, NULL);
+  elapsedTime = (endTime.tv_sec - startTime.tv_sec) * 1000.0;      // sec to ms
+  elapsedTime += (endTime.tv_usec - startTime.tv_usec) / 1000.0;   // us to ms
+  elapsedTime /= 1000.;
+  sprintf(timenow, "%10.3f", elapsedTime);
+  return(timenow);
+}
+
 //================================================
 
 class Universe {
 
 private:
 
-	double alpha_i;
-	double alpha_m;
-	double beta;
-	double gamma;
-	double delta;
+  double alpha_i;
+  double alpha_m;
+  double beta;
+  double gamma;
+  double delta;
 
-    double TargetNovelty;
-    double CumulativeRelativeLoss;
-    double CRLsquare;
-    string id;
+  double TargetNovelty;
+  double CumulativeRelativeLoss;
+  double CRLsquare;
+  string id;
 
 
-	int N_nodes;
-	int M_edges;
+  int N_nodes;
+  int M_edges;
 
-	int N_epochs;
-	int N_steps;
-	int N_repeats;
+  int N_epochs;
+  int N_steps;
+  int N_repeats;
 
-	int current_epoch;
-	double current_loss;
-	int current_repeat;
-    double current_novelty;
+  int current_epoch;
+  double current_loss;
+  int current_repeat;
+  double current_novelty;
 
-	int mode_identify_failed;
-    int verbose_level; // 0 is silent, higher is more
+  int mode_identify_failed;
+  int verbose_level; // 0 is silent, higher is more
 
-	double k_max;
+  double k_max;
 
-	graph_t Full_g;
+  graph_t Full_g;
 
 #define GraphRes float // was double
 
-	GraphRes **Prob;
-	GraphRes **Tried;
-	GraphRes **Dist;
-	GraphRes **Final;
-        GraphRes **EdgeIndex;
-	GraphRes *Rank;
+  GraphRes **Prob;
+  GraphRes **Tried;
+  GraphRes **Dist;
+  GraphRes **Final;
+  GraphRes **EdgeIndex;
+  GraphRes *Rank;
 
-    base_generator_type generator;
-    boost::uniform_real<> uni_dist;
-    boost::geometric_distribution<double> geo;
+  double max_loss;
 
+  base_generator_type generator;
+  boost::uniform_real<> uni_dist;
+  boost::geometric_distribution<double> geo;
+
 public:
 
+  //======  Constructor ======
+  Universe(const std::string FileToOpen, int Epochs, int Steps, int Repeats,
+	   int identify_failed, double target, const std::string idd) {
+    //typedef array_type2::index index2;
 
+    std::ifstream inFile;
+    //string line;
 
-	//======  Constructor ======
-	Universe(const std::string FileToOpen, int Epochs, int Steps, int Repeats, int identify_failed, double target, const std::string idd)
-	{
-		//typedef array_type2::index index2;
+    base_generator_type gene(42u);
+    generator = gene;
+    generator.seed(static_cast<unsigned int>(std::time(0)));
+    boost::uniform_real<> uni_d(0,1);
+    uni_dist = uni_d;
 
+    int i, k;
+    int x, y;
+    Edge* edge_array_mine;
+    int num_arcs_mine, num_nodes_mine;
+    int* weights_mine;
 
-		std::ifstream inFile;
-        //string line;
+    TargetNovelty = target;
+    CumulativeRelativeLoss = 0.;
+    CRLsquare = 0.;
 
-        //-------------------------------
+    N_epochs  = Epochs;
+    N_steps   = Steps;
+    N_repeats = Repeats;
 
-        base_generator_type gene(42u);
-        generator = gene;
-        generator.seed(static_cast<unsigned int>(std::time(0)));
-        boost::uniform_real<> uni_d(0,1);
-        uni_dist = uni_d;
+    current_epoch = 0;
+    current_loss = 0.;
+    current_repeat = 0;
 
-        //--------------------------------
+    id = idd;
 
-		int i, k;
-        int x, y;
-		Edge* edge_array_mine;
-		int num_arcs_mine, num_nodes_mine;
-		int* weights_mine;
+    verbose_level = 1;
+    mode_identify_failed = identify_failed;
 
-        TargetNovelty = target;
-        CumulativeRelativeLoss = 0.;
-        CRLsquare = 0.;
+    // The first pass though file with the graph
+    inFile.open(FileToOpen.c_str());
+    if (inFile.fail()) {
+      cout << "Unable to open file";
+      exit(1); // terminate with error
+    }else {
 
+      if (verbose_level > 2){
+	std::cout <<  " Opened <" << FileToOpen << ">"<<std::endl;
+      }
+    }
 
-		N_epochs  = Epochs;
-		N_steps   = Steps;
-		N_repeats = Repeats;
+    i=0;
+    std::string line;
+    //while (! inFile.eof() && ! inFile.fail()) {
+    while (1==1) {
 
-		current_epoch = 0;
-		current_loss = 0.;
-		current_repeat = 0;
+      inFile >> x;
+      inFile >> y;
 
-        id = idd;
+      if (verbose_level > 2){
+	std::cout << " x: " << x;
+	std::cout << " y: " << y << std::endl;
+      }
 
-        verbose_level = 1;
+      if (i==0){
+	N_nodes=x;
+	M_edges=y;
+	break;
+      }
+      i++;
+    }
+    inFile.close();
 
-		mode_identify_failed = identify_failed;
+    if (verbose_level == 2){
+      std::cout << N_nodes <<  " nodes, " << M_edges << " edges"<<std::endl;
+    }
 
+    // k_max is the longest distance possible
 
-		//-------------------------------
-		// The first pass though file with the graph
-		inFile.open(FileToOpen.c_str());
-		if (inFile.fail()) {
-			cout << "Unable to open file";
-			exit(1); // terminate with error
-		}else {
+    //k_max = M_edges;
+    k_max = 70;
 
-            if (verbose_level > 2){
-                std::cout <<  " Opened <" << FileToOpen << ">"<<std::endl;
-            }
-        }
+    //------------------------------------
+    // Get memory allocated for all class members
 
-		i=0;
-        std::string line;
-		//while (! inFile.eof() && ! inFile.fail()) {
-        while (1==1) {
+    Prob = allocate_2Dmatrix(N_nodes, N_nodes);
+    Tried = allocate_2Dmatrix(N_nodes, N_nodes);
+    Dist = allocate_2Dmatrix(N_nodes, N_nodes);
+    Final = allocate_2Dmatrix(N_nodes, N_nodes);
+    EdgeIndex = allocate_2Dmatrix(N_nodes, N_nodes);
+    Rank = allocate_1Dmatrix(N_nodes);
 
-            inFile >> x;
-            inFile >> y;
+    //The second pass through file with the graph
 
-            if (verbose_level > 2){
-                std::cout << " x: " << x;
-                std::cout << " y: " << y << std::endl;
-            }
+    for(int i = 0; i < N_nodes; ++i) {
+      Rank[i]=0.;
+      for(int j = 0; j < N_nodes; ++j) {
+	Final[i][j] = 0.;
+	Prob[i][j]=0.;
+	Dist[i][j]=-1.;
+	Tried[i][j]=0.;
+	EdgeIndex[i][j]=-1;
+      }
+    }
 
-			if (i==0){
-				N_nodes=x;
-				M_edges=y;
-                break;
-			}
-			i++;
+    // Fill in the final graph -- and we are ready to go!
 
+    inFile.open(FileToOpen.c_str());
+    if (!inFile) {
+      std::cout << "Unable to open file";
+      exit(1); // terminate with error
+    }
+    else {
+      if (verbose_level > 2){
+	std::cout <<  " Opened <" << FileToOpen << ">"<<std::endl;
+      }
+    }
+    i=0;
+    while (inFile >> x && inFile >>y) {
+      if (i > 0) {
+	Final[x][y]=1.;
+	Final[y][x]=1.;
+	if (verbose_level == 2){
+	  std::cout << ".";
+	}
+      }
+      i++;
+    }
+    if (verbose_level == 2){
+      std::cout << std::endl;
+    }
+    inFile.close();
+    k=0;
+    for (int i=0; i<N_nodes-1; i++){
+      for (int j=i+1;j<N_nodes; j++){
+	if(Final[i][j] > 0.){
+	  EdgeIndex[i][j]=k;
+	  k++;
+	}
+      }
+    }
 
-		}
-		inFile.close();
+    // create graph -- hopefully, we can keep it, just modifying edge weights
 
-        if (verbose_level == 2){
-            std::cout << N_nodes <<  " nodes, " << M_edges << " edges"<<std::endl;
-        }
+    edge_array_mine = new Edge[2*M_edges];
+    num_arcs_mine = 2*M_edges;
+    num_nodes_mine = N_nodes;
+    weights_mine = new int[2*M_edges];
+    for (int i=0; i<2*M_edges; i++){ weights_mine[i]=1;}
 
-		// k_max is the longest distance possible
+    k=0;
+    for(int i=0; i<N_nodes-1; i++){
+      for( int j=i+1; j<N_nodes; j++){
+	if (Final[i][j]>0.){
+	  edge_array_mine[2*k]  =Edge(i,j);
+	  edge_array_mine[2*k+1]=Edge(j,i);
+	  k++;
+	}
+      }
+    }
+    graph_t g(edge_array_mine, edge_array_mine + num_arcs_mine, weights_mine, num_nodes_mine);
 
-        //k_max = M_edges;
-		k_max = 70;
+    Full_g = g;
+    delete edge_array_mine;
+    delete weights_mine;
 
-		//------------------------------------
-		// Get memory allocated for all class members
+    std::vector<edge_descriptor> p(num_edges(Full_g));
+    std::vector<int> d(num_edges(Full_g));
+    edge_descriptor s;
+    boost::graph_traits<graph_t>::vertex_descriptor u, v;
 
-		Prob = allocate_2Dmatrix(N_nodes, N_nodes);
-		Tried = allocate_2Dmatrix(N_nodes, N_nodes);
-		Dist = allocate_2Dmatrix(N_nodes, N_nodes);
-		Final = allocate_2Dmatrix(N_nodes, N_nodes);
-        EdgeIndex = allocate_2Dmatrix(N_nodes, N_nodes);
-		Rank = allocate_1Dmatrix(N_nodes);
+    for (int i=0; i<N_nodes-1; i++){
+      for (int j=i+1; j<N_nodes; j++){
+	if (Final[i][j] > 0.){
+	  u = vertex(i, Full_g);
+	  v = vertex(j, Full_g);
+	  remove_edge(u,v,Full_g);
+	  remove_edge(v,u,Full_g);
 
-        //The second pass through file with the graph
+	}
+      }
+    }
+    set_max_loss();
+  }
 
-		for(int i = 0; i < N_nodes; ++i) {
-			Rank[i]=0.;
-			for(int j = 0; j < N_nodes; ++j) {
-				Final[i][j] = 0.;
-				Prob[i][j]=0.;
-				Dist[i][j]=-1.;
-				Tried[i][j]=0.;
-                EdgeIndex[i][j]=-1;
-			}
-		}
+  void set_max_loss() {
+    // Based on formulas from random_analytical.pdf
+    // (9): E[RLt] = (1/t) * SUM(i=0 to T of: (V*(V-1) / (2 * (E-i))
+    // (12) Var[RLt] = 1 / (T**2) * SUM( i=0 to T of: ((V*(V-1))/2) - E + 1 ) / ((E-i)**2)
+    // (9) + 3sigma = E[RLt] + 3 * SQRT(Var)
 
+    int E = M_edges;
+    int V = N_nodes;
+    int T = TargetNovelty;
+    double sum, ERLt, VarRLt;
 
-		// Fill in the final graph -- and we are ready to go!
+    sum = 0;
+    for(int i=0;i<=T;i++) {
+      sum += (V*(V-1)) / (2*(E-i));
+    }
+    ERLt = (1.0/T) * sum;
 
-	    inFile.open(FileToOpen.c_str());
-		if (!inFile) {
-            std::cout << "Unable to open file";
-			exit(1); // terminate with error
-		}
-		else {
-
-            if (verbose_level > 2){
-                std::cout <<  " Opened <" << FileToOpen << ">"<<std::endl;
-            }
-        }
-
-		i=0;
-		while (inFile >> x && inFile >>y) {
-			if (i > 0) {
-				Final[x][y]=1.;
-				Final[y][x]=1.;
-
-
-                if (verbose_level == 2){
-                    std::cout << ".";
-                }
-			}
-			i++;
-
-		}
-        if (verbose_level == 2){
-            std::cout << std::endl;
-        }
-		inFile.close();
-
-        k=0;
-        for (int i=0; i<N_nodes-1; i++){
-            for (int j=i+1;j<N_nodes; j++){
-                if(Final[i][j] > 0.){
-                    EdgeIndex[i][j]=k;
-                    k++;
-                }
-            }
-        }
-
-
-
-		//+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-		// create graph -- hopefully, we can keep it, just modifying edge weights
-
-
-		edge_array_mine = new Edge[2*M_edges];
-		num_arcs_mine = 2*M_edges;
-		num_nodes_mine = N_nodes;
-		weights_mine = new int[2*M_edges];
-		for (int i=0; i<2*M_edges; i++){ weights_mine[i]=1;}
-
-		k=0;
-		for(int i=0; i<N_nodes-1; i++){
-			for( int j=i+1; j<N_nodes; j++){
-				if (Final[i][j]>0.){
-					edge_array_mine[2*k]  =Edge(i,j);
-					edge_array_mine[2*k+1]=Edge(j,i);
-					k++;
-				}
-			}
-		}
-		graph_t g(edge_array_mine, edge_array_mine + num_arcs_mine, weights_mine, num_nodes_mine);
-
-		Full_g = g;
-		delete edge_array_mine;
-		delete weights_mine;
-
-		//===========================================================================
-		std::vector<edge_descriptor> p(num_edges(Full_g));
-		std::vector<int> d(num_edges(Full_g));
-		edge_descriptor s;
-		boost::graph_traits<graph_t>::vertex_descriptor u, v;
-
-		for (int i=0; i<N_nodes-1; i++){
-			for (int j=i+1; j<N_nodes; j++){
-				if (Final[i][j] > 0.){
-					u = vertex(i, Full_g);
-					v = vertex(j, Full_g);
-					remove_edge(u,v,Full_g);
-					remove_edge(v,u,Full_g);
-
-				}
-			}
-		}
-
-
+    sum = 0;
+    for(int i=0;i<=T;i++) {
+      sum += (((V*(V-1))/2.0) - E + 1.0 ) / ((E-i)*(E-i));
     }
+    VarRLt = (1.0 / (T*T)) * sum;
+    max_loss = ERLt + (3.0 * sqrt(VarRLt));
+    cout << "set_max_loss: V=" << V << " E=" << E << " T=" << T << "  ERLt=" << ERLt << " VarRLt=" << VarRLt << " max_loss=" << max_loss << endl;
+  }
 
+  int sample_failed_number(double pfail) {
 
-	//=====================================================================
-	int sample_failed_number(double pfail){
+    //boost::geometric_distribution<double> geo(pfail);
+    //boost::variate_generator<base_generator_type&, geometric_distribution<double> > geom(generator, geo);
 
-		//boost::geometric_distribution<double> geo(pfail);
-		//boost::variate_generator<base_generator_type&, geometric_distribution<double> > geom(generator, geo);
+    double r, u, g;
 
-		double r, u, g;
+    r=0.;
+    for(int i=0; i<N_steps; i++){
 
-        r=0.;
-		for(int i=0; i<N_steps; i++){
+      u=(double)rand();
+      u = 1.-u /(double)(pow(2.,31)-1.);
+      g=(int)(ceil(log(u) / log(pfail)));
 
-            u=(double)rand();
-            u = 1.-u /(double)(pow(2.,31)-1.);
-            g=(int)(ceil(log(u) / log(pfail)));
+      //r += geom();
 
-			//r += geom();
-
-            r+=g;
-		}
-
-        if (verbose_level>=3){
-            std::cout << id << " failed " << r << std::endl;
-		}
-	return (int) round(r);  // FIXME: Andrey: please verify that round() is correct.
-
-	}
-
-    //=============================================
-    double get_target(void){
-        return TargetNovelty;
+      r+=g;
     }
 
-    //=============================================
-    void set_target(double target){
-        TargetNovelty=target;
+    if (verbose_level>=3){
+      std::cout << id << " failed " << r << std::endl;
     }
+    return (int) round(r);  // FIXME: Andrey: please verify that round() is correct.
 
-	//=============================================
-	int sample(){
+  }
 
-        //boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
-        // double r = uni(), Summa = 0.;
+  double get_target(void){
+    return TargetNovelty;
+  }
 
+  void set_target(double target){
+    TargetNovelty=target;
+  }
 
+  int sample(){
 
-        double r = rand(), Summa = 0.;
-        r /= (double)(pow(2.,31)-1.);
-		int result = 0;
-		int finished = 0;
+    //boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
+    // double r = uni(), Summa = 0.;
+    double r = rand(), Summa = 0.;
+    r /= (double)(pow(2.,31)-1.);
+    int result = 0;
+    int finished = 0;
 
-        if (verbose_level==4){
-            std::cout << id << " sampled " << r << std::endl;
-        }
+    if (verbose_level==4){
+      std::cout << id << " sampled " << r << std::endl;
+    }
 
-		for(int i=0; i<N_nodes-1 && finished==0; i++){
-			for( int j=i+1; j<N_nodes && finished==0; j++){
-
-				Summa += Prob[i][j];
-
-				if (Summa > r){
-
-					Tried[i][j]+=1.;
-
-					if (Final[i][j] > 0.){
-						result = 1;
-					}
-					finished = 1;
-				}
-			}
-		}
-
-		return result;
-
+    for (int i=0; i<N_nodes-1 && finished==0; i++) {
+      for ( int j=i+1; j<N_nodes && finished==0; j++) {
+	Summa += Prob[i][j];
+	if (Summa > r){
+	  Tried[i][j]+=1.;
+	  if (Final[i][j] > 0.){
+	    result = 1;
+	  }
+	  finished = 1;
 	}
+      }
+    }
+    return result;
+  }
 
-	//===============================
-	void update_current_graph(void){
 
-		std::vector<edge_descriptor> p(num_edges(Full_g));
-		std::vector<int> d(num_edges(Full_g));
-		edge_descriptor s;
-		boost::graph_traits<graph_t>::vertex_descriptor u, v;
+  void update_current_graph(void){
 
-		//property_map<graph_t, edge_weight_t>::type weightmap = get(edge_weight, Full_g);
-		for (int i=0; i<N_nodes-1; i++){
-			for (int j=i+1; j<N_nodes; j++){
-				if (Final[i][j] > 0. && Tried[i][j]>0){
-					//s = edge(i, j, Full_g);
-					boost::graph_traits<graph_t>::edge_descriptor e1,e2;
-					bool found1, found2;
-					u = vertex(i, Full_g);
-					v = vertex(j, Full_g);
-					tie(e1, found1) = edge(u, v, Full_g);
-					tie(e2, found2) = edge(v, u, Full_g);
-					if (!found1 && !found2){
-						add_edge(u,v,1,Full_g);
-					    add_edge(v,u,1,Full_g);
-					}
+    std::vector<edge_descriptor> p(num_edges(Full_g));
+    std::vector<int> d(num_edges(Full_g));
+    edge_descriptor s;
+    boost::graph_traits<graph_t>::vertex_descriptor u, v;
 
-				}
-			}
+    //property_map<graph_t, edge_weight_t>::type weightmap = get(edge_weight, Full_g);
+    for (int i=0; i<N_nodes-1; i++){
+      for (int j=i+1; j<N_nodes; j++){
+	if (Final[i][j] > 0. && Tried[i][j]>0){
+	  //s = edge(i, j, Full_g);
+	  boost::graph_traits<graph_t>::edge_descriptor e1,e2;
+	  bool found1, found2;
+	  u = vertex(i, Full_g);
+	  v = vertex(j, Full_g);
+	  tie(e1, found1) = edge(u, v, Full_g);
+	  tie(e2, found2) = edge(v, u, Full_g);
+	  if (!found1 && !found2){
+	    add_edge(u,v,1,Full_g);
+	    add_edge(v,u,1,Full_g);
+	  }
 
-		}
 	}
+      }
 
-	//===============================
-	void update_distances(void){
-		// put shortest paths to the *Dist[][]
-		std::vector<vertex_descriptor> p(num_vertices(Full_g));
-		std::vector<int> d(num_vertices(Full_g));
-		vertex_descriptor s;
+    }
+  }
 
+  void update_distances(void){
+    // put shortest paths to the *Dist[][]
+    std::vector<vertex_descriptor> p(num_vertices(Full_g));
+    std::vector<int> d(num_vertices(Full_g));
+    vertex_descriptor s;
 
-		// put shortest paths to the *Dist[][]
-		for (int j=0; j<num_vertices(Full_g); j++){
-
-			if(Rank[j] > 0.){
-				s = vertex(j, Full_g);
-				dijkstra_shortest_paths(Full_g, s, predecessor_map(&p[0]).distance_map(&d[0]));
-
-				//std::cout <<" Vertex "<< j << std::endl;
-				graph_traits < graph_t >::vertex_iterator vi, vend;
-
-				for (boost::tie(vi, vend) = vertices(Full_g); vi != vend; ++vi) {
-
-					if (p[*vi]!=*vi){
-						Dist[*vi][j]=d[*vi];
-						Dist[j][*vi]=d[*vi];
-
-						if ( (int)round(Dist[*vi][j]>max_dist)) {
-						  // FIXME: Andrey: please verify that (int) cast is correct. Do we need to round()?
-						  // also, the indent on this iff statement was way off -
-						  // perhaps due to space v. tab?
-						  max_dist=(int)round(Dist[*vi][j]);
-						}
-
-
-					} else {
-						Dist[*vi][j]=-1.;
-						Dist[j][*vi]=-1.;
-					}
-				}
-			}
-
-		}
-
-
+    // put shortest paths to the *Dist[][]
+    for (int j=0; j<num_vertices(Full_g); j++){
+      if(Rank[j] > 0.){
+	s = vertex(j, Full_g);
+	dijkstra_shortest_paths(Full_g, s, predecessor_map(&p[0]).distance_map(&d[0]));
+	//std::cout <<" Vertex "<< j << std::endl;
+	graph_traits < graph_t >::vertex_iterator vi, vend;
+	for (boost::tie(vi, vend) = vertices(Full_g); vi != vend; ++vi) {
+	  if (p[*vi]!=*vi){
+	    Dist[*vi][j]=d[*vi];
+	    Dist[j][*vi]=d[*vi];
+	    if ( (int)round(Dist[*vi][j]>max_dist)) {
+	      // FIXME: Andrey: please verify that (int) cast is correct. Do we need to round()?
+	      // also, the indent on this iff statement was way off -
+	      // perhaps due to space v. tab?
+	      max_dist=(int)round(Dist[*vi][j]);
+	    }
+	  } else {
+	    Dist[*vi][j]=-1.;
+	    Dist[j][*vi]=-1.;
+	  }
 	}
+      }
+    }
+  }
 
-	//======================================================
-	void update_ranks(void){
 
-		for(int i=0; i<N_nodes; i++){
-			Rank[i]=0.;
-		}
+  void update_ranks(void){
 
-		for(int i=0; i<N_nodes-1; i++){
-			for( int j=i+1; j<N_nodes; j++){
-				if (Tried[i][j]>0. && Final[i][j] >0.){
-					Rank[i]++;
-					Rank[j]++;
-				}
-			}
-		}
+    for(int i=0; i<N_nodes; i++){
+      Rank[i]=0.;
+    }
 
+    for(int i=0; i<N_nodes-1; i++){
+      for( int j=i+1; j<N_nodes; j++){
+	if (Tried[i][j]>0. && Final[i][j] >0.){
+	  Rank[i]++;
+	  Rank[j]++;
 	}
+      }
+    }
 
-	//====================================================================
-	void set_world(double a_i, double a_m, double b, double g, double d){
+  }
 
-		alpha_i=a_i;
-		alpha_m=a_m;
-		gamma=g;
-		beta=b;
-		delta=d;
+  //====================================================================
+  void set_world(double a_i, double a_m, double b, double g, double d){
 
-	}
+    alpha_i=a_i;
+    alpha_m=a_m;
+    gamma=g;
+    beta=b;
+    delta=d;
 
-	//====================================================================
-	void reset_world(){
+  }
 
-        //====================================================
-		std::vector<edge_descriptor> p(num_edges(Full_g));
-		std::vector<int> d(num_edges(Full_g));
-		edge_descriptor s;
-		boost::graph_traits<graph_t>::vertex_descriptor u, v;
+  //====================================================================
+  void reset_world(){
 
+    //====================================================
+    std::vector<edge_descriptor> p(num_edges(Full_g));
+    std::vector<int> d(num_edges(Full_g));
+    edge_descriptor s;
+    boost::graph_traits<graph_t>::vertex_descriptor u, v;
 
-		for (int i=0; i<N_nodes-1; i++){
-			for (int j=i+1; j<N_nodes; j++){
-				if (Final[i][j] > 0. && Tried[i][j] > 0){
-					u = vertex(i, Full_g);
-					v = vertex(j, Full_g);
-					remove_edge(u,v,Full_g);
-					remove_edge(v,u,Full_g);
 
-				}
-			}
-		}
+    for (int i=0; i<N_nodes-1; i++){
+      for (int j=i+1; j<N_nodes; j++){
+	if (Final[i][j] > 0. && Tried[i][j] > 0){
+	  u = vertex(i, Full_g);
+	  v = vertex(j, Full_g);
+	  remove_edge(u,v,Full_g);
+	  remove_edge(v,u,Full_g);
 
-        //==================================================
+	}
+      }
+    }
 
-		current_loss=0;
-		current_epoch=0;
-		current_repeat++;
-        current_novelty=0;
+    //==================================================
 
-		for(int i = 0; i < N_nodes; ++i) {
-			Rank[i]=0.;
-			for(int j = 0; j < N_nodes; ++j) {
-				Prob[i][j]=0.;
-				Dist[i][j]=-1.;
-				Tried[i][j]=0.;
-			}
-		}
-	}
+    current_loss=0;
+    current_epoch=0;
+    current_repeat++;
+    current_novelty=0;
 
+    for(int i = 0; i < N_nodes; ++i) {
+      Rank[i]=0.;
+      for(int j = 0; j < N_nodes; ++j) {
+	Prob[i][j]=0.;
+	Dist[i][j]=-1.;
+	Tried[i][j]=0.;
+      }
+    }
+  }
 
-    //==============================================
-    void show_parameters(void){
 
-        std::cout << "Parameters: "
-        << alpha_i << " "
-        << alpha_m << " | "
-        << beta << " "
-        << gamma << " | "
-        << delta << std::endl;
+  //==============================================
+  void show_parameters(void){
 
-    }
+    std::cout << "Parameters: "
+	      << alpha_i << " "
+	      << alpha_m << " | "
+	      << beta << " "
+	      << gamma << " | "
+	      << delta << std::endl;
 
+  }
 
 
-    //===============================================
-    string file_name(){
 
-        std::ostringstream s;
-        s << "world_"
-        << lexical_cast<std::string>(alpha_i) << "_"
-        << lexical_cast<std::string>(alpha_m) << "_"
-        << lexical_cast<std::string>(beta) << "_"
-        << lexical_cast<std::string>(gamma) << "_"
-        << lexical_cast<std::string>(delta) << "_"
-        << lexical_cast<std::string>(N_epochs) << "_"
-        << lexical_cast<std::string>(N_steps) << "_"
-        << lexical_cast<std::string>(N_repeats) << ".txt";
+  //===============================================
+  string file_name(){
 
-        return s.str();
+    std::ostringstream s;
+    s << "world_"
+      << lexical_cast<std::string>(alpha_i) << "_"
+      << lexical_cast<std::string>(alpha_m) << "_"
+      << lexical_cast<std::string>(beta) << "_"
+      << lexical_cast<std::string>(gamma) << "_"
+      << lexical_cast<std::string>(delta) << "_"
+      << lexical_cast<std::string>(N_epochs) << "_"
+      << lexical_cast<std::string>(N_steps) << "_"
+      << lexical_cast<std::string>(N_repeats) << ".txt";
 
-    }
+    return s.str();
 
+  }
 
 
 
-    //=================================================
-    void set_verbose(int verbose){
 
-        verbose_level = verbose;
-    }
+  //=================================================
+  void set_verbose(int verbose){
 
+    verbose_level = verbose;
+  }
 
-    //=============================================================
+
+  //=============================================================
   void update_probabilities(void){
 
 
@@ -807,13 +757,11 @@
     // Compute sampling probabilities
     // first pass: \xi_i,j
     int i, j;
-    //#pragma omp parallel for private (j)
-    //#pragma omp parallel for 
 
-    //    #pragma omp parallel for default(none) shared( Prob, alpha_i, alpha_m, beta, k_max, gamma, delta, Rank, Dist) private(i,j)
-    #pragma omp parallel for private(i,j)
+    std::cout << now() << " pass1 update_probabilities" << std::endl;
 
     for( i=0; i<N_nodes-1; i++){
+#pragma omp parallel for private(j)
       for(  j=i+1; j<N_nodes; j++){
 
 	double bg = 0.;
@@ -838,686 +786,441 @@
       }
     }
 
+    std::cout << now() << " pass2 update_probabilities" << std::endl;
 
     // second pass: sum
     double Summa = 0.;
 
-    #pragma omp parallel
+// pragma omp parallel
     for(i=0; i<N_nodes-1; i++){
       for(j=i+1; j<N_nodes; j++){
 	Summa += Prob[i][j];
       }
     }
 
+    std::cout << now() << " pass3 update_probabilities" << std::endl;
+
     // third pass: normalize
-    #pragma omp parallel 
     for( i=0; i<N_nodes-1; i++){
-      for(  j=i+1; j<N_nodes; j++){
+#pragma omp parallel for private(j)
+      for( j=i+1; j<N_nodes; j++){
 	Prob[i][j] /= Summa;
       }
     }
 
+    std::cout << now() << " exit  update_probabilities" << std::endl;
   }
 
-	// Now we are ready for simulations
-	//==============================================
-	void update_world(){
+  // Now we are ready for simulations
+  //==============================================
+  void update_world(){
 
-		int failed = 0;
+    int failed = 0;
 
-		// Given current universe compute shortest paths
-		//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    // Given current universe compute shortest paths
+    //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-std::cout << "Before updates" << std::endl;
-		update_current_graph();
-std::cout << "after current" << std::endl;
-		update_ranks();
-std::cout << "after ranks" << std::endl;
-		update_distances();
-std::cout << "after distances" << std::endl;
-		update_probabilities();
-std::cout << "after probs" << std::endl;
+    std::cout << now() << " Before updates" << std::endl;
+    update_current_graph();
+    std::cout << now() << " after current" << std::endl;
+    update_ranks();
+    std::cout << now() << " after ranks" << std::endl;
+    update_distances();
+    std::cout << now() << " after distances" << std::endl;
+    update_probabilities();
+    std::cout << now() << " after probs" << std::endl;
 
-		//===============================
-		// sampling
-		int result;
-		double cost=0., novel=0.;
-		int publishable = 0;
+    // sampling
+    int result;
+    double cost=0., novel=0.;
+    int publishable = 0;
 
+    if (mode_identify_failed == 1){
+      while(publishable < N_steps){
+	std::cout << now() << " failed:1 before sample\n";
+	result = sample();
+	std::cout << now() << " failed:1 after sample\n";
+	publishable += result;
+	failed += (1-result);
+      }
 
-		//^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-		if (mode_identify_failed == 1){
+      std::cout << now() << " failed:1 before for\n";
+      for(int i=0; i<N_nodes-1; i++){
+	int j;
+        #pragma omp parallel for private(j)
+	for( j=i+1; j<N_nodes; j++){
 
-			while(publishable < N_steps){
+	  cost+=Tried[i][j];
 
-std::cout << "failed:1 before sample\n";
-		    	result = sample();
-std::cout << "failed:1 after sample\n";
-			    publishable += result;
-			    failed += (1-result);
+	  if (Tried[i][j]>0. && Final[i][j]>0.){
+	    novel+=1.;
+	    std::cout << now() << " failed:1 novel: " << novel << std::endl;
+	  }
+	}
+      }
+      std::cout << now() << " failed:1 after for\n";
+    }
+    else {
+      double pfail=0.;
+      int n_failed;
+      //, n_check = 0;
 
-			}
-
-std::cout << "failed:1 before for\n";
-			for(int i=0; i<N_nodes-1; i++){
-				for( int j=i+1; j<N_nodes; j++){
-
-					cost+=Tried[i][j];
-
-					if (Tried[i][j]>0. && Final[i][j]>0.){
-						novel+=1.;
-std::cout << "failed:1 novel: " << novel << std::endl;
-					}
-				}
-			}
-std::cout << "failed:1 after for\n";
-
-		}
-		//^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-		else {
-
-			double pfail=0.;
-			int n_failed;
-			//, n_check = 0;
-
-std::cout << "failed:0 before for\n";
-			for(int i=0; i<N_nodes-1; i++){
-				for( int j=i+1; j<N_nodes; j++){
-					if (Final[i][j] == 0.){
-						pfail += Prob[i][j];
-						Prob[i][j] = 0.;
-					}
-
-				}
-			}
-
-			for(int i=0; i<N_nodes-1; i++){
-				for( int j=i+1; j<N_nodes; j++){
-					Prob[i][j] /= (1.-pfail);
-				}
-				//std::cout << std::endl;
-			}
-
-std::cout << "failed:0 after for\n";
-			n_failed = sample_failed_number(pfail);
-
-
-std::cout << "failed:0 before while\n";
-			while(publishable < N_steps){
-
-		    	result = sample();
-			    publishable += result;
-			}
-std::cout << "failed:0 after while\n";
-
-
-			current_loss += (n_failed + N_steps);
-			cost = current_loss;
-
-			for(int i=0; i<N_nodes-1; i++){
-				for( int j=i+1; j<N_nodes; j++){
-
-					if (Tried[i][j]>0. && Final[i][j]>0.){
-						novel+=1.;
-std::cout << "failed:0 novel: " << novel << std::endl;
-
-					}
-				}
-			}
-		}
-
-        current_novelty = novel;
-
-
-		//^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-verbose_level = 2;
-		if (verbose_level == 2){
-            std::cout << (current_repeat+1) << "  epoch=" << (current_epoch+1)
-
-		    << "  cost=" << cost
-		    << " novel=" << novel
-		    << " rel_loss=" << cost/novel
-		    << std::endl;
-        }
-
-		current_epoch++;
+      std::cout << now() << " failed:0 before for\n";
+      for (int i=0; i<N_nodes-1; i++) {
+	int j;
+	// #pragma omp parallel for private(j)
+	for (int j=i+1; j<N_nodes; j++) {
+	  if (Final[i][j] == 0.) {
+	    pfail += Prob[i][j];
+	    Prob[i][j] = 0.;
+	  }
 	}
+      }
 
-
-	//======  Destructor ======
-	~Universe(){
-
-		delete_2Dmatrix(Final, N_nodes);
-		delete_2Dmatrix(Dist, N_nodes);
-		delete_2Dmatrix(Tried, N_nodes);
-		delete_2Dmatrix(Prob, N_nodes);
-        delete_2Dmatrix(EdgeIndex, N_nodes);
-		delete_1Dmatrix(Rank);
+      for(int i=0; i<N_nodes-1; i++){
+	int j;
+	// #pragma omp parallel for private(j)
+	for(j=i+1; j<N_nodes; j++){
+	  Prob[i][j] /= (1.-pfail);
 	}
+	//std::cout << std::endl;
+      }
 
-    //================================================
-    // Allocate memory
-    double** allocate_2Dmatrix_double(int N, int M)
-    {
-        double **pointer;
+      std::cout << now() << " failed:0 after for\n";
+      n_failed = sample_failed_number(pfail);
+      std::cout << now() << " failed:0 before while\n";
+      while(publishable < N_steps){
+	result = sample();
+	publishable += result;
+      }
+      std::cout << now() << " failed:0 after while\n";
 
-        if (verbose_level == 2){
-            std::cout<< "["<<N<<"|"<<M<<"]"<<std::endl;
-        }
-        pointer = new double*[N];
-        for (int i = 0; i < N; ++i)
-            pointer[i] = new double[M];
+      current_loss += (n_failed + N_steps);
+      cost = current_loss;
 
-        return pointer;
+      for(int i=0; i<N_nodes-1; i++){
+	for( int j=i+1; j<N_nodes; j++){
+	  if (Tried[i][j]>0. && Final[i][j]>0.){
+	    novel+=1.;
+	    std::cout << now() << " failed:0 novel: " << novel << std::endl;
+	  }
+	}
+      }
     }
-    // Allocate memory
-    GraphRes** allocate_2Dmatrix(int N, int M)
-    {
-        GraphRes **pointer;
+    current_novelty = novel;
 
-        if (verbose_level == 2){
-            std::cout<< "["<<N<<"|"<<M<<"]"<<std::endl;
-        }
-        pointer = new GraphRes*[N];
-        for (int i = 0; i < N; ++i)
-            pointer[i] = new GraphRes[M];
-
-        return pointer;
+    verbose_level = 2;
+    if (verbose_level == 2) {
+      std::cout << (current_repeat+1) << "  epoch=" << (current_epoch+1)
+		<< "  cost=" << cost
+		<< " novel=" << novel
+		<< " rel_loss=" << cost/novel
+		<< std::endl;
     }
-    //===================
-    GraphRes* allocate_1Dmatrix(int N)
-    {
-        GraphRes *pointer;
+    current_epoch++;
+  }
 
-        if(N > 0){
+  //======  Destructor ======
+  ~Universe(){
+    delete_2Dmatrix(Final, N_nodes);
+    delete_2Dmatrix(Dist, N_nodes);
+    delete_2Dmatrix(Tried, N_nodes);
+    delete_2Dmatrix(Prob, N_nodes);
+    delete_2Dmatrix(EdgeIndex, N_nodes);
+    delete_1Dmatrix(Rank);
+  }
 
-            pointer = new GraphRes[N];
-
-        }else {
-
-            pointer = NULL;
-        }
-
-        return pointer;
-
+  // Allocate memory
+  double** allocate_2Dmatrix_double(int N, int M) {
+    double **pointer;
+    
+    if (verbose_level == 2){
+      std::cout<< "["<<N<<"|"<<M<<"]"<<std::endl;
     }
+    pointer = new double*[N];
+    for (int i = 0; i < N; ++i)
+      pointer[i] = new double[M];
+    
+    return pointer;
+  }
+  
+  // Allocate memory
+  GraphRes** allocate_2Dmatrix(int N, int M) {
+    GraphRes **pointer;
 
-    //==============================================
-    // De-Allocate memory to prevent memory leak
-    void delete_2Dmatrix_double(double **pointer, int N){
-
-        if (pointer != NULL){
-
-            for (int i = 0; i < N; ++i){
-                delete [] pointer[i];
-            }
-            delete [] pointer;
-        }
+    if (verbose_level == 2){
+      std::cout<< "["<<N<<"|"<<M<<"]"<<std::endl;
     }
-    void delete_2Dmatrix(GraphRes **pointer, int N){
+    pointer = new GraphRes*[N];
+    for (int i = 0; i < N; ++i)
+      pointer[i] = new GraphRes[M];
 
-        if (pointer != NULL){
+    return pointer;
+  }
 
-            for (int i = 0; i < N; ++i){
-                delete [] pointer[i];
-            }
-            delete [] pointer;
-        }
+  GraphRes* allocate_1Dmatrix(int N) {
+    GraphRes *pointer;
+    if(N > 0){
+      pointer = new GraphRes[N];
+    }else {
+      pointer = NULL;
     }
-    //====================
-    void delete_1Dmatrix(GraphRes *pointer){
+    return pointer;
+  }
 
-        delete [] pointer;
-    }
+  // De-Allocate memory to prevent memory leak
 
-    //===========================================
-    double get_rel_loss(){
-
-        return CumulativeRelativeLoss ;
+  void delete_2Dmatrix_double(double **pointer, int N) {
+    if (pointer != NULL){
+      for (int i = 0; i < N; ++i){
+	delete [] pointer[i];
+      }
+      delete [] pointer;
     }
+  }
 
-    //===========================================
-    double get_rel_loss_err(){
+  void delete_2Dmatrix(GraphRes **pointer, int N) {
+    if (pointer != NULL){
 
-        return CRLsquare ;
+      for (int i = 0; i < N; ++i){
+	delete [] pointer[i];
+      }
+      delete [] pointer;
     }
+  }
 
+  void delete_1Dmatrix(GraphRes *pointer) {
+    delete [] pointer;
+  }
 
+  double get_rel_loss() {
+    return CumulativeRelativeLoss ;
+  }
 
-    //==================================================================================
-    void evolve_to_target_and_save(int istart, int iend, double* storage, int* counters){
+  double get_rel_loss_err() {
+    return CRLsquare ;
+  }
 
-        double ALOT=100000000000.;
-        double ratio = 0.0;
-        int check = 0;
+  void evolve_to_target_and_save(int istart, int iend, double* storage, int* counters) {
+    double ALOT=100000000000.;
+    double ratio = 0.0;
 
-        reset_world();
+    reset_world();
+    for (int k = istart; k < iend; k++){
+      for(int i=0; i< N_epochs &&  current_novelty < TargetNovelty; i++){
+	if(ratio < max_loss) {
+	  update_world();
+	}
+	else{
+	  break;
+	}
+	ratio = current_loss/current_novelty;
+      }
+      if (ratio < max_loss) {
+	storage[k]=current_loss/current_novelty;
+      }
+      else{
+	storage[k]=ALOT;
+      }
+      counters[k]=1;
+      reset_world();
+    }
+  }
 
-        for (int k = istart; k < iend; k++){
+  double Omax_loss_value(int tn) {
+    if( tn == 58 )           return 128.286;
+    else if( tn == 108 )     return 131.866;
+    else if( tn == 158 )     return 135.551;
+    else if( tn == 208 )     return 139.694;
+    else if( tn == 258 )     return 144.163;
+    else if( tn == 308 )     return 148.967;
+    else if( tn == 358 )     return 154.201;
+    else if( tn == 408 )     return 159.962;
+    else if( tn == 458 )     return 166.441;
+    else if( tn == 508 )     return 173.655;
+    else if( tn == 558 )     return 181.921;
+    else if( tn == 608 )     return 191.246;
+    else if( tn == 658 )     return 202.150;
+    else if( tn == 708 )     return 215.197;
+    else if( tn == 758 )     return 202.150;  // Verify with Andrey. Same as TargetNovelty of 658
+    else if( tn == 808 )     return 251.698;
+    else if( tn == 858 )     return 279.201;
+    else if( tn == 908 )     return 320.112;
+    else if( tn == 958 )     return 394.774;
+    else if( tn == 1008 )    return 1052.38;  // Huge number here. Why?
+    else                      return 10000.;   /* Pray that this does not occur. Ask Andrey what to do */
+  }
 
-            for(int i=0; i< N_epochs &&  current_novelty < TargetNovelty; i++){
-
-                if(ratio < max_loss_value((int)TargetNovelty)){
-                    update_world();
-                }
-                else{
-                    check = 1;
-                    break;
-                }
-                ratio = current_loss/current_novelty;
-            }
-            if( check ){
-                storage[k]=ALOT;
-            }
-            else{
-                storage[k]=current_loss/current_novelty;
-            }
-            counters[k]=1;
-
-            reset_world();
-        }
-
+  double max_loss_value(int tn){
+    switch(tn) {
+    case 58:      return 128.286;
+    case 108:     return 131.866;
+    case 158:     return 135.551;
+    case 208:     return 139.694;
+    case 258:     return 144.163;
+    case 308:     return 148.967;
+    case 358:     return 154.201;
+    case 408:     return 159.962;
+    case 458:     return 166.441;
+    case 508:     return 173.655;
+    case 558:     return 181.921;
+    case 608:     return 191.246;
+    case 658:     return 202.150;
+    case 708:     return 215.197;
+    case 758:     return 202.150;  // Verify with Andrey. Same as TargetNovelty of 658
+    case 808:     return 251.698;
+    case 858:     return 279.201;
+    case 908:     return 320.112;
+    case 958:     return 394.774;
+    case 1008:    return 1052.38;  // Huge number here. Why?
+    default:      return 10000.;   /* Pray that this does not occur. Ask Andrey what to do */
     }
+  }
 
-    //==============================================
-    double Omax_loss_value(int tn){
+  int get_reruns(void) {
+    return N_repeats;
+  }
 
-        if( tn == 58 )           return 128.286;
-        else if( tn == 108 )     return 131.866;
-        else if( tn == 158 )     return 135.551;
-        else if( tn == 208 )     return 139.694;
-        else if( tn == 258 )     return 144.163;
-        else if( tn == 308 )     return 148.967;
-        else if( tn == 358 )     return 154.201;
-        else if( tn == 408 )     return 159.962;
-        else if( tn == 458 )     return 166.441;
-        else if( tn == 508 )     return 173.655;
-        else if( tn == 558 )     return 181.921;
-        else if( tn == 608 )     return 191.246;
-        else if( tn == 658 )     return 202.150;
-        else if( tn == 708 )     return 215.197;
-        else if( tn == 758 )     return 202.150;  // Verify with Andrey. Same as TargetNovelty of 658
-        else if( tn == 808 )     return 251.698;
-        else if( tn == 858 )     return 279.201;
-        else if( tn == 908 )     return 320.112;
-        else if( tn == 958 )     return 394.774;
-        else if( tn == 1008 )    return 1052.38;  // Huge number here. Why?
-        else                      return 10000.;   /* Pray that this does not occur. Ask Andrey what to do */
+  double get_parameter(int i) {
+    switch(i){
+    case 0:
+      return alpha_i;
+    case 1:
+      return alpha_m;
+    case 2:
+      return beta;
+    case 3:
+      return gamma;
+    case 4:
+      return delta;
+    default:
+      std::cout << "Erroneous parameter id!!!!\n\n\n";
+      return 0.;
     }
-    double max_loss_value(int tn){
+  }
 
-      switch(tn) {
-        case 58:      return 128.286;
-        case 108:     return 131.866;
-        case 158:     return 135.551;
-        case 208:     return 139.694;
-        case 258:     return 144.163;
-        case 308:     return 148.967;
-        case 358:     return 154.201;
-        case 408:     return 159.962;
-        case 458:     return 166.441;
-        case 508:     return 173.655;
-        case 558:     return 181.921;
-        case 608:     return 191.246;
-        case 658:     return 202.150;
-        case 708:     return 215.197;
-        case 758:     return 202.150;  // Verify with Andrey. Same as TargetNovelty of 658
-        case 808:     return 251.698;
-        case 858:     return 279.201;
-        case 908:     return 320.112;
-        case 958:     return 394.774;
-        case 1008:    return 1052.38;  // Huge number here. Why?
-        default:      return 10000.;   /* Pray that this does not occur. Ask Andrey what to do */
+  void evolve_to_target(){
+    reset_world();
+    if (beta < -1. || gamma < -1.){
+      CumulativeRelativeLoss = 100000000000.;
+      CRLsquare = 0.;
+      return;
+    }
+    for (int k=0; k< N_repeats; k++){
+      for(int i=0; i<N_epochs &&  current_novelty < TargetNovelty; i++){
+	update_world();
       }
+      CumulativeRelativeLoss += current_loss/current_novelty;
+      CRLsquare += (current_loss/current_novelty)*(current_loss/current_novelty);
+      if(verbose_level==3){
+	std::cout <<  CumulativeRelativeLoss << " | " << CRLsquare << std::endl;
+      }
+      if(verbose_level==1){
+	std::cout <<  "." ;
+      }
+      else if(verbose_level==2){
+	std::cout <<  "**" << (k+1) <<  "**  curr loss " << current_loss << "; curr novelty " << current_novelty << std::endl;
+      }
+      reset_world();
     }
 
+    CumulativeRelativeLoss /= double(N_repeats);
+    CRLsquare /= double(N_repeats);
 
-    //==============================================
-    int get_reruns(void){
-        return N_repeats;
+    if(verbose_level==1){
+      std::cout << std::endl;
     }
-
-    //==============================================
-    double get_parameter(int i){
-
-        switch(i){
-            case 0:
-                return alpha_i;
-            case 1:
-                return alpha_m;
-            case 2:
-                return beta;
-            case 3:
-                return gamma;
-            case 4:
-                return delta;
-            default:
-
-                std::cout << "Erroneous parameter id!!!!\n\n\n";
-                return 0.;
-        }
+    if(verbose_level==2){
+      std::cout <<  CumulativeRelativeLoss << " || " << CRLsquare << std::endl;
     }
+    CRLsquare = 2*sqrt((CRLsquare - CumulativeRelativeLoss*CumulativeRelativeLoss)/double(N_repeats));
+  }
 
+  int set_parameter(double value, int position){
 
-    //==============================================
-    void evolve_to_target(){
+    if (position < 0 || position > 4) {return 0;}
 
-        reset_world();
-        if (beta < -1. || gamma < -1.){
-            CumulativeRelativeLoss = 100000000000.;
-            CRLsquare = 0.;
-            return;
-        }
+    else {
 
-
-        for (int k=0; k< N_repeats; k++){
-
-
-            for(int i=0; i<N_epochs &&  current_novelty < TargetNovelty; i++){
-                update_world();
-            }
-
-            CumulativeRelativeLoss += current_loss/current_novelty;
-            CRLsquare += (current_loss/current_novelty)*(current_loss/current_novelty);
-            if(verbose_level==3){
-                std::cout <<  CumulativeRelativeLoss << " | " << CRLsquare << std::endl;
-            }
-
-            if(verbose_level==1){
-                std::cout <<  "." ;
-
-            }
-            else if(verbose_level==2){
-                std::cout <<  "**" << (k+1) <<  "**  curr loss " << current_loss << "; curr novelty " << current_novelty << std::endl;
-            }
-
-
-            reset_world();
-        }
-
-        CumulativeRelativeLoss /= double(N_repeats);
-        CRLsquare /= double(N_repeats);
-
-        if(verbose_level==1){
-            std::cout << std::endl;
-        }
-
-        if(verbose_level==2){
-            std::cout <<  CumulativeRelativeLoss << " || " << CRLsquare << std::endl;
-        }
-
-        CRLsquare = 2*sqrt((CRLsquare - CumulativeRelativeLoss*CumulativeRelativeLoss)/double(N_repeats));
-
+      switch(position){
+      case 0:
+	alpha_i=value;
+	return 1;
+      case 1:
+	alpha_m=value;
+	return 1;
+      case 2:
+	beta=value;
+	return 1;
+      case 3:
+	gamma=value;
+	return 1;
+      case 4:
+	delta=value;
+	return 1;
+      }
     }
-
-
-    //================================================================
-    int set_parameter(double value, int position){
-
-        if (position < 0 || position > 4) {return 0;}
-
-        else {
-
-            switch(position){
-                case 0:
-                    alpha_i=value;
-                    return 1;
-                case 1:
-                    alpha_m=value;
-                    return 1;
-                case 2:
-                    beta=value;
-                    return 1;
-                case 3:
-                    gamma=value;
-                    return 1;
-                case 4:
-                    delta=value;
-                    return 1;
-            }
-
-        }
-
-        return 0;
-    }
-
-#ifdef notdef
-    //=================================================================
-    void try_annealing(double starting_jump, int iterations,
-                       double temp_start, double temp_end, double target_rejection){
-
-        double dx[5]={0.,0.,0.,0.,0};
-        double x[5]={0.,0.,0.,0.,0};
-        double rejection[5]={0., 0., 0., 0., 0.};
-        double curr_x, curr_err, x_tmp;
-        double temperature;
-        double ratio, r;
-        int cycle=10;
-        boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
-
-        // set up parameter for annealing
-
-        x[0]=alpha_i;
-        x[1]=alpha_m;
-        x[2]=beta;
-        x[3]=gamma;
-        x[4]=delta;
-
-        for(int i=0;i<5;i++){
-            dx[i] = starting_jump;
-        }
-
-        // establish the current value
-
-        //..........................................
-        evolve_to_target();
-        std::cout << CumulativeRelativeLoss << " +- " << CRLsquare << std::endl;
-
-        curr_x   = CumulativeRelativeLoss;
-        curr_err = CRLsquare;
-        CumulativeRelativeLoss = 0;
-        CRLsquare = 0;
-        //...........................................
-
-        // optimization cycle
-        for(int i=0; i<iterations; i++){
-
-            temperature = temp_start*exp( i*(log(temp_end)-log(temp_start))/(double)iterations);
-            std::cout  << std::endl << "....T = " << wrap_double(temperature,3) << std::endl << std::endl;
-
-            if (i % cycle == 0 && i > 0){
-
-                for (int k=0; k<5; k++){
-
-                    rejection[k]/=(double)cycle;
-                    if (rejection[k] > 0){
-                        dx[k] = dx[k]/(rejection[k]/target_rejection);
-                        rejection[k]=0.;
-                    }
-                    else{
-                        dx[k]*=2.;
-                    }
-                    std::cout  << dx[k] << " ";
-                }
-                std::cout  << std::endl;
-            }
-
-
-            for (int j=0; j<5; j++){
-
-                // get new value of x[j]
-                x_tmp = get_new_x(x[j],dx[j]);
-
-
-
-                //.............................................
-                set_parameter(x_tmp, j);
-
-
-                evolve_to_target();
-
-                std::cout  << std::endl << "......... " << std::endl;
-                std::cout << "Trying... " << CumulativeRelativeLoss << " +- " << CRLsquare << std::endl;
-
-                ratio = min(1.,exp(-(CumulativeRelativeLoss-curr_x)/temperature));
-                r = uni();
-                std::cout << r << " vs " << ratio << std::endl;
-
-                if (r > ratio){
-
-                    std::cout << string_wrap(id, 4) <<" "<< (i+1) << ","<< (j)
-                    <<" "<< (i+1) << " Did not accept "
-                    << x_tmp << "(" << j << ")" << std::endl;
-                    std::cout << alpha_i << " "<< alpha_m << " "
-                    << beta << " " << gamma << " "
-                    << delta << " " << std::endl;
-                    set_parameter(x[j], j);
-                    CumulativeRelativeLoss = 0;
-                    CRLsquare = 0;
-
-                    rejection[j]+=1.;
-                }
-
-                else {
-
-                    curr_x   = CumulativeRelativeLoss;
-                    curr_err = CRLsquare;
-                    x[j] = x_tmp;
-                    CumulativeRelativeLoss = 0;
-                    CRLsquare = 0;
-                    std::cout << (i+1) << string_wrap((string) " Rejection counts: ", 8)
-                    << wrap_double(rejection[0],2)
-                    << " "<< wrap_double(rejection[1], 7) << " "
-                    << wrap_double(rejection[2],5) << " " << wrap_double(rejection[2],9) << " "
-                    << wrap_double(rejection[4],6) << " "
-                    << std::endl << std::endl;
-
-                    std::cout << string_wrap(id, 4) <<" "<< (i+1) <<","<< (j)
-                    <<" "
-                    << string_wrap((string) "***** Did accept! ", 3)
-                    << wrap_double(alpha_i,2)
-                    << " "<< wrap_double(alpha_m, 7) << " "
-                    << wrap_double(beta,5) << " "
-                    << wrap_double(gamma,9) << " "
-                    << wrap_double(delta,6) << " "
-                    << std::endl << std::endl;
-
-                }
-                //........................................................
-
-            }
-
-        }
-
-    }
-
-#endif
-
+    return 0;
+  }
 };
 
-//============================================================
-
-#ifdef P_DISPATCH
-std::pair<double,double> multi_loss(dispatch_group_t group,
-                                    Universe* un[],
-                                    dispatch_queue_t* CustomQueues,
-                                    double* Results,
-                                    int*    Counters,
-                                    double* params){
-#else
 std::pair<double,double> multi_loss(Universe* un[],
                                     double* Results,
                                     int*    Counters,
                                     double* params){
 
-#endif
+  int N = un[0]->get_reruns();
+  int step = (int)floor((double)N/(double)(Nworkers)); // FIXME: Andrey: please check change in cast grouping and use of floor
+  int istart=0;
+  int iend = istart+step;
 
-    int N = un[0]->get_reruns();
-    int step = (int)floor((double)N/(double)(Nworkers)); // FIXME: Andrey: please check change in cast grouping and use of floor
-    int istart=0;
-    int iend = istart+step;
+  double Loss=0., LossSquare=0.;
 
-    double Loss=0., LossSquare=0.;
+  // timeval startTime, endTime;
+  // double elapsedTime;
+  gettimeofday(&startTime, NULL);
 
-    timeval startTime, endTime;
-    double elapsedTime;
-    gettimeofday(&startTime, NULL);
+  if ( N > NUniverse ) {
+    std::cerr << "Error: Number of reruns=" << N << " is greater than max NUniverse=" << NUniverse << "\n";
+    exit(1);
+  }
 
-    if ( N > NUniverse ) {
-      std::cerr << "Error: Number of reruns=" << N << " is greater than max NUniverse=" << NUniverse << "\n";
-      exit(1);
+  for(int i=0; i<N; i++){
+    for(int j=0; j<5; j++){
+      un[i]->set_parameter(params[j],j);
     }
+  }
 
-    for(int i=0; i<N; i++){
-        for(int j=0; j<5; j++){
-            un[i]->set_parameter(params[j],j);
-        }
-    }
+  int i;
 
-#ifdef P_DISPATCH
-    for(int i=0; i<Nworkers; i++){
+  // Execute rerun loop in parallel
 
-        dispatch_group_async(group, CustomQueues[i], ^{
+  //#pragma omp parallel for private (i)
+  for(i=0; i<N; i++){
+    un[i]->evolve_to_target_and_save(i, i+1, Results, Counters);
+  }
 
-            // un[i]->evolve_to_target_and_save(istart, iend, Results, Counters);
-            un[i]->evolve_to_target_and_save(i*step, min((i+1)*step,N), Results, Counters);
-        });
+  for (int i=0; i<N; i++){
+    Loss+=Results[i]/(double)N;
+    LossSquare+=Results[i]*Results[i]/(double)N;
+  }
 
-        std::cout << "queued: i=" << i << " N=" << N << " istart=" << istart << " iend=" << iend << "\n";
-        // istart += step;
-        // iend = min(istart+step,N);
+  double two_std = ((LossSquare - Loss*Loss)/(double)N);
 
-    }
-    dispatch_group_wait(group, DISPATCH_TIME_FOREVER);
-    //dispatch_release(group);
-#else
-    int i;
+  two_std = 2.*sqrt(two_std);
+  std::pair<double,double> Res;
+  Res.first=Loss;
+  Res.second=two_std;
 
-    // Execute rerun loop in parallel
+  gettimeofday(&endTime, NULL);
+  elapsedTime = (endTime.tv_sec - startTime.tv_sec) * 1000.0;      // sec to ms
+  elapsedTime += (endTime.tv_usec - startTime.tv_usec) / 1000.0;   // us to ms
+  elapsedTime /= 1000.;
+  cout << "multi_loss(N=" << N << ", target=" << un[0]->get_target() << ") elapsed time: " << elapsedTime << " seconds " << elapsedTime/60. << " minutes\n\n";
 
-    #pragma omp parallel for private (i)
-    for(i=0; i<N; i++){
-        un[i]->evolve_to_target_and_save(i, i+1, Results, Counters);
-     }
-#endif
-
-    for (int i=0; i<N; i++){
-        Loss+=Results[i]/(double)N;
-        LossSquare+=Results[i]*Results[i]/(double)N;
-    }
-
-    double two_std = ((LossSquare - Loss*Loss)/(double)N);
-
-    two_std = 2.*sqrt(two_std);
-    std::pair<double,double> Res;
-    Res.first=Loss;
-    Res.second=two_std;
-
-    gettimeofday(&endTime, NULL);
-    elapsedTime = (endTime.tv_sec - startTime.tv_sec) * 1000.0;      // sec to ms
-    elapsedTime += (endTime.tv_usec - startTime.tv_usec) / 1000.0;   // us to ms
-    elapsedTime /= 1000.;
-    cout << "multi_loss(N=" << N << ", target=" << un[0]->get_target() << ") elapsed time: " << elapsedTime << " seconds " << elapsedTime/60. << " minutes\n\n";
-
-    return Res;
+  return Res;
 }
-//============================================================
 
-
-//============================================================
-#ifdef P_DISPATCH
-void multi_annealing( dispatch_group_t group,
-                     Universe* un[],
-                     dispatch_queue_t* CustomQueues,
-                     double T_start, double T_end,
-                     double Target_rejection,
-                     int Annealing_repeats,
-                     double starting_jump,
-                     double* Results,
-                     int*    Counters,
-                     double* params0,
-                     double annealing_cycles){
-#else
 void multi_annealing(Universe* un[],
                      double T_start, double T_end,
                      double Target_rejection,
@@ -1527,190 +1230,173 @@
                      int*    Counters,
                      double* params0,
                      double annealing_cycles){
-#endif
-    //.................................
-    // re-implement annealing
+  //.................................
+  // re-implement annealing
 
-    double dx[5]={0.,0.,0.,0.,0};
-    double x[5]={0.,0.,0.,0.,0};
-    double rejection[5]={0., 0., 0., 0., 0.};
-    double curr_x, curr_err, x_tmp;
-    double temperature;
-    double ratio, r;
-    int cycle=10;
-    //boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
+  double dx[5]={0.,0.,0.,0.,0};
+  double x[5]={0.,0.,0.,0.,0};
+  double rejection[5]={0., 0., 0., 0., 0.};
+  double curr_x, curr_err, x_tmp;
+  double temperature;
+  double ratio, r;
+  int cycle=10;
+  //boost::variate_generator<base_generator_type&, boost::uniform_real<> > uni(generator, uni_dist);
 
-    // set up parameter for annealing
+  // set up parameter for annealing
 
-    x[0]=params0[0];
-    x[1]=params0[1];
-    x[2]=params0[2];
-    x[3]=params0[3];
-    x[4]=params0[4];
+  x[0]=params0[0];
+  x[1]=params0[1];
+  x[2]=params0[2];
+  x[3]=params0[3];
+  x[4]=params0[4];
 
-    for(int i=0;i<5;i++){
-        dx[i] = starting_jump;
-    }
+  for(int i=0;i<5;i++){
+    dx[i] = starting_jump;
+  }
 
-    // establish the current value
-    std::pair<double,double>Res;
+  // establish the current value
+  std::pair<double,double>Res;
 
-#ifdef P_DISPATCH
-    Res = multi_loss(group, un, CustomQueues, Results, Counters, x);
-#else
-    Res = multi_loss(       un,               Results, Counters, x);
-#endif
-    std::cout << "Returned from initial multi_loss:" << std::endl;
-    std::cout << Res.first << " +- " << Res.second << std::endl;
+  Res = multi_loss(       un,               Results, Counters, x);
 
-    if ( operation == 'm' ) {
-      FILE *f;
-      int N = un[0]->get_reruns();
+  std::cout << "Returned from initial multi_loss:" << std::endl;
+  std::cout << Res.first << " +- " << Res.second << std::endl;
 
-      f = fopen("multi_loss.data","w");
-      for(int i=0; i<N; i++) {
-        fprintf(f,"%.20e\n",Results[i]);
-      }
-      fclose(f);
-      exit(0);
+  if ( operation == 'm' ) {
+    FILE *f;
+    int N = un[0]->get_reruns();
+
+    f = fopen("multi_loss.data","w");
+    for(int i=0; i<N; i++) {
+      fprintf(f,"%.20e\n",Results[i]);
     }
+    fclose(f);
+    exit(0);
+  }
 
-    curr_x   = Res.first;
-    curr_err = Res.second;
+  curr_x   = Res.first;
+  curr_err = Res.second;
 
-    // optimization cycle
+  // optimization cycle
 
-    for(int i=0; i<annealing_cycles; i++){
+  for(int i=0; i<annealing_cycles; i++){
 
-        temperature = T_start*exp( i*(log(T_end)-log(T_start))/(double)annealing_cycles);
-        std::cout  << std::endl << "....T = " << wrap_double(temperature,3) << std::endl << std::endl;
+    temperature = T_start*exp( i*(log(T_end)-log(T_start))/(double)annealing_cycles);
+    std::cout  << std::endl << "....T = " << wrap_double(temperature,3) << std::endl << std::endl;
 
-        if (i % cycle == 0 && i > 0){
+    if (i % cycle == 0 && i > 0){
+      for (int k=0; k<5; k++){
+	rejection[k]/=(double)cycle;
+	if (rejection[k] > 0){
+	  dx[k] = dx[k]/(rejection[k]/Target_rejection);
+	  rejection[k]=0.;
+	}
+	else{
+	  dx[k]*=2.;
+	}
+	std::cout  << dx[k] << " ";
+      }
+      std::cout  << std::endl;
+    }
 
-            for (int k=0; k<5; k++){
-                rejection[k]/=(double)cycle;
+    for (int j=0; j<5; j++){
+      if (FIX_VARIABLES==0 || var_fixed[j]==0){
+	// get new value of x[j]
+	double x_hold=x[j];
+	x_tmp = get_new_x(x[j],dx[j]);
+	x[j]=x_tmp;
 
-                if (rejection[k] > 0){
-                    dx[k] = dx[k]/(rejection[k]/Target_rejection);
-                    rejection[k]=0.;
-                }
-                else{
-                    dx[k]*=2.;
-                }
-                std::cout  << dx[k] << " ";
-            }
-            std::cout  << std::endl;
-        }
+	std::cout << wrap_double(x_tmp,10) << " " << wrap_double(j,9) << "\n\n";
+	//=======================================
+	//.............................................
+	for(int w=0; w<Nworkers; w++){
+	  un[w]->set_parameter(x_tmp, j);
+	}
 
+	Res = multi_loss(un, Results, Counters, x);
+	std::cout << Res.first << " +- " << Res.second << std::endl;
 
-        for (int j=0; j<5; j++){
+	ratio = min(1.,exp(-(Res.first-curr_x)/temperature));
+	r = rand()/(double)(pow(2.,31)-1.);
+	std::cout << r << " vs " << ratio << std::endl;
 
-            ///////////////////////////////
-            if (FIX_VARIABLES==0 || var_fixed[j]==0){
+	double ALOT=100000000000.;
 
+	if (Res.first < ALOT)
+	{
+	  ofstream filestr;
 
+	  filestr.open ("best_opt_some.txt", ofstream::app);
 
-                // get new value of x[j]
-                double x_hold=x[j];
-                x_tmp = get_new_x(x[j],dx[j]);
-                x[j]=x_tmp;
+	  // >> i/o operations here <<
+	  filestr
 
-                std::cout << wrap_double(x_tmp,10) << " " << wrap_double(j,9) << "\n\n";
-                //=======================================
-                //.............................................
-                for(int w=0; w<Nworkers; w++){
-                    un[w]->set_parameter(x_tmp, j);
-                }
+	    << "N, " << i << ", " << j << ", " << dx[j] << ", " << rejection[j] << ", |, " // FIXME: MW-DEBUGGING
 
-#ifdef P_DISPATCH
-                Res = multi_loss(group, un, CustomQueues, Results, Counters, x);
-#else
-                Res = multi_loss(       un,               Results, Counters, x);
-#endif
-                std::cout << Res.first << " +- " << Res.second << std::endl;
+	    << un[0]->get_target() << ", "
+	    << Res.first
+	    << ", " << un[0]->get_parameter(0)
+	    << ", " << un[0]->get_parameter(1)
+	    << ", " << un[0]->get_parameter(2)
+	    << ", " << un[0]->get_parameter(3)
+	    << ", " << un[0]->get_parameter(4) << ", " << Res.second << ",\n";
 
-                ratio = min(1.,exp(-(Res.first-curr_x)/temperature));
-                r = rand()/(double)(pow(2.,31)-1.);
-                std::cout << r << " vs " << ratio << std::endl;
+	  filestr.close();
 
-                double ALOT=100000000000.;
 
-                if (Res.first < ALOT)
-                {
-                    ofstream filestr;
+	  filestr.open ("max_dist.txt", ofstream::app);
 
-                    filestr.open ("best_opt_some.txt", ofstream::app);
+	  // >> i/o operations here <<
+	  filestr << max_dist << ",\n";
 
-                    // >> i/o operations here <<
-                    filestr
+	  filestr.close();
 
-		    << "N, " << i << ", " << j << ", " << dx[j] << ", " << rejection[j] << ", |, " // FIXME: MW-DEBUGGING
+	  FILE *bf;
+	  bf = fopen("bestdb.txt","a");
+	  fprintf(bf, "N %2d %2d %10.5f %5.2f | %5.2f %10.5f [ %5.2f %5.2f %10.5f %10.5f %10.5f ] %10.5f\n", i, j, dx[j], rejection[j],
+		  un[0]->get_target(),
+		  Res.first,
+		  un[0]->get_parameter(0),
+		  un[0]->get_parameter(1),
+		  un[0]->get_parameter(2),
+		  un[0]->get_parameter(3),
+		  un[0]->get_parameter(4),
+		  Res.second);
+	  fclose(bf);
+	}
 
-                    << un[0]->get_target() << ", "
-                    << Res.first
-                    << ", " << un[0]->get_parameter(0)
-                    << ", " << un[0]->get_parameter(1)
-                    << ", " << un[0]->get_parameter(2)
-                    << ", " << un[0]->get_parameter(3)
-                    << ", " << un[0]->get_parameter(4) << ", " << Res.second << ",\n";
+	if (r > ratio){
 
-                    filestr.close();
-
-
-                    filestr.open ("max_dist.txt", ofstream::app);
-
-                    // >> i/o operations here <<
-                    filestr << max_dist << ",\n";
-
-                    filestr.close();
-
-                    FILE *bf;
-                    bf = fopen("bestdb.txt","a");
-                    fprintf(bf, "N %2d %2d %10.5f %5.2f | %5.2f %10.5f [ %5.2f %5.2f %10.5f %10.5f %10.5f ] %10.5f\n", i, j, dx[j], rejection[j],
-			    un[0]->get_target(),
-			    Res.first,
-			    un[0]->get_parameter(0),
-			    un[0]->get_parameter(1),
-			    un[0]->get_parameter(2),
-			    un[0]->get_parameter(3),
-			    un[0]->get_parameter(4),
-			    Res.second);
-                    fclose(bf);
-                }
-
-
-                if (r > ratio){
-
-                    std::cout << " "<< (i+1) << ","<< (j)
+	  std::cout << " "<< (i+1) << ","<< (j)
                     <<" "<< (i+1) << " Did not accept "
                     << x_tmp << "(" << j << ")" << std::endl;
-                    std::cout << un[0]->get_parameter(0)
+	  std::cout << un[0]->get_parameter(0)
                     << " " << un[0]->get_parameter(1)
                     << " " << un[0]->get_parameter(2)
                     << " " << un[0]->get_parameter(3)
                     << " " << un[0]->get_parameter(4) << " " << std::endl;
 
-                    x[j]=x_hold;
-                    for(int w=0; w<Nworkers; w++){
-                        un[w]->set_parameter(x[j], j);
-                    }
+	  x[j]=x_hold;
+	  for(int w=0; w<Nworkers; w++){
+	    un[w]->set_parameter(x[j], j);
+	  }
 
 
-                    //set_parameter(x[j], j);
-                    rejection[j]+=1.;
-                }
+	  //set_parameter(x[j], j);
+	  rejection[j]+=1.;
+	}
 
-                else {
+	else {
 
-                    curr_x   = Res.first;
-                    curr_err = Res.second;
-                    x[j] = x_tmp;
+	  curr_x   = Res.first;
+	  curr_err = Res.second;
+	  x[j] = x_tmp;
 
-                    for(int w=0; w<Nworkers; w++){
-                        un[w]->set_parameter(x[j], j);
-                    }
+	  for(int w=0; w<Nworkers; w++){
+	    un[w]->set_parameter(x[j], j);
+	  }
 
-                    std::cout << (i+1) << string_wrap((string) " Rejection counts: ", 8)
+	  std::cout << (i+1) << string_wrap((string) " Rejection counts: ", 8)
                     << wrap_double(rejection[0],2) << " "
                     << wrap_double(rejection[1],7) << " "
                     << wrap_double(rejection[2],5) << " "
@@ -1718,7 +1404,7 @@
                     << wrap_double(rejection[4],6) << " "
                     << std::endl << std::endl;
 
-                    std::cout << " "<< (i+1) <<","<< (j)
+	  std::cout << " "<< (i+1) <<","<< (j)
                     <<" "
                     << string_wrap((string) "***** Did accept! ", 3)
                     << wrap_double(un[0]->get_parameter(0),2) << " "
@@ -1727,238 +1413,176 @@
                     << wrap_double(un[0]->get_parameter(3),9) << " "
                     << wrap_double(un[0]->get_parameter(4),6) << " "
                     << std::endl << std::endl;
-
-
-
-                }
-                //........................................................
-
-            }
-        }
-
+	}
+      }
     }
-
+  }
 }
 
-
-
-//================================================
 int
 main(int argc, char* argv[])
 {
+  double params0[6] = {0., 0., 0., 0., 0., 0.2}, target=50., range;
+  string par_names0[6] = {"alpha_i", "alpha_m", "beta", "gamma", "delta", "target"};
+  string par_names1[4] = {"n_epochs", "n_steps", "n_reruns", "range"};
+  string par_names2[5] = {"T_start", "T_end", "Annealing_steps","Target_rejection","Starting_jump"};
+  string par_names3[5] = {"FREEZE_alpha_i", "FREEZE_alpha_m", "FREEZE_beta", "FREEZE_gamma", "FREEZE_delta"};
+  string par_names4[3] = {"Operation", "Nworkers", "initSeed"};
 
-    double params0[6] = {0., 0., 0., 0., 0., 0.2}, target=50., range;
-    string par_names0[6] = {"alpha_i", "alpha_m", "beta", "gamma", "delta", "target"};
-    string par_names1[4] = {"n_epochs", "n_steps", "n_reruns", "range"};
-    string par_names2[5] = {"T_start", "T_end", "Annealing_steps","Target_rejection","Starting_jump"};
-    string par_names3[5] = {"FREEZE_alpha_i", "FREEZE_alpha_m", "FREEZE_beta", "FREEZE_gamma", "FREEZE_delta"};
-    string par_names4[3] = {"Operation", "Nworkers", "initSeed"};
+  int params1[4] = {300, 50, 1000, 10};
+  int params3[5] = { 0, 0, 0, 0, 0};
 
-    int params1[4] = {300, 50, 1000, 10};
-    int params3[5] = { 0, 0, 0, 0, 0};
+  //          temperature_start,  temperature_end,  annealing_steps target_rejection  Starting_jump
+  double params2[5] = {1,             0.001,               100,              0.3,           1.5};
 
-    //          temperature_start,  temperature_end,  annealing_steps target_rejection  Starting_jump
-    double params2[5] = {1,             0.001,               100,              0.3,           1.5};
+  int verbose_level = 2;
+  const std::string one="one", two="two";
+  static Universe* un[NUniverse];
+  static double* Results;
+  static int*    Counters;
 
-    int verbose_level = 2;
-    const std::string one="one", two="two";
-    static Universe* un[NUniverse];
-#ifdef P_DISPATCH
-    static dispatch_queue_t CustomQueues[MAXNworkers];
-#endif
-    static double* Results;
-    static int*    Counters;
+  timeval t1, t2;
+  double elapsedTime;
 
-    timeval t1, t2;
-    double elapsedTime;
-    // start timer
-    gettimeofday(&t1, NULL);
+  gettimeofday(&t1, NULL);   // start timer
 
-
-    if (argc < 8) {
-        std::cout << "Usage: super_optimizer alpha_i alpha_m beta gamma delta target_innov [n_epochs n_steps n_reruns] [range] [verbose_level]\n";
-        std::cout << "         [T_start T_end Annealing_steps Target_rejection Starting_jump]\n";
-        std::cout << "         [FREEZE_alpha_i FREEZE_alpha_m FREEZE_beta FREEZE_gamma FREEZE_delta]\n";
-
-        system("pwd");
-
-
-        return(1);
+  if (argc < 8) {
+    std::cout << "Usage: super_optimizer alpha_i alpha_m beta gamma delta target_innov [n_epochs n_steps n_reruns] [range] [verbose_level]\n";
+    std::cout << "         [T_start T_end Annealing_steps Target_rejection Starting_jump]\n";
+    std::cout << "         [FREEZE_alpha_i FREEZE_alpha_m FREEZE_beta FREEZE_gamma FREEZE_delta]\n";
+    system("pwd");
+    return(1);
+  }
+  else {
+    for (int nArg=0; nArg < argc; nArg++){
+      //std::cout << nArg << " " << argv[nArg] << std::endl;
+      if (nArg > 0 && nArg < 7){
+	params0[nArg-1]= atof(argv[nArg]);
+	std::cout << par_names0[nArg-1] << ": " << params0[nArg-1] <<  std::endl;
+      }
+      if (nArg > 6 && nArg < 11){
+	params1[nArg-7]= atoi(argv[nArg]);
+	std::cout << par_names1[nArg-7] << ": " << params1[nArg-7] <<  std::endl;
+      }
+      if (nArg == 11){
+	verbose_level = atoi(argv[nArg]);
+	std::cout << "verbose level: " << verbose_level <<  std::endl;
+      }
+      if (nArg > 11 && nArg < 17){
+	params2[nArg-12]= atof(argv[nArg]);
+	std::cout << par_names2[nArg-12] << ": " << params2[nArg-12] <<  std::endl;
+      }
+      if (nArg > 16 && nArg < 22){
+	params3[nArg-17]= (int)round(atof(argv[nArg]));   // FIXME: Andrey: please verify that round() is correct.
+	var_fixed[nArg-17]= (int)round(atof(argv[nArg])); // FIXME: ditto
+	std::cout << par_names3[nArg-17] << ": " << var_fixed[nArg-17] <<  std::endl;
+      }
+      if (nArg == 22 ){
+	operation = *argv[nArg];
+	std::cout << par_names4[0] << ": " << operation <<  std::endl;
+      }
+      if (nArg == 23 ){
+	Nworkers = atoi(argv[nArg]);
+	std::cout << par_names4[1] << ": " << Nworkers <<  std::endl;
+      }
+      if (nArg == 24 ){
+	initSeed = atoi(argv[nArg]);
+	std::cout << par_names4[2] << ": " << initSeed <<  std::endl;
+      }
     }
-    else {
-        for (int nArg=0; nArg < argc; nArg++){
-            //std::cout << nArg << " " << argv[nArg] << std::endl;
-            if (nArg > 0 && nArg < 7){
-                params0[nArg-1]= atof(argv[nArg]);
-                std::cout << par_names0[nArg-1] << ": " << params0[nArg-1] <<  std::endl;
-            }
-            if (nArg > 6 && nArg < 11){
-                params1[nArg-7]= atoi(argv[nArg]);
-                std::cout << par_names1[nArg-7] << ": " << params1[nArg-7] <<  std::endl;
-            }
-            if (nArg == 11){
-                verbose_level = atoi(argv[nArg]);
-                std::cout << "verbose level: " << verbose_level <<  std::endl;
-            }
-            if (nArg > 11 && nArg < 17){
-                params2[nArg-12]= atof(argv[nArg]);
-                std::cout << par_names2[nArg-12] << ": " << params2[nArg-12] <<  std::endl;
-            }
-            if (nArg > 16 && nArg < 22){
-	        params3[nArg-17]= (int)round(atof(argv[nArg]));   // FIXME: Andrey: please verify that round() is correct.
-	        var_fixed[nArg-17]= (int)round(atof(argv[nArg])); // FIXME: ditto
-                std::cout << par_names3[nArg-17] << ": " << var_fixed[nArg-17] <<  std::endl;
-            }
-            if (nArg == 22 ){
-                operation = *argv[nArg];
-                std::cout << par_names4[0] << ": " << operation <<  std::endl;
-            }
-            if (nArg == 23 ){
-                Nworkers = atoi(argv[nArg]);
-                std::cout << par_names4[1] << ": " << Nworkers <<  std::endl;
-            }
-            if (nArg == 24 ){
-                initSeed = atoi(argv[nArg]);
-                std::cout << par_names4[2] << ": " << initSeed <<  std::endl;
-            }
+  }
 
+  for (int j=0; j<5; j++){
+    cout << j << " | " << var_fixed[j] << " (fixed) \n";
+  }
 
-        }
+  target=params0[5];
+  range = (double)params1[3];
+  int identify_failed = 0;
+  char* filename= (char *)"movie_graph.txt";
+  int n_ep=params1[0], n_st=params1[1], n_rep=params1[2];
 
-    }
+  for(int i=0; i<NUniverse; i++){
+    un[i] = new Universe((char *)filename,n_ep,n_st,
+			 (int)n_rep,
+			 identify_failed, target, i2string(i));
+  }
 
-    for (int j=0; j<5; j++){
+  if(n_rep > 0){
+    Results = new double[n_rep];
+    Counters = new int[n_rep];
+  }else {
+    Results =  NULL;
+    Counters = NULL;
+    std::cout << " Number of reruns should be positive! " <<  std::endl;
+    return 0;
+  }
 
-        cout << j << " | " << var_fixed[j] << " (fixed) \n";
-    }
+  //srand(time(0));
+  //srandomdev();
 
-    target=params0[5];
-    range = (double)params1[3];
-	int identify_failed = 0;
-	char* filename= (char *)"movie_graph.txt";
- 	int n_ep=params1[0], n_st=params1[1], n_rep=params1[2];
+  if ( initSeed != 0.0 ) {
+    srand(initSeed);
+  }
+  else {
+    timeval t;
+    gettimeofday(&t, NULL);
+    srand(t.tv_usec);
+  }
 
-    //...............................
-
-    for(int i=0; i<NUniverse; i++){
-        un[i] = new Universe((char *)filename,n_ep,n_st,
-                             (int)n_rep,
-                             identify_failed, target, i2string(i));
-#ifdef P_DISPATCH
-        CustomQueues[i] = dispatch_queue_create(i2char(i), NULL);
-#endif
+  {
+    double r=0;
+    for (int j=0; j<100; j++){
+      r = rand()/(double)(pow(2.,31)-1.);
+      std::cout << r << " ";
     }
+    std::cout << "\n";
+  }
 
-    //...............................
-    if(n_rep > 0){
+  //random initiation of starting parameters
 
-        Results = new double[n_rep];
-        Counters = new int[n_rep];
-
-    }else {
-
-        Results =  NULL;
-        Counters = NULL;
-        std::cout << " Number of reruns should be positive! " <<  std::endl;
-        return 0;
-
+  if (range > 0.){
+    for (int i=0; i < 5; i++){
+      if (params0[i]==-100.){
+	double r1 = (rand()/(double)(pow(2.,31)-1.));
+	double r2 = (rand()/(double)(pow(2.,31)-1.));
+	double sign = 1.;
+	if(r1 > 0.5){
+	  sign=-1.;
+	}
+	params0[i] = sign*r2*range;
+	std::cout << par_names0[i] << ": " << params0[i] <<  std::endl;
+      }
     }
-    //...............................
-    //srand(time(0));
-    //srandomdev();
+  }
 
-    if ( initSeed != 0.0 ) {
-      srand(initSeed);
-    }
-    else {
-        timeval t;
-        gettimeofday(&t, NULL);
-        srand(t.tv_usec);
-    }
+  double T_start=params2[0], T_end=params2[1], Target_rejection=params2[3], starting_jump=params2[4];
+  int Annealing_repeats = (int) params2[2];
 
-    {
-        double r=0;
-        for (int j=0; j<100; j++){
+  // print_memory_status();
 
+  multi_annealing(un, T_start, T_end, Target_rejection, Annealing_repeats,
+		  starting_jump, Results, Counters, params0, Annealing_repeats);
 
+  // stop timer
 
-            r = rand()/(double)(pow(2.,31)-1.);
-            std::cout << r << " ";
-        }
-        std::cout << "\n";
-    }
-  	//random initiation of starting parameters
+  gettimeofday(&t2, NULL);
 
-    if (range > 0.){
+  // compute and print the elapsed time in millisec
 
-        for (int i=0; i < 5; i++){
+  elapsedTime = (t2.tv_sec - t1.tv_sec) * 1000.0;      // sec to ms
+  elapsedTime += (t2.tv_usec - t1.tv_usec) / 1000.0;   // us to ms
+  elapsedTime /= 1000.;
+  cout << "\n*** optimizer completed, elapsed time=" << elapsedTime << " seconds " << elapsedTime/60. << " minutes)\n\n";
 
-            if (params0[i]==-100.){
+  for(int i=0; i<Nworkers; i++){
+    delete un[i];
+  }
 
-                double r1 = (rand()/(double)(pow(2.,31)-1.));
-                double r2 = (rand()/(double)(pow(2.,31)-1.));
-                double sign = 1.;
-
-                if(r1 > 0.5){
-                    sign=-1.;
-                }
-
-                params0[i] = sign*r2*range;
-
-                std::cout << par_names0[i] << ": " << params0[i] <<  std::endl;
-            }
-        }
-
-    }
-
-
-    double T_start=params2[0], T_end=params2[1], Target_rejection=params2[3], starting_jump=params2[4];
-    int Annealing_repeats = (int) params2[2];
-
-    // print_memory_status();
-
-#ifdef P_DISPATCH
-    dispatch_group_t group = dispatch_group_create();
-
-    //.............................
-    multi_annealing(group, un, CustomQueues, T_start, T_end, Target_rejection, Annealing_repeats,
-                    starting_jump, Results, Counters, params0, Annealing_repeats);
-
-    //dispatch_group_wait(group, DISPATCH_TIME_FOREVER);
-    dispatch_release(group);
-    //.............................
-#else
-    multi_annealing(       un,                T_start, T_end, Target_rejection, Annealing_repeats,
-                    starting_jump, Results, Counters, params0, Annealing_repeats);
-#endif
-
-
-    // stop timer
-    gettimeofday(&t2, NULL);
-
-    // compute and print the elapsed time in millisec
-    elapsedTime = (t2.tv_sec - t1.tv_sec) * 1000.0;      // sec to ms
-    elapsedTime += (t2.tv_usec - t1.tv_usec) / 1000.0;   // us to ms
-    elapsedTime /= 1000.;
-    cout << "\n*** optimizer completed, elapsed time=" << elapsedTime << " seconds " << elapsedTime/60. << " minutes)\n\n";
-
-    //.....................
-
-    for(int i=0; i<Nworkers; i++){
-        delete un[i];
-    }
-
-    //....................
-    if(n_rep > 0){
-
-        delete [] Results;
-        delete [] Counters;
-
-    }
-
-    return 0;
-
-
-
+  if(n_rep > 0){
+    delete [] Results;
+    delete [] Counters;
+  }
+  return 0;
 }
 

Added: SwiftApps/SciColSim/maxloss.cpp
===================================================================
--- SwiftApps/SciColSim/maxloss.cpp	                        (rev 0)
+++ SwiftApps/SciColSim/maxloss.cpp	2012-12-23 04:33:21 UTC (rev 6110)
@@ -0,0 +1,101 @@
+#include <fstream>
+#include <iostream>
+#include <stdio.h>
+#include <time.h>
+#include <ctime>
+#include <algorithm>
+#include <string>
+
+#include <sys/param.h>
+#include <sys/time.h>
+#include <sys/types.h>
+#include <unistd.h>
+#include <stdlib.h>
+
+#include <math.h>
+
+using namespace std;
+
+void set_max_loss(long long v, long long e, long long t) {
+
+  // Based on formulas from random_analytical.pdf
+
+  // t-=100;
+  double E = e;
+  double V = v;
+  double T = t;
+
+  double max_loss;
+  double sum, ERLt, VarRLt, absVarRLt;
+
+  // (9): E[RLt] = (1/t) * SUM(i=0 to T of: (V*(V-1) / (2 * (E-i))
+
+  sum = 0;
+  for(int i=0;i<t;i++) {
+    sum += ((double)(v*(v-1))) / ((double)(2*(e-i)));
+  }
+  ERLt = (1.0/(double) t) * sum;
+
+  // (12): Var[RLt] = 1 / (T**2) * SUM( i=0 to T of: ((V*(V-1))/2) - E + 1 ) / ((E-i)**2)
+
+  sum = 0;
+  for(int i=0;i<t;i++) {
+    sum +=  
+      ( (((double)(v*(v-1)))/ 2.0) - (double)e + (double)i )
+      /  
+      (double)((e-i)*(e-i))
+      ;
+    if ( (double)((e-i)*(e-i)) == 0.0 ) {
+      printf( "zero denom: %d %d\n", e, i);
+    }
+  }
+  int tmp = t*t;
+  VarRLt = (1.0/(double)((t) * t)) * sum;
+  if (VarRLt < 0.0) absVarRLt=0.0;
+  else absVarRLt = VarRLt;
+
+  // (9) + 3sigma = E[RLt] + 3 * SQRT(Var)
+  max_loss = ERLt + (3.0 * sqrt(absVarRLt));
+  printf("%12d %12.3f %12.8e %12.3f\n", t, ERLt, VarRLt, max_loss);
+}
+
+struct Graph {
+  const char *n;
+  int v;
+  int e;
+} G[] =
+
+{
+  "movie",    500,    1008,
+  "big.001", 1857,    1312,
+  "big.002", 3094,    2683,
+  "big.005", 5405,    6776,
+  "big.01",  7765,   13421,
+  "big.10", 19281,  134594,
+  "big.20", 23258,  269133,
+  "big.30", 25484,  403401,
+  "big.40", 26821,  537106,
+  "big.50", 27774,  671179,
+  "big.60", 28482,  804774,
+  "big.70", 29055,  938061,
+  "big.80", 29487, 1072415,
+  "big.90", 29779, 1205741,
+  "big",    30060, 1338753,   
+  "",        0,     0
+};
+
+int main()
+{
+  int E, V, T;
+  int i=0;
+  while (G[i].v > 0) {
+    cout << "\nGraph " << G[i].n << " V=" << G[i].v << " E=" << G[i].e << endl;
+    printf("Pct          T          ERLt       VarRLt       max_loss\n");
+    for(double p = 0.1; p<=1.0; p+=0.1) {
+      printf("%.2f",p);
+      set_max_loss(G[i].v, G[i].e, (int)((G[i].e * p)+0.5));
+    }
+    i++;
+  }
+}
+

Added: SwiftApps/SciColSim/maxloss.py
===================================================================
--- SwiftApps/SciColSim/maxloss.py	                        (rev 0)
+++ SwiftApps/SciColSim/maxloss.py	2012-12-23 04:33:21 UTC (rev 6110)
@@ -0,0 +1,39 @@
+#! /usr/bin/env python
+
+n = 0
+v = 1
+e = 2
+
+graphs = [ 
+     [ "movie",    500,    1008 ],
+     [ "big.001", 1857,    1312 ],
+     [ "big.002", 3094,    2683 ],
+     [ "big.005", 5405,    6776 ],
+     [ "big.01",  7765,   13421 ],
+     [ "big.10", 19281,  134594 ],
+     [ "big.20", 23258,  269133 ],
+     [ "big.30", 25484,  403401 ],
+     [ "big.40", 26821,  537106 ],
+     [ "big.50", 27774,  671179 ],
+     [ "big.60", 28482,  804774 ],
+     [ "big.70", 29055,  938061 ],
+     [ "big.80", 29487, 1072415 ],
+     [ "big.90", 29779, 1205741 ],
+     [ "big",    30060, 1338753 ], 
+     ]
+
+for G in graphs:
+	N = G[n]
+	V = G[v]
+	E = G[e]
+	print "\nGraph %s: V=%d E=%d\n" % (N,V,E)
+	for pct in range(1,11):
+		Tmax = int(E * (pct/10.0))
+		tl = 0.
+		vl = 0.
+		for t in range(Tmax):
+			tl = tl + float(V*(V-1.))/float(2.*(E-t))
+			vl = vl + float(V*(V-1.)/2. - E + t)/float((E-t)*(E-t))
+		tl /= float(Tmax)
+		vl /= float(Tmax)*float(Tmax)
+		print pct, Tmax, tl, vl


Property changes on: SwiftApps/SciColSim/maxloss.py
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftApps/SciColSim/maxloss_ar.py
===================================================================
--- SwiftApps/SciColSim/maxloss_ar.py	                        (rev 0)
+++ SwiftApps/SciColSim/maxloss_ar.py	2012-12-23 04:33:21 UTC (rev 6110)
@@ -0,0 +1,15 @@
+V = [500]
+E = [1008]
+
+curr = 0
+
+
+for Tmax in range(101,1009,101):
+        tl = 0.
+        vl = 0.
+        for t in range(Tmax):
+                tl = tl + float(V[0]*(V[0]-1.))/float(2.*(E[0]-t))
+                vl = vl + float(V[0]*(V[0]-1.)/2. - E[0] + t)/float((E[0]-t)*(E[0]-t))
+        tl /= float(Tmax)
+        vl /= float(Tmax)*float(Tmax)
+        print Tmax, tl, vl

Modified: SwiftApps/SciColSim/samplegraph.sh
===================================================================
--- SwiftApps/SciColSim/samplegraph.sh	2012-12-19 14:06:35 UTC (rev 6109)
+++ SwiftApps/SciColSim/samplegraph.sh	2012-12-23 04:33:21 UTC (rev 6110)
@@ -2,7 +2,7 @@
 
 fraction=${1:-1.0}
 
-tmp=$(mktemp -t samplegraph)
+tmp=$(mktemp -t samplegraph.XXXX)
 
 awk '
 
@@ -16,6 +16,7 @@
      
 BEGIN { 
   getmsec="perl -MTime::HiRes=gettimeofday -e \"print int(1000*gettimeofday()).qq(\\n);\""
+  getmsec="date +%N"
   getmsec | getline msec
   close(getmsec)
   _cliff_seed = (msec % 10000) / 10000

Modified: SwiftApps/SciColSim/testgraph.py
===================================================================
--- SwiftApps/SciColSim/testgraph.py	2012-12-19 14:06:35 UTC (rev 6109)
+++ SwiftApps/SciColSim/testgraph.py	2012-12-23 04:33:21 UTC (rev 6110)
@@ -138,12 +138,14 @@
   endTarget        = startTarget+1
   incrTarget       = 50
   optimizerRepeats = 1
+  # evolveReruns     = 1
   evolveReruns     = 1
   annealingSteps   = 1
-  NWorkers         = "2"
+  NWorkers         = "8"
   openmp           = "OMP_NUM_THREADS=" + NWorkers
   operation        = "m"  # n=normal, m=manual (runs 1 multi_loss call)
   seed             = "" # "123456"
+  app              = "./openmp-optimizer";
   app              = "./graphsim";
 
 # Ensure we dont pass new parameters to original optimizer versions
@@ -158,9 +160,7 @@
 
 for target in range(startTarget,endTarget,incrTarget):
   for i in range(optimizerRepeats):
-    args = "rm -f bestdb.txt; " + \
-           openmp + " " + "/usr/bin/time -l " + \
-                          app + " 0 0 0 0 0 " + str(target) + " 40000 20 " + str(evolveReruns) + \
+    args = "rm -f bestdb.txt;" +  openmp +" " + "/usr/bin/time --verbose " + app + " 0 0 0 0 0 " + str(target) + " 40000 20 " + str(evolveReruns) + \
            " 2 2 2. 0.01 " + str(annealingSteps) + " 0.3 2.3 0 0 0 0 0 " + operation + " " + NWorkers + " " + seed + \
            " # >& out.T"+str(target)+".i"+str(i) + "; #mv bestdb.txt best.T" + str(target) + ".i" + str(i) 
     print("\n**** Calling optimizer: "+args+"\n")



From davidk at ci.uchicago.edu  Wed Dec  5 14:21:36 2012
From: davidk at ci.uchicago.edu (davidk at ci.uchicago.edu)
Date: Wed, 05 Dec 2012 20:21:36 -0000
Subject: [Swift-commit] r6099 - in SwiftTutorials/UofC_2012-11-27-fusion: .
	bin data scripts
Message-ID: <20121205202135.D92CA9D050@svn.ci.uchicago.edu>

Author: davidk
Date: 2012-12-05 14:21:35 -0600 (Wed, 05 Dec 2012)
New Revision: 6099

Added:
   SwiftTutorials/UofC_2012-11-27-fusion/README
   SwiftTutorials/UofC_2012-11-27-fusion/bin/
   SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
   SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
   SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
   SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl
   SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
   SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
   SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c
   SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
   SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
   SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
   SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
   SwiftTutorials/UofC_2012-11-27-fusion/data/
   SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt
   SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp
   SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx
Log:
Files needed to run tutorials on fusion, with the additional of two new mpi examples


Added: SwiftTutorials/UofC_2012-11-27-fusion/README
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/README	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/README	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,100 @@
+
+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
+
+An output directory will be created by the Swift scripts
+
+
+Use bin/setup.sh to add tutorial programs to your PATH
+
+Run:
+
+source bin/setup.sh
+
+EXERCISE 1 - Run a simple command under Swift
+
+This script simply runs the getinfo command found in bin/getinfo.sh
+
+You can run this on the login node by typing:
+
+bin/getinfo.sh
+
+Inspect getinfo.sh to see what it does.
+
+The Swift syntax in scripts/script01.swift directs the output of
+getinfo.sh to file output/info.txt
+
+Run the Swift script by typing:
+
+runswift scripts/script01.swift
+
+Check that the output is created in the output directory
+
+EXERCISE 2 - Run parallel jobs
+
+The Swift syntax in scripts/script02.swift runs the getinfo
+script 25 times in parallel.  Each job produces an output
+file with a different name.
+
+runswift scripts/script02.swift
+
+Check that the output is created successfully
+
+EXERCISE 3 - Run parallel jobs with pipelines
+
+The Swift syntax in scripts/script02.swift runs the getinfo
+script 25 times in parallel.  Each job produces an output
+file with a different name.  Each output file is then read by the
+filterinfo task, which produces output in _concurrent
+
+Inspect bin/filterinfo.sh to see what it does to the output of getinfo.sh
+
+runswift scripts/script03.swift
+
+EXERCISE 4 - Name files in pipelines
+
+In Exercise 3, the final outputs were named by Swift.
+Exercise 4 is similar to 3 but allows you to name the final
+outputs.  Edit script04.swift to name the files in an appropriate
+way.
+
+EXERCISE 5 - Reduction
+
+Exercise 5 allows you to collect all of the filtered outputs
+and summarize them into one file.  This Swift script allows
+suminfo.sh to read all the files and collect a statistic.
+
+Inspect bin/suminfo.sh to see what it will do to the files it reads.
+
+EXERCISE 6 - Simple MPI test
+
+Exercise 6 is a simple MPI test. Each rank of the MPI job
+runs a "hostname" command and creates a file. The files
+get added to a tar file - output/results.tar. A wrapper
+script, bin/testmpi.sh runs mpiexec to launch the test 
+mpi program. This application uses the Fusion batch
+queue to request 2 nodes.
+
+View output/results.tar to see the results.
+
+EXERCISE 7 - NAMD MPI test
+
+Exercise 7 is a real application that runs NAMD
+using MPI. It is a simple parameter sweep that
+changes some values in the input files then does
+the run. Like exercise 6, this uses the batch queue
+with 2 nodes.
+
+CLEAN UP
+
+Simply run: bin/cleanup and enter y to confirm

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+echo Removing:
+echo
+ls -ltd script??-* swiftwork _concurrent output *.kml *.swiftx swift.log applist config sites.xml pathlist 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 script??-* swiftwork _concurrent output *.kml *.swiftx swift.log applist config sites.xml pathlist
+else
+  echo
+  echo No files removed.
+fi
+


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,2 @@
+#! /bin/sh
+grep getinfo.sh $1 | wc -l >$2


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,10 @@
+cat <<END
+cluster cat        /bin/cat               null null null
+cluster sh         /bin/sh                null null null
+cluster getinfo    $PWD/bin/getinfo.sh    null null null
+cluster filterinfo $PWD/bin/filterinfo.sh null null null
+cluster suminfo    $PWD/bin/suminfo.sh    null null null
+clustermpi rmsd    $PWD/bin/rmsd.sh       null null null
+clustermpi plot_pd $PWD/bin/plot_pd.pl    null null null
+clustermpi testmpi $PWD/bin/testmpi.sh    null null null
+END


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+hostname -f
+date
+sleep 2
+ps -u $USER -H


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+hostname -f
+date
+sleep 3
+ps -u $USER -H -f


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,70 @@
+#!/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, ">", "output/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 "output/rmsd.$b1name${b1}_$b2name${b2}.dat")
+		{	
+			open(INPUT, "<", "output/rmsd.$b1name${b1}_$b2name${b2}.dat");
+			$_ = <INPUT>;
+
+			my @data = split(/ +/,$_);
+        		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/UofC_2012-11-27-fusion/bin/plot_pd.pl
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,47 @@
+#!/bin/bash 
+
+b1=$1
+b2=$2
+b1name=$3
+b2name=$4
+namd_input=$5
+namd_parameters=$6
+vmd_script=$7
+
+echo Command line arguments: $@
+echo
+
+echo Hostname: $( hostname )
+echo
+
+echo File listing
+echo ------------
+find
+echo
+
+echo Running the following sed commands
+echo sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
+sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
+sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
+sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
+echo Done with sed
+echo
+
+namd2=$( which namd2 )
+echo Found namd2 at $namd2
+echo About to run mpiexec -machinefile $PBS_NODEFILE $namd2 $namd_input 
+mpiexec -machinefile $PBS_NODEFILE $namd2 $namd_input 
+
+echo
+echo About to run vmd -dispdev text -e $vmd_script 
+vmd -dispdev text -e $vmd_script 
+
+mv output/cg_clath_cage.dcd output/cg_clath_cage-$b1-$b2.dcd
+mv rmsd.dat output/rmsd.$b1name${b1}_$b2name${b2}.dat
+
+echo
+echo Files at end of run
+find
+echo


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,75 @@
+#! /bin/sh
+
+cat <<END >pathlist
+rule .*_concurrent/.* DIRECT $PWD/tmp
+rule .*               DIRECT /
+END
+
+cat <<END >config
+status.mode=provider
+use.provider.staging=false
+use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+file.gc.enabled=false
+tcp.port.range=50000,51000
+END
+
+reservationID=${reservationID:-swift}
+
+cat <<END >sites.xml
+
+<config>
+
+<pool handle="local">
+  <execution provider="local"/>
+  <profile namespace="karajan" key="jobThrottle">0.03</profile>
+  <profile namespace="karajan" key="initialScore">10000</profile>
+  <filesystem provider="local" url="none" />
+  <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+<pool handle="cluster">
+        <execution jobmanager="local:pbs" provider="coaster" url="none"/>
+        <filesystem provider="local" url="none" />
+        <profile namespace="globus" key="maxtime">3600</profile>
+        <profile namespace="globus" key="jobsPerNode">8</profile>
+        <profile namespace="globus" key="queue">shared</profile>
+        <profile namespace="globus" key="nodeGranularity">1</profile>
+        <profile namespace="globus" key="maxNodes">1</profile>
+        <profile namespace="karajan" key="jobThrottle">1.0</profile>
+        <profile namespace="karajan" key="initialScore">100</profile>
+        <profile namespace="globus" key="HighOverAllocation">100</profile>
+        <profile namespace="globus" key="LowOverAllocation">100</profile>
+        <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+<pool handle="clustermpi">
+  <execution jobmanager="local:pbs" provider="pbs" url="none"/>
+  <filesystem provider="local" url="none" />
+  <profile namespace="globus" key="maxtime">60</profile>
+  <profile namespace="globus" key="jobsPerNode">1</profile>
+  <profile namespace="globus" key="ppn">8</profile>
+  <profile namespace="karajan" key="jobThrottle">5.99</profile>
+  <profile namespace="karajan" key="initialScore">10000</profile>
+  <profile namespace="globus" key="count">2</profile>
+  <profile namespace="globus" key="jobType">single</profile>
+  <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+</config>
+
+END
+
+genapplist >applist
+
+set -x
+#swift -config config -tc.file applist -sites.file sites.xml -cdm.file pathlist $*
+swift -config config -tc.file applist -sites.file sites.xml $*
+
+
+
+


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1 @@
+PATH=/homes/davidk/swift-0.94/cog/modules/swift/dist/swift-svn/bin:/homes/davidk/namd_2.8-intel-openmpi:/homes/davidk/vmd:$PWD/bin:$PATH

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,2 @@
+#! /bin/sh
+awk '{ sum += $1 } END { print "Total processes observed: " sum }' $*


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
___________________________________________________________________
Added: svn:executable
   + *
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,51 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <mpi.h>
+#include <string.h>
+
+int main (argc, argv)
+     int argc;
+     char *argv[];
+{
+  int rank, size;
+
+  MPI_Init (&argc, &argv);			/* starts MPI */
+  MPI_Comm_rank (MPI_COMM_WORLD, &rank);	/* get current process id */
+  MPI_Comm_size (MPI_COMM_WORLD, &size);	/* get number of processes */
+
+  FILE *fp, *command;
+  char filename[100];
+  char hostname[1024];
+
+  sprintf(filename, "output.%d.txt", rank);
+  printf("Trying to write output to %s\n", filename);
+  fp = fopen(filename, "w");
+
+  if (fp == NULL) {
+     printf("Unable to write file\n");
+     exit(0);
+  } 
+
+  command = popen("/bin/hostname -f", "r");
+  if(command == NULL) {
+     printf("Failed to run command\n");
+     exit(1);
+  }
+
+  while (fgets(hostname, sizeof(hostname)-1, command) != NULL) {
+    hostname[(strlen(hostname)-1)] = '\0';
+    fprintf(fp, "Hostname: %s, rank: %d\n", hostname, rank);
+  }
+
+  fclose(fp);
+  printf("Done writing output file %s\n", filename);
+
+  MPI_Finalize();
+
+  // Create a tar file of results (only once)
+  if(rank == 0) {
+     system("mkdir output");
+     system("tar cvf output/results.tar output*.txt");
+  }
+  return 0;
+}

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+mpiexec -machinefile $PBS_NODEFILE /homes/davidk/testmpi/testmpi


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,83 @@
+# NAMD Config file - autogenerated by NAMDgui plugin
+# Author: Jan Saam,  saam at charite.de
+
+# input
+coordinates             cg_clath_cage.pdb
+structure               cg_clath_cage.psf
+parameters              par_cg_clath.inp
+paratypecharmm          on
+
+# output
+set output              output/cg_clath_cage
+outputname              $output
+dcdfile                 ${output}.dcd
+xstFile                 ${output}.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			350
+switching               on
+switchdist              348                 
+pairlistdist            352
+
+# Multiple timestepping
+firsttimestep           0
+timestep                10
+stepspercycle           1
+nonbondedFreq           1
+fullElectFrequency      1
+rigidBonds              all
+
+# Temperature control
+
+set temperature         310
+temperature             $temperature;  # initial temperature
+
+# Langevin Dynamics
+langevin                on;            # do langevin dynamics
+langevinDamping         0.001             # 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 310
+#minimize 10000
+#for { set TEMP 310 } { $TEMP <= 650 } { incr TEMP 5 } {
+#  run 10000
+#  reassignTemp $TEMP
+#  langevinTemp $TEMP
+#}
+#
+#run 1000000
+#
+#for { set TEMP 650 } { $TEMP >= 310 } { incr TEMP -5 } {
+#  reassignTemp $TEMP
+#  langevinTemp $TEMP
+#  run 10000
+#} 
+#run 1000000
+
+minimize            1000
+reinitvels          $temperature
+run                 2000
+


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb	2012-12-05 20:21:35 UTC (rev 6099)
@@ -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


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf	2012-12-05 20:21:35 UTC (rev 6099)
@@ -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
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+       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
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+     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
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+     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
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+     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
+     209     218     219     209     214     215     209     210     211
+     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
+     222     231     232     222     227     228     222     223     224
+     223     224     225     223     222     231     223     222     227
+     224     225     226     227     228     229     227     222     231
+     228     229     230     231     232     233     232     233     234
+     235     244     245     235     240     241     235     236     237
+     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
+     261     270     271     261     266     267     261     262     263
+     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
+     280     281     282     283     284     285     284     285     286
+     287     296     297     287     292     293     287     288     289
+     288     289     290     288     287     296     288     287     292
+     289     290     291     292     293     294     292     287     296
+     293     294     295     296     297     298     297     298     299
+     300     309     310     300     305     306     300     301     302
+     301     302     303     301     300     309     301     300     305
+     302     303     304     305     306     307     305     300     309
+     306     307     308     309     310     311     310     311     312
+     313     322     323     313     318     319     313     314     315
+     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
+     456     465     466     456     461     462     456     457     458
+     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
+     114     115     116     117     118     119     120     121
+     118     123     124     125     118     127     128     129
+     119     123     118     127     119     118     123     124
+     119     118     127     128     119     120     121     122
+     123     118     119     120     123     118     127     128
+     123     124     125     126     127     118     119     120
+     127     118     123     124     127     128     129     130
+     131     132     133     134     131     136     137     138
+     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
+     140     141     142     143     144     145     146     147
+     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
+     157     158     159     160     157     162     163     164
+     157     166     167     168     158     162     157     166
+     158     157     162     163     158     157     166     167
+     158     159     160     161     162     157     158     159
+     162     157     166     167     162     163     164     165
+     166     157     158     159     166     157     162     163
+     166     167     168     169     170     171     172     173
+     170     175     176     177     170     179     180     181
+     171     175     170     179     171     170     175     176
+     171     170     179     180     171     172     173     174
+     175     170     171     172     175     170     179     180
+     175     176     177     178     179     170     171     172
+     179     170     175     176     179     180     181     182
+     183     184     185     186     183     188     189     190
+     183     192     193     194     184     188     183     192
+     184     183     188     189     184     183     192     193
+     184     185     186     187     188     183     184     185
+     188     183     192     193     188     189     190     191
+     192     183     184     185     192     183     188     189
+     192     193     194     195     196     197     198     199
+     196     201     202     203     196     205     206     207
+     197     201     196     205     197     196     201     202
+     197     196     205     206     197     198     199     200
+     201     196     197     198     201     196     205     206
+     201     202     203     204     205     196     197     198
+     205     196     201     202     205     206     207     208
+     209     210     211     212     209     214     215     216
+     209     218     219     220     210     214     209     218
+     210     209     214     215     210     209     218     219
+     210     211     212     213     214     209     210     211
+     214     209     218     219     214     215     216     217
+     218     209     210     211     218     209     214     215
+     218     219     220     221     222     223     224     225
+     222     227     228     229     222     231     232     233
+     223     227     222     231     223     222     227     228
+     223     222     231     232     223     224     225     226
+     227     222     223     224     227     222     231     232
+     227     228     229     230     231     222     223     224
+     231     222     227     228     231     232     233     234
+     235     236     237     238     235     240     241     242
+     235     244     245     246     236     240     235     244
+     236     235     240     241     236     235     244     245
+     236     237     238     239     240     235     236     237
+     240     235     244     245     240     241     242     243
+     244     235     236     237     244     235     240     241
+     244     245     246     247     248     249     250     251
+     248     253     254     255     248     257     258     259
+     249     253     248     257     249     248     253     254
+     249     248     257     258     249     250     251     252
+     253     248     249     250     253     248     257     258
+     253     254     255     256     257     248     249     250
+     257     248     253     254     257     258     259     260
+     261     262     263     264     261     266     267     268
+     261     270     271     272     262     266     261     270
+     262     261     266     267     262     261     270     271
+     262     263     264     265     266     261     262     263
+     266     261     270     271     266     267     268     269
+     270     261     262     263     270     261     266     267
+     270     271     272     273     274     275     276     277
+     274     279     280     281     274     283     284     285
+     275     279     274     283     275     274     279     280
+     275     274     283     284     275     276     277     278
+     279     274     275     276     279     274     283     284
+     279     280     281     282     283     274     275     276
+     283     274     279     280     283     284     285     286
+     287     288     289     290     287     292     293     294
+     287     296     297     298     288     292     287     296
+     288     287     292     293     288     287     296     297
+     288     289     290     291     292     287     288     289
+     292     287     296     297     292     293     294     295
+     296     287     288     289     296     287     292     293
+     296     297     298     299     300     301     302     303
+     300     305     306     307     300     309     310     311
+     301     305     300     309     301     300     305     306
+     301     300     309     310     301     302     303     304
+     305     300     301     302     305     300     309     310
+     305     306     307     308     309     300     301     302
+     309     300     305     306     309     310     311     312
+     313     314     315     316     313     318     319     320
+     313     322     323     324     314     318     313     322
+     314     313     318     319     314     313     322     323
+     314     315     316     317     318     313     314     315
+     318     313     322     323     318     319     320     321
+     322     313     314     315     322     313     318     319
+     322     323     324     325     326     327     328     329
+     326     331     332     333     326     335     336     337
+     327     331     326     335     327     326     331     332
+     327     326     335     336     327     328     329     330
+     331     326     327     328     331     326     335     336
+     331     332     333     334     335     326     327     328
+     335     326     331     332     335     336     337     338
+     339     340     341     342     339     344     345     346
+     339     348     349     350     340     344     339     348
+     340     339     344     345     340     339     348     349
+     340     341     342     343     344     339     340     341
+     344     339     348     349     344     345     346     347
+     348     339     340     341     348     339     344     345
+     348     349     350     351     352     353     354     355
+     352     357     358     359     352     361     362     363
+     353     357     352     361     353     352     357     358
+     353     352     361     362     353     354     355     356
+     357     352     353     354     357     352     361     362
+     357     358     359     360     361     352     353     354
+     361     352     357     358     361     362     363     364
+     365     366     367     368     365     370     371     372
+     365     374     375     376     366     370     365     374
+     366     365     370     371     366     365     374     375
+     366     367     368     369     370     365     366     367
+     370     365     374     375     370     371     372     373
+     374     365     366     367     374     365     370     371
+     374     375     376     377     378     379     380     381
+     378     383     384     385     378     387     388     389
+     379     383     378     387     379     378     383     384
+     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
+


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1 @@
+Hi Swift!

Added: SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,80 @@
+* 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/UofC_2012-11-27-fusion/rmsd.temp.tcl
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl	2012-12-05 20:21:35 UTC (rev 6099)
@@ -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 cg_clath_cage.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.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/UofC_2012-11-27-fusion/scripts/catsn.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,12 @@
+type file;
+
+app (file o) cat (file i)
+{
+  cat @i stdout=@o;
+}
+
+file out[]<simple_mapper; location="outdir", prefix="f.",suffix=".out">;
+foreach j in [1:@toint(@arg("n","1"))] {
+  file data<"data.txt">;
+  out[j] = cat(data);
+}

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,9 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+file info <"output/info.txt">;
+info = getinfo();

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,13 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+foreach i in [0:24] {
+  string fname = @strcat("output/info.",i,".txt");
+  file info <single_file_mapper; file=fname>;
+  info = getinfo();
+}
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,19 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+app (file o) filterinfo (file i)
+{
+  filterinfo @i @o;
+}
+
+foreach i in [0:24] {
+  string fname = @strcat("output/info.",i,".txt");
+  file info <single_file_mapper; file=fname>;
+  info = getinfo();
+  file filtered = filterinfo(info);
+}
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,25 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+app (file o) filter (file i)
+{
+  filterinfo @i @o;
+}
+
+file filtered[];
+
+foreach i in [0:24] {
+  string fname = @strcat("output/info.",i,".txt");
+  file info <single_file_mapper; file=fname>;
+  info = getinfo();
+  // replace: filtered[i] = filter(info);
+  // with:
+  string filfname = ???
+  filfname = 
+  filtered[i] = 
+}
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,30 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+app (file o) filter (file i)
+{
+  filterinfo @i @o;
+}
+
+app (file o) reduce (file i[])
+{
+  suminfo @filenames(i) stdout=@o;
+}
+
+file filtered[];
+
+foreach i in [0:24] {
+  string fname = @strcat("output/info.",i,".txt");
+  file info <single_file_mapper; file=fname>;
+  info = getinfo();
+  filtered[i] = filter(info);
+}
+
+file sum<"output/sum.data">;
+
+sum = reduce(filtered);
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,9 @@
+type file;
+
+app (file r) testmpi ()
+{
+  testmpi;
+}
+
+file results <"output/results.tar">;
+results = testmpi();

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,451 @@
+<project><!-- CACHE ID fde29c67-b524-4558-b5f9-1228186b92ec-no-provenance -->
+  <import file="sys.xml"/>
+  <import file="scheduler.xml"/>
+  <import file="rlog.xml"/>
+  <import file="vdl.k"/>
+  <types>
+     <xs:schema targetNamespace="http://ci.uchicago.edu/swift/2009/02/swiftscript" xmlns="http://ci.uchicago.edu/swift/2009/02/swiftscript" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+      	   <xs:simpleType name="file">
+      	   <xs:restriction base="string"/>
+      	   </xs:simpleType>
+     </xs:schema>
+  </types>
+  <global name="swift#string#17013">
+    <vdl:new type="string" value=".dcd" />
+  </global>
+  <global name="swift#string#17006">
+    <vdl:new type="string" value="logs/rmsd-" />
+  </global>
+  <global name="swift#string#17012">
+    <vdl:new type="string" value="output/cg_clath_cage-" />
+  </global>
+  <global name="swift#string#17010">
+    <vdl:new type="string" value=".err.txt" />
+  </global>
+  <global name="swift#string#17001">
+    <vdl:new type="string" value="DT" />
+  </global>
+  <global name="swift#string#17017">
+    <vdl:new type="string" value=".dat" />
+  </global>
+  <global name="swift#string#17016">
+    <vdl:new type="string" value="_" />
+  </global>
+  <global name="swift#string#17000">
+    <vdl:new type="string" value="PX" />
+  </global>
+  <global name="swift#string#17015">
+    <vdl:new type="string" value="output/rmsd." />
+  </global>
+  <global name="swift#string#17008">
+    <vdl:new type="string" value=".out.txt" />
+  </global>
+  <global name="swift#string#17007">
+    <vdl:new type="string" value="-" />
+  </global>
+  <global name="swift#float#17003">
+    <vdl:new type="float" value="1.0" />
+  </global>
+  <global name="swift#float#17002">
+    <vdl:new type="float" value="0.0" />
+  </global>
+  <global name="swift#float#17004">
+    <vdl:new type="float" value="0.5" />
+  </global>
+  <element name="rmsd" arguments="o,e,dcdf,datf,b1_val,b2_val,b1_name,b2_name,namd_input_file,namd_params_file,vmd_script_file,psf_file,pdb_file" _defline="3">
+     
+     
+     
+     
+     
+     
+     
+     
+     
+     
+     
+     
+     
+    <unitStart name="rmsd" line="3" type="PROCEDURE" outputs="o,e,dcdf,datf"/>
+    <vdl:execute>
+      <vdl:tr>rmsd</vdl:tr>
+      <vdl:stagein var="{b1_val}"/>
+      <vdl:stagein var="{b2_val}"/>
+      <vdl:stagein var="{b1_name}"/>
+      <vdl:stagein var="{b2_name}"/>
+      <vdl:stagein var="{namd_input_file}"/>
+      <vdl:stagein var="{namd_params_file}"/>
+      <vdl:stagein var="{vmd_script_file}"/>
+      <vdl:stagein var="{psf_file}"/>
+      <vdl:stagein var="{pdb_file}"/>
+      <vdl:stageout var="{o}"/>
+      <vdl:stageout var="{e}"/>
+      <vdl:stageout var="{dcdf}"/>
+      <vdl:stageout var="{datf}"/>
+
+      <vdl:arguments>
+        <variable>b1_val</variable>
+        <variable>b2_val</variable>
+        <variable>b1_name</variable>
+        <variable>b2_name</variable>
+        <swiftscript:filename _traceline="5">
+         <variable>namd_input_file</variable> 
+        </swiftscript:filename>
+        <swiftscript:filename _traceline="5">
+         <variable>namd_params_file</variable> 
+        </swiftscript:filename>
+        <swiftscript:filename _traceline="5">
+         <variable>vmd_script_file</variable> 
+        </swiftscript:filename>
+      </vdl:arguments>
+      <vdl:stdout>
+        <swiftscript:filename _traceline="5">
+         <variable>o</variable> 
+        </swiftscript:filename>
+      </vdl:stdout><vdl:stderr>
+        <swiftscript:filename _traceline="5">
+         <variable>e</variable> 
+        </swiftscript:filename>
+      </vdl:stderr>
+    </vdl:execute>
+    <vdl:closedataset var="{o}"/>
+    <vdl:closedataset var="{e}"/>
+    <vdl:closedataset var="{dcdf}"/>
+    <vdl:closedataset var="{datf}"/>
+    <unitEnd name="rmsd" line="3" type="PROCEDURE"/></element>
+
+  <set name="b1name">
+        <vdl:new type="string" dbgname="b1name" waitfor="88000" _defline="9"/>
+  </set>
+   
+  <set name="b2name">
+        <vdl:new type="string" dbgname="b2name" waitfor="88001" _defline="10"/>
+  </set>
+   
+  <set name="b1min">
+        <vdl:new type="float" dbgname="b1min" waitfor="88002" _defline="13"/>
+  </set>
+   
+  <set name="b1max">
+        <vdl:new type="float" dbgname="b1max" waitfor="88003" _defline="14"/>
+  </set>
+   
+  <set name="b2min">
+        <vdl:new type="float" dbgname="b2min" waitfor="88004" _defline="15"/>
+  </set>
+   
+  <set name="b2max">
+        <vdl:new type="float" dbgname="b2max" waitfor="88005" _defline="16"/>
+  </set>
+   
+  <set name="delta">
+        <vdl:new type="float" dbgname="delta" waitfor="88006" _defline="19"/>
+  </set>
+   
+  <set name="namd_params">
+        <vdl:new type="file" dbgname="namd_params" _defline="22">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="par_cg_clath.inp"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="namd_input">
+        <vdl:new type="file" dbgname="namd_input" _defline="23">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="cg_clath_cage.conf"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="vmd_script">
+        <vdl:new type="file" dbgname="vmd_script" _defline="24">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="rmsd.temp.tcl"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="psf">
+        <vdl:new type="file" dbgname="psf" _defline="25">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="cg_clath_cage.psf"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="pdb">
+        <vdl:new type="file" dbgname="pdb" _defline="26">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="cg_clath_cage.pdb"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="dats">
+    <vdl:new type="file[float][float]" dbgname="dats" waitfor="88013" _defline="27">
+      <vdl:mapping descriptor="concurrent_mapper">
+        <vdl:parameter name="prefix">dats-345532ce-25ec-45f9-933b-4d188d42079b</vdl:parameter>
+      </vdl:mapping>
+    </vdl:new>
+  </set>
+   
+  <restartLog>
+  	<vdl:mains>
+		<vdl:startprogressticker />
+		<vdl:mainp>
+		    <uparallel>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b1name"/>
+		             <vdl:setfieldvalue _traceline="10">
+		                 <variable>b1name</variable>
+		                 <variable>swift#string#17000</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b1name}" closeID="88000" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b2name"/>
+		             <vdl:setfieldvalue _traceline="13">
+		                 <variable>b2name</variable>
+		                 <variable>swift#string#17001</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b2name}" closeID="88001" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b1min"/>
+		             <vdl:setfieldvalue _traceline="14">
+		                 <variable>b1min</variable>
+		                 <variable>swift#float#17002</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b1min}" closeID="88002" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b1max"/>
+		             <vdl:setfieldvalue _traceline="15">
+		                 <variable>b1max</variable>
+		                 <variable>swift#float#17003</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b1max}" closeID="88003" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b2min"/>
+		             <vdl:setfieldvalue _traceline="16">
+		                 <variable>b2min</variable>
+		                 <variable>swift#float#17002</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b2min}" closeID="88004" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b2max"/>
+		             <vdl:setfieldvalue _traceline="19">
+		                 <variable>b2max</variable>
+		                 <variable>swift#float#17003</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b2max}" closeID="88005" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="delta"/>
+		             <vdl:setfieldvalue _traceline="22">
+		                 <variable>delta</variable>
+		                 <variable>swift#float#17004</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{delta}" closeID="88006" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="dats"/>
+		          <vdl:tparallelFor name="$"  _traceline="29" 
+		           _vvar="b1">
+		            <getarrayiterator><sequential>
+		           <set name="swift#from"><variable>b1min</variable></set>
+		           <set name="swift#to"><variable>b1max</variable></set>
+		           <set name="swift#step"><variable>delta</variable></set>
+		           <set name="swift#rangeout">
+		            <vdl:range>
+		              <argument name="from"><variable>swift#from</variable></argument>
+		              <argument name="to"><variable>swift#to</variable></argument>
+		              <argument name="step"><variable>swift#step</variable></argument>
+		            </vdl:range>
+		           </set>
+		            
+		           <variable>swift#rangeout</variable>
+		          </sequential></getarrayiterator>
+		            <set names="$$, b1">
+		              <each items="{$}"/>
+		            </set>
+		          	<unitStart line="29" type="FOREACH_IT"/>
+
+		                <sequentialWithID>
+		                    <sequential>
+		                      <vdl:tparallelFor name="$"  
+		                       _vvar="b2">
+		                        <getarrayiterator><sequential>
+		                       <set name="swift#from"><variable>b2min</variable></set>
+		                       <set name="swift#to"><variable>b2max</variable></set>
+		                       <set name="swift#step"><variable>delta</variable></set>
+		                       <set name="swift#rangeout">
+		                        <vdl:range>
+		                          <argument name="from"><variable>swift#from</variable></argument>
+		                          <argument name="to"><variable>swift#to</variable></argument>
+		                          <argument name="step"><variable>swift#step</variable></argument>
+		                        </vdl:range>
+		                       </set>
+		                        
+		                       <variable>swift#rangeout</variable>
+		                      </sequential></getarrayiterator>
+		                        <set names="$$, b2">
+		                          <each items="{$}"/>
+		                        </set>
+		                      	<unitStart line="30" type="FOREACH_IT"/>
+
+		                          <set name="swift#mapper#17005">
+		                                <vdl:new type="string" dbgname="swift#mapper#17005" waitfor="" _defline=""/>
+		                          </set>
+		                           
+		                          <set name="output">
+		                            <vdl:new type="file" dbgname="output" waitfor="88008" _defline="31">
+		                              <vdl:mapping descriptor="single_file_mapper">
+		                                <vdl:parameter name="file"><variable>swift#mapper#17005</variable></vdl:parameter>
+		                              </vdl:mapping>
+		                            </vdl:new>
+		                          </set>
+		                           
+		                          <set name="swift#mapper#17009">
+		                                <vdl:new type="string" dbgname="swift#mapper#17009" waitfor="" _defline=""/>
+		                          </set>
+		                           
+		                          <set name="error">
+		                            <vdl:new type="file" dbgname="error" waitfor="88009" _defline="32">
+		                              <vdl:mapping descriptor="single_file_mapper">
+		                                <vdl:parameter name="file"><variable>swift#mapper#17009</variable></vdl:parameter>
+		                              </vdl:mapping>
+		                            </vdl:new>
+		                          </set>
+		                           
+		                          <set name="swift#mapper#17011">
+		                                <vdl:new type="string" dbgname="swift#mapper#17011" waitfor="" _defline=""/>
+		                          </set>
+		                           
+		                          <set name="dcd">
+		                            <vdl:new type="file" dbgname="dcd" waitfor="88010" _defline="33">
+		                              <vdl:mapping descriptor="single_file_mapper">
+		                                <vdl:parameter name="file"><variable>swift#mapper#17011</variable></vdl:parameter>
+		                              </vdl:mapping>
+		                            </vdl:new>
+		                          </set>
+		                           
+		                          <set name="swift#mapper#17014">
+		                                <vdl:new type="string" dbgname="swift#mapper#17014" waitfor="" _defline=""/>
+		                          </set>
+		                           
+		                          <set name="dat">
+		                            <vdl:new type="file" dbgname="dat" waitfor="88011" _defline="34">
+		                              <vdl:mapping descriptor="single_file_mapper">
+		                                <vdl:parameter name="file"><variable>swift#mapper#17014</variable></vdl:parameter>
+		                              </vdl:mapping>
+		                            </vdl:new>
+		                          </set>
+		                           
+		                            <uparallel>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="-1">
+		                                         <variable>swift#mapper#17005</variable>
+		                                         <swiftscript:strcat _traceline="31">
+		                                          <variable>swift#string#17006</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17008</variable> 
+		                                         </swiftscript:strcat>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="-1">
+		                                         <variable>swift#mapper#17009</variable>
+		                                         <swiftscript:strcat _traceline="32">
+		                                          <variable>swift#string#17006</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17010</variable> 
+		                                         </swiftscript:strcat>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="-1">
+		                                         <variable>swift#mapper#17011</variable>
+		                                         <swiftscript:strcat _traceline="33">
+		                                          <variable>swift#string#17012</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17013</variable> 
+		                                         </swiftscript:strcat>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="-1">
+		                                         <variable>swift#mapper#17014</variable>
+		                                         <swiftscript:strcat _traceline="34">
+		                                          <variable>swift#string#17015</variable><variable>b1name</variable><variable>b1</variable><variable>swift#string#17016</variable><variable>b2name</variable><variable>b2</variable><variable>swift#string#17017</variable> 
+		                                         </swiftscript:strcat>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="36">
+		                                         <vdl:getfieldsubscript>
+		                                           <argument name="var"><vdl:getfieldsubscript>
+		                                           <argument name="var"><variable>dats</variable></argument>
+		                                           <argument name="subscript"><variable>b1</variable></argument>
+		                                         </vdl:getfieldsubscript></argument>
+		                                           <argument name="subscript"><variable>b2</variable></argument>
+		                                         </vdl:getfieldsubscript>
+		                                         <variable>dat</variable>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                    <unitStart type="SCOPE" outputs="output,error,dcd,dat"/>
+		                                  <rmsd _traceline="36">
+		                                      <variable>output</variable>
+		                                      <variable>error</variable>
+		                                      <variable>dcd</variable>
+		                                      <variable>dat</variable>
+		                                      <variable>b1</variable>
+		                                      <variable>b2</variable>
+		                                      <variable>b1name</variable>
+		                                      <variable>b2name</variable>
+		                                      <variable>namd_input</variable>
+		                                      <variable>namd_params</variable>
+		                                      <variable>vmd_script</variable>
+		                                      <variable>psf</variable>
+		                                      <variable>pdb</variable>
+		                                  </rmsd>
+		                                    <unitEnd type="SCOPE"/>
+		                                </sequential>
+		                            </uparallel>
+		                            <vdl:cleandataset var="{dat}"/>
+		                            <vdl:cleandataset var="{error}"/>
+		                            <vdl:cleandataset var="{dcd}"/>
+		                            <vdl:cleandataset var="{output}"/>
+		                          <unitEnd line="30" type="FOREACH_IT"/>
+		                      </vdl:tparallelFor>
+		                    </sequential>
+		                </sequentialWithID>
+
+		              <unitEnd line="29" type="FOREACH_IT"/>
+		          </vdl:tparallelFor>
+		            <partialCloseDataset var="{dats}" closeID="88013" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		    </uparallel>
+		</vdl:mainp>
+		<vdl:stopprogressticker />
+	</vdl:mains>
+  </restartLog>
+  <vdl:cleandataset var="{namd_params}"/>
+  <vdl:cleandataset var="{vmd_script}"/>
+  <vdl:cleandataset var="{psf}"/>
+  <vdl:cleandataset var="{namd_input}"/>
+  <vdl:cleandataset var="{pdb}"/>
+  <vdl:cleandataset var="{dats}"/>
+  <vdl:cleandataset shutdown="true"/>
+</project>

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,38 @@
+type file;
+
+app (file o, file e, file dcdf, file datf) rmsd (float b1_val, float b2_val, string b1_name, string b2_name, file namd_input_file, file namd_params_file, file vmd_script_file, file psf_file, file pdb_file)
+{
+  rmsd b1_val b2_val b1_name b2_name @namd_input_file @namd_params_file @vmd_script_file stdout=@o stderr=@e;
+}
+
+# Bead names
+string b1name = "PX";
+string b2name = "DT";
+
+# Bead ranges
+float b1min=0.0;
+float b1max=1.0;
+float b2min=0.0;
+float b2max=1.0;
+
+# Delta
+float delta=0.5;
+
+# Files
+file namd_params <"par_cg_clath.inp">;
+file namd_input <"cg_clath_cage.conf">;
+file vmd_script <"rmsd.temp.tcl">;
+file psf <"cg_clath_cage.psf">;
+file pdb <"cg_clath_cage.pdb">;
+file[float][float] dats;
+
+foreach b1 in [b1min:b1max:delta] {
+   foreach b2 in [b2min:b2max:delta] {
+      file output <single_file_mapper; file=@strcat("logs/rmsd-", b1, "-", b2, ".out.txt")>;
+      file error <single_file_mapper; file=@strcat("logs/rmsd-", b1, "-", b2, ".err.txt")>;
+      file dcd <single_file_mapper; file=@strcat("output/cg_clath_cage-", b1, "-", b2, ".dcd")>;
+      file dat <single_file_mapper; file=@strcat("output/rmsd.", b1name, b1, "_", b2name, b2, ".dat")>;
+      dats[b1][b2] = dat;
+      (output, error, dcd, dat) = rmsd(b1, b2, b1name, b2name, namd_input, namd_params, vmd_script, psf, pdb);
+   }
+}

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,157 @@
+<program xmlns="http://ci.uchicago.edu/swift/2009/02/swiftscript"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xmlns:xs="http://www.w3.org/2001/XMLSchema">
+  <types>
+     	<type>
+     		<typename>file</typename>
+     		<typealias>string</typealias>
+     		<typestructure></typestructure>
+     	</type>
+  </types>
+  <procedure name="rmsd" src="line 3">
+
+    <output name="o" type="file"  xsi:nil="true"/>
+
+    <output name="e" type="file"  xsi:nil="true"/>
+
+    <output name="dcdf" type="file"  xsi:nil="true"/>
+
+    <output name="datf" type="file"  xsi:nil="true"/>
+
+    <input name="b1_val" type="float"  xsi:nil="true"/>
+
+    <input name="b2_val" type="float"  xsi:nil="true"/>
+
+    <input name="b1_name" type="string"  xsi:nil="true"/>
+
+    <input name="b2_name" type="string"  xsi:nil="true"/>
+
+    <input name="namd_input_file" type="file"  xsi:nil="true"/>
+
+    <input name="namd_params_file" type="file"  xsi:nil="true"/>
+
+    <input name="vmd_script_file" type="file"  xsi:nil="true"/>
+
+    <input name="psf_file" type="file"  xsi:nil="true"/>
+
+    <input name="pdb_file" type="file"  xsi:nil="true"/>
+    <binding>
+      <application src="line 3">
+        <executable>rmsd</executable>
+        <stdout><function name="filename" src="line 5">
+          <variableReference>o</variableReference></function></stdout><stderr><function name="filename" src="line 5">
+          <variableReference>e</variableReference></function></stderr><variableReference>b1_val</variableReference><variableReference>b2_val</variableReference><variableReference>b1_name</variableReference><variableReference>b2_name</variableReference><function name="filename" src="line 5">
+          <variableReference>namd_input_file</variableReference></function><function name="filename" src="line 5">
+          <variableReference>namd_params_file</variableReference></function><function name="filename" src="line 5">
+          <variableReference>vmd_script_file</variableReference></function>  </application>
+    </binding>
+  </procedure>
+  <variable name="b1name" type="string" isGlobal="false" xsi:nil="true" src="line 9"/>
+  <assign src="line 10">
+   <variableReference>b1name</variableReference>
+   <stringConstant>PX</stringConstant>
+  </assign>
+  <variable name="b2name" type="string" isGlobal="false" xsi:nil="true" src="line 10"/>
+  <assign src="line 13">
+   <variableReference>b2name</variableReference>
+   <stringConstant>DT</stringConstant>
+  </assign>
+  <variable name="b1min" type="float" isGlobal="false" xsi:nil="true" src="line 13"/>
+  <assign src="line 14">
+   <variableReference>b1min</variableReference>
+   <floatConstant>0.0</floatConstant>
+  </assign>
+  <variable name="b1max" type="float" isGlobal="false" xsi:nil="true" src="line 14"/>
+  <assign src="line 15">
+   <variableReference>b1max</variableReference>
+   <floatConstant>1.0</floatConstant>
+  </assign>
+  <variable name="b2min" type="float" isGlobal="false" xsi:nil="true" src="line 15"/>
+  <assign src="line 16">
+   <variableReference>b2min</variableReference>
+   <floatConstant>0.0</floatConstant>
+  </assign>
+  <variable name="b2max" type="float" isGlobal="false" xsi:nil="true" src="line 16"/>
+  <assign src="line 19">
+   <variableReference>b2max</variableReference>
+   <floatConstant>1.0</floatConstant>
+  </assign>
+  <variable name="delta" type="float" isGlobal="false" xsi:nil="true" src="line 19"/>
+  <assign src="line 22">
+   <variableReference>delta</variableReference>
+   <floatConstant>0.5</floatConstant>
+  </assign>
+  <variable name="namd_params" type="file" isGlobal="false" src="line 22"><file name="par_cg_clath.inp"/></variable>
+  <variable name="namd_input" type="file" isGlobal="false" src="line 23"><file name="cg_clath_cage.conf"/></variable>
+  <variable name="vmd_script" type="file" isGlobal="false" src="line 24"><file name="rmsd.temp.tcl"/></variable>
+  <variable name="psf" type="file" isGlobal="false" src="line 25"><file name="cg_clath_cage.psf"/></variable>
+  <variable name="pdb" type="file" isGlobal="false" src="line 26"><file name="cg_clath_cage.pdb"/></variable>
+  <variable name="dats" type="file[float][float]" isGlobal="false" xsi:nil="true" src="line 27"/>
+  <foreach var="b1"  src="line 29">
+  <in>
+    <range>
+      <variableReference>b1min</variableReference>
+      <variableReference>b1max</variableReference>
+      <variableReference>delta</variableReference>
+    </range>
+  </in>
+  <body><foreach var="b2"  src="line 30">
+    <in>
+      <range>
+        <variableReference>b2min</variableReference>
+        <variableReference>b2max</variableReference>
+        <variableReference>delta</variableReference>
+      </range>
+    </in>
+    <body><variable name="output" type="file" isGlobal="false" src="line 31">
+        <mapping descriptor="single_file_mapper">
+          <param name="file"><function name="strcat" src="line 31">
+            <stringConstant>logs/rmsd-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.out.txt</stringConstant></function></param>
+        </mapping>
+      </variable>
+      <variable name="error" type="file" isGlobal="false" src="line 32">
+        <mapping descriptor="single_file_mapper">
+          <param name="file"><function name="strcat" src="line 32">
+            <stringConstant>logs/rmsd-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.err.txt</stringConstant></function></param>
+        </mapping>
+      </variable>
+      <variable name="dcd" type="file" isGlobal="false" src="line 33">
+        <mapping descriptor="single_file_mapper">
+          <param name="file"><function name="strcat" src="line 33">
+            <stringConstant>output/cg_clath_cage-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.dcd</stringConstant></function></param>
+        </mapping>
+      </variable>
+      <variable name="dat" type="file" isGlobal="false" src="line 34">
+        <mapping descriptor="single_file_mapper">
+          <param name="file"><function name="strcat" src="line 34">
+            <stringConstant>output/rmsd.</stringConstant><variableReference>b1name</variableReference><variableReference>b1</variableReference><stringConstant>_</stringConstant><variableReference>b2name</variableReference><variableReference>b2</variableReference><stringConstant>.dat</stringConstant></function></param>
+        </mapping>
+      </variable>
+      <assign src="line 36">
+       <arraySubscript>
+        <arraySubscript>
+         <variableReference>dats</variableReference>
+         <variableReference>b1</variableReference>
+        </arraySubscript>
+        <variableReference>b2</variableReference>
+       </arraySubscript>
+       <variableReference>dat</variableReference>
+      </assign>
+      <call proc="rmsd" src="line 36">
+        <output><variableReference>output</variableReference></output>
+        <output><variableReference>error</variableReference></output>
+        <output><variableReference>dcd</variableReference></output>
+        <output><variableReference>dat</variableReference></output>
+        <input><variableReference>b1</variableReference></input>
+        <input><variableReference>b2</variableReference></input>
+        <input><variableReference>b1name</variableReference></input>
+        <input><variableReference>b2name</variableReference></input>
+        <input><variableReference>namd_input</variableReference></input>
+        <input><variableReference>namd_params</variableReference></input>
+        <input><variableReference>vmd_script</variableReference></input>
+        <input><variableReference>psf</variableReference></input>
+        <input><variableReference>pdb</variableReference></input>
+      </call></body>
+    </foreach></body>
+  </foreach>
+</program>