[Swift-commit] r6559 - in SwiftTutorials/CMTS_2013-06-17: . basic_swift basic_swift/data basic_swift/part01 basic_swift/part02 basic_swift/part03 basic_swift/part04 basic_swift/part05 basic_swift/part06 basic_swift/part07 bin namd_sweep
wilde at ci.uchicago.edu
wilde at ci.uchicago.edu
Sun Jun 16 08:30:30 CDT 2013
Author: wilde
Date: 2013-06-16 08:30:27 -0500 (Sun, 16 Jun 2013)
New Revision: 6559
Added:
SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
SwiftTutorials/CMTS_2013-06-17/basic_swift/
SwiftTutorials/CMTS_2013-06-17/basic_swift/README
SwiftTutorials/CMTS_2013-06-17/basic_swift/data/
SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt
SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/
SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README
SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift
SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc
SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/
SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README
SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift
SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift
SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc
SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/
SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README
SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift
SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc
SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/
SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README
SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift
SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc
SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/
SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README
SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift
SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc
SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/
SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README
SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift
SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc
SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/
SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README
SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift
SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml
SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc
SwiftTutorials/CMTS_2013-06-17/bin/
SwiftTutorials/CMTS_2013-06-17/bin/avg.sh
SwiftTutorials/CMTS_2013-06-17/bin/cleanup
SwiftTutorials/CMTS_2013-06-17/bin/highest.sh
SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh
SwiftTutorials/CMTS_2013-06-17/bin/makeinput
SwiftTutorials/CMTS_2013-06-17/bin/myapp
SwiftTutorials/CMTS_2013-06-17/bin/random.sh
SwiftTutorials/CMTS_2013-06-17/bin/random2.sh
SwiftTutorials/CMTS_2013-06-17/bin/random3.sh
SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
SwiftTutorials/CMTS_2013-06-17/namd_sweep/
SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO
SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl
SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf
SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb
SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf
SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf
SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp
SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl
SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh
SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift
SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl
SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh
SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc
SwiftTutorials/CMTS_2013-06-17/setup.csh
SwiftTutorials/CMTS_2013-06-17/setup.sh
Log:
Initial revision for this tutorial.
Added: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
===================================================================
(Binary files differ)
Property changes on: SwiftTutorials/CMTS_2013-06-17/SwiftCMTSLecture.2013.0617.pptx
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,52 @@
+
+INTRODUCTION TO SWIFT
+
+SETUP
+
+Obtain the tutorial package
+
+Change directory into the created directory called "tutorial"
+
+This directory contains:
+
+bin: script tools for the tutorial
+scripts: Swift scripts for the tutorial
+
+TO START, do:
+
+$ source setup.sh # to add tutorial programs to your PATH
+
+...and then verify:
+
+$ random.sh # should be found in your PATH now
+
+
+
+The tutorial is arranged in parts. To begin:
+
+$ cd part01
+$ cat README
+
+When finished:
+
+$ cd ../part02 # etc
+
+In each part, you can type "cleanup" after running a few swift scripts
+to remove the old logs that build up, and (usually) the output files.
+
+
+The topics of the tutorial parts are:
+
+part01: First Swift script - run a "simulation" program, random.sh
+
+part02: Specifying the output filenames
+
+part03: Run many instances of a "simulation" program in a foreach() loop
+
+part04: run a program in a foreach() loop with explicitly named output files.
+
+part05: Add a program that "analyzes" the output the parallel simulations
+
+part06: Add arguments to the "simulation" program
+
+part07: Run the "simulations" on the parallel cluster
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/data/data.txt 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+Hi Swift!
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,40 @@
+
+TOPIC: First Swift script - run a "simulation" program, random.sh
+
+
+Verify that random.sh is in your path, and that it works:
+
+$ which random.sh
+$ random.sh
+
+Study the Swift program:
+
+$ cat p1.swift
+
+Examine the tool catalog file:
+
+$ cat tc
+
+Run the program:
+
+$ swift -tc.file tc p1.swift
+
+Look at the output:
+
+$ cat _concurrent/*
+
+Look at the other files generated:
+
+$ ls -l
+
+We'll talk more about these files later
+
+$ cleanup
+
+Then test the sript a few more times.
+
+$ swift -tc.file tc p1.swift; cat _concurrent/*
+
+$ swift -tc.file tc p1.swift; cat _concurrent/*
+
+$ swift -tc.file tc p1.swift; cat _concurrent/*
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/p1.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,8 @@
+type file;
+
+app (file o) mysim ()
+{
+ random stdout=@filename(o);
+}
+
+file f = mysim();
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part01/tc 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+localhost random random.sh
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,33 @@
+
+TOPIC: specifying the output filenames
+
+Study the Swift program:
+
+$ cat p2.swift
+
+Examine the tool catalog file:
+
+$ cat tc
+
+Run the program:
+
+$ swift -tc.file tc p2.swift
+
+Look at the output:
+
+$ cat sim.out
+
+Then test the sript a few more times.
+
+$ swift -tc.file tc p1.swift; cat sim.out
+
+$ swift -tc.file tc p1.swift; cat sim.out
+
+$ swift -tc.file tc p1.swift; cat sim.out
+
+Things to try:
+
+- change the output filename
+
+- add a dir component to the output filename
+
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,9 @@
+type file;
+
+app (file o) mysim ()
+{
+ random stdout=@filename(o);
+}
+
+file f<"sim.out">;
+f = mysim();
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/p2b.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,9 @@
+type file;
+
+app (file o) mysim ()
+{
+ random stdout=@filename(o);
+}
+
+file f<"output/sim.out">;
+f = mysim();
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part02/tc 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+localhost random random.sh
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,20 @@
+
+TOPIC: run many instances of a "simulation" program in a foreach() loop
+
+
+Run the program:
+
+$ swift -tc.file tc p3.swift
+
+Look at the output:
+
+$ cd _concurrent
+$ ls -l
+$ cat *
+
+Look at the order in which the files were written:
+
+$ ls -lt
+
+We'll come back to this...
+
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/p3.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,11 @@
+type file;
+
+app (file o) mysim ()
+{
+ random stdout=@filename(o);
+}
+
+foreach i in [0:9] {
+ file f = mysim();
+}
+
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part03/tc 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+localhost random random.sh
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,42 @@
+
+TOPIC: run a program in a foreach() loop with explicitly named output files.
+
+
+Study the program:
+
+- @strcat() is a Swift builtin function (the @name() form is used for many but not all builtins)
+
+- Note that @strcat() coerces numeric args to strings
+
+- <"filename"> was a shorthand for <single_file_mapper;...> but the latter is more flexible.
+
+Run the program:
+
+$ swift -tc.file tc p4.swift
+
+Look at the output:
+
+$ cd output
+$ ls -l
+$ cat *
+
+
+Try:
+
+- Adjust the script to take the number of simulations to do from the command line
+
+ @arg("argname") returns arguments after the .swift script on the swift command line:
+
+ swift -tc.file tc p4.swift -myarg1=value1 ...
+
+ @arg("argname","default") returns "default" if the argname is not given on the command line
+
+ @toInt() converts strings to integers:
+
+ @toInt(@arg("myArg1"))
+
+
+- trace(expr1,...) traces expressions on stdout.
+
+ Try inserting a few traces. But remember: Swift is *very* concurrent!
+
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/p4.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,12 @@
+type file;
+
+app (file o) mysim ()
+{
+ random stdout=@filename(o);
+}
+
+foreach i in [0:9] {
+ file f <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+ f = mysim();
+}
+
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part04/tc 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1 @@
+localhost random random.sh
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,51 @@
+
+
+TOPIC: Add a program that "analyzes" the output the parallel simulations
+
+
+Study the program:
+
+We added a new app to "analyze" all the simulation outputs:
+
+app (file o) analyze (file s[])
+{
+ average @filenames(s) stdout=@filename(o);
+}
+
+Nots that it expects an array of files as its input, and that
+it uses @filenames() to place the names of all the files on
+the command line to the "average" program.
+
+Average does:
+--------------------
+#! /bin/sh
+
+awk '
+
+{ sum += $1}
+
+END { print sum/NR }
+' $*
+-------------------
+
+
+At the end of the script we insert:
+
+file stats<"output/average.out">;
+stats = analyze(sims);
+
+...which runs the analysis *after* all the simulations complete.
+
+
+Run the program:
+
+$ swift -tc.file tc p5.swift
+
+Look at the output:
+
+$ cd output
+$ ls -l
+$ cat sim*.out
+$ cat average.out
+
+
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/p5.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,24 @@
+type file;
+
+app (file o) mysim ()
+{
+ random stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+ average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+
+int nsim = @toInt(@arg("nsim","10"));
+
+foreach i in [0:nsim-1] {
+ file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+ simout = mysim();
+ sims[i] = simout;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part05/tc 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+localhost random random.sh
+localhost average avg.sh
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,28 @@
+
+TOPIC: add arguments to the "simulation" program
+(to control number of steps, range of output, and number of output lines)
+
+
+Test new versions of the "simulation" program:
+
+ random.sh # original
+ random2.sh [runtime] # runtime in seconds; defaults to 1 sec
+ random3.sh [runtime] [range] # requests random numbers in {0:range-1}
+ random4.sh [runtime] [range] [count] # requests "count" random numbers in {0:range}
+
+p6.swift changes to random2 for the simulation program and adds an argument.
+
+Run the program:
+
+$ swift -tc.file tc p6.swift -steps=3 # each simulation takes 3 seconds
+
+Next we need to use the parallel cluster for our simulations!
+
+Try:
+
+- change to random3.sh and add the extra argument "range"
+
+- change to random4.sh and add yet another argument "count"
+
+
+
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/p6.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,25 @@
+type file;
+
+app (file o) mysim2 (int timesteps)
+{
+ random2 timesteps stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+ average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+int nsim = @toInt(@arg("nsim","10"));
+
+int steps = @toInt(@arg("steps","1"));
+
+foreach i in [0:nsim-1] {
+ file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+ simout = mysim2(steps);
+ sims[i] = simout;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part06/tc 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+localhost random2 random2.sh
+localhost average avg.sh
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,81 @@
+
+TOPIC: Run the "simulations" on the parallel cluster
+
+
+Til now we've been running our "simulations" on the local login host.
+
+Now we'll run them on the parallel cluster.
+
+The script will be the same as previous, but we change the tool catalog to
+indicate that our "simulation app" (random4.sh) should be run on the
+"westmere" partition of the Midway cluster using the "slurm" scheduler:
+
+We changed file "tc" from:
+
+localhost random4 random4.sh
+localhost average avg.sh
+
+to:
+
+westmere random4 random4.sh
+localhost average avg.sh
+
+And we added the "sites.xml" file which specifies two "pools" of resources,
+the "local host" pool (which we've been using till now) and the "westmere" pool.
+
+To run, we now add the sites.xml file to the swift command line:
+
+$ swift -tc.file tc -sites.file sites.xml p7.swift -steps=10 -range=1000 -count=6 -nsim=100
+
+Note that we're now asking for 100 simulations to be run, each of which
+is to run for 10 steps (ie 10 seconds).
+
+The sites file looks like this:
+
+<config>
+
+ <pool handle="localhost">
+ <execution provider="local"/>
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ </pool>
+
+ <pool handle="westmere">
+ <execution provider="coaster" jobmanager="local:slurm"/>
+
+ <!-- Set partition and account here: -->
+ <profile namespace="globus" key="queue">westmere</profile>
+ <profile namespace="globus" key="ppn">12</profile>
+ <!-- <profile namespace="globus" key="project">pi-wilde</profile> -->
+
+ <!-- Set number of jobs and nodes per job here: -->
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxnodes">1</profile>
+ <profile namespace="globus" key="nodegranularity">1</profile>
+ <profile namespace="globus" key="jobsPerNode">12</profile> <!-- apps per node! -->
+ <profile namespace="karajan" key="jobThrottle">.11</profile> <!-- eg .11 -> 12 -->
+
+ <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+ <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+ <profile namespace="globus" key="maxtime">1800</profile> <!-- in seconds! -->
+
+ <!-- Set data staging model and work dir here: -->
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+ <!-- Typically leave these constant: -->
+ <profile namespace="globus" key="slurm.exclusive">false</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ </pool>
+
+</config>
+
+Try:
+
+- running more app() calls at once: change jobsPerNode and jobThrottle
+
+- requesting more than 1 slurm job at once: change slots
+
+- requesting nodes in units greater than 1: change maxnodes and nodeGranularity
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/p7.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,27 @@
+type file;
+
+app (file o) mysim4 (int timesteps, int range, int count)
+{
+ random4 timesteps range count stdout=@filename(o);
+}
+
+app (file o) analyze (file s[])
+{
+ average @filenames(s) stdout=@filename(o);
+}
+
+file sims[];
+int nsim = @toInt(@arg("nsim", "10"));
+
+int steps = @toInt(@arg("steps", "1"));
+int range = @toInt(@arg("range", "100"));
+int count = @toInt(@arg("count", "10"));
+
+foreach i in [0:nsim-1] {
+ file simout <single_file_mapper; file=@strcat("output/sim_",i,".out")>;
+ simout = mysim4(steps,range,count);
+ sims[i] = simout;
+}
+
+file stats<"output/average.out">;
+stats = analyze(sims);
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/sites.xml 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,39 @@
+<config>
+
+ <pool handle="localhost">
+ <execution provider="local"/>
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ </pool>
+
+ <pool handle="westmere">
+ <execution provider="coaster" jobmanager="local:slurm"/>
+
+ <!-- Set partition and account here: -->
+ <profile namespace="globus" key="queue">westmere</profile>
+ <profile namespace="globus" key="ppn">12</profile>
+ <!-- <profile namespace="globus" key="project">pi-wilde</profile> -->
+
+ <!-- Set number of jobs and nodes per job here: -->
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxnodes">1</profile>
+ <profile namespace="globus" key="nodegranularity">1</profile>
+ <profile namespace="globus" key="jobsPerNode">12</profile> <!-- apps per node! -->
+ <profile namespace="karajan" key="jobThrottle">.11</profile> <!-- eg .11 -> 12 -->
+
+ <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+ <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+ <profile namespace="globus" key="maxtime">1800</profile> <!-- in seconds! -->
+
+ <!-- Set data staging model and work dir here: -->
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+
+ <!-- Typically leave these constant: -->
+ <profile namespace="globus" key="slurm.exclusive">false</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ </pool>
+
+</config>
Added: SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/basic_swift/part07/tc 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+westmere random4 random4.sh
+localhost average avg.sh
Added: SwiftTutorials/CMTS_2013-06-17/bin/avg.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/avg.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/avg.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,9 @@
+#! /bin/sh
+
+awk '
+
+{ sum += $1}
+
+END { print sum/NR }
+' $*
+
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/avg.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/cleanup
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/cleanup (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/cleanup 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+echo Removing:
+echo
+ls -ltd *log *.d swiftwork _concurrent output *.kml *.swiftx swift.log 2>/dev/null
+echo
+echo Enter y to proceed:
+read ok
+if [ _$ok = _y -o _$ok = _Y -o _$ok = _yes ]; then
+ echo
+ set -x
+ rm -rf *log *.d swiftwork _concurrent output *.kml *.swiftx swift.log
+else
+ echo
+ echo No files removed.
+fi
+
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/cleanup
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/highest.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/highest.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/highest.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+#! /bin/sh
+sort -nr | head -$1
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/highest.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,5 @@
+#! /bin/sh
+
+# Print the lowest N numbers from standard input (deafult: lowest 3)
+
+sort -n | head -${1:-3}
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/lowest.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/makeinput
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/makeinput (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/makeinput 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,22 @@
+#! /bin/sh
+
+nfiles=${1:-10}
+
+rm -rf input
+mkdir input
+cp ../data/sat/t? input/
+( cd input
+ n=0
+ for h in $(seq -w 00 99); do
+ for v in $(seq -w 00 99); do
+ n=$((n+1))
+ if [ $n -gt $nfiles ]; then
+ break;
+ else
+ f=t$(($RANDOM%10))
+ ln $f h${h}v${v}.rgb
+ fi
+ done
+ done
+ rm t?
+)
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/makeinput
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/myapp
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/myapp (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/myapp 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+hostname -f
+date
+sleep 3
+ps -u $USER -H -f
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/myapp
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/random.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,2 @@
+#! /bin/sh
+echo $RANDOM
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/random2.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random2.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random2.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,7 @@
+#! /bin/sh
+
+runtime=${1:-0}
+
+sleep $runtime
+
+echo $(($RANDOM))
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random2.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/random3.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random3.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random3.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,10 @@
+#! /bin/sh
+
+runtime=${1:-0}
+range=${2:-30000}
+
+sleep $runtime
+
+echo $(($RANDOM%range))
+
+
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random3.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/bin/random4.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/bin/random4.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,12 @@
+#! /bin/sh
+
+runtime=${1:-0}
+range=${2:-30000}
+n=${3:-10}
+
+sleep $runtime
+
+for ((i=0;i<n;i++)); do
+ echo $(($RANDOM%range))
+done
+
Property changes on: SwiftTutorials/CMTS_2013-06-17/bin/random4.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/README
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/README (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/README 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,17 @@
+These files perform a brute force parameter search in two dimensions
+in order to find the parameters that minimize the root mean square
+deviation (RMSD) of the system from an ideal structure.
+
+sweep_pd.pl – Loops over all possible parameter pairs, creates from
+templates a parameter file (par_cg_clath.temp.inp), a NAMD input file
+(cg_clath_cage.temp.conf), and a VMD script (rmsd.temp.tcl) for
+calculating the RMSD. The script then submits a single pbs job (pxdt.pbs)
+for each parameter pair.
+
+plot_pd.pl – After all of the simulations have been performed, this
+script reads in the RMSD values for each parameter pair and writes the
+data in a gnuplot 2D plot data format. This script also prints to screen
+the minimum RMSD and the parameter values corresponding to that value.
+
+-Frank X. Vazquez fxv at uchicago.edu
+7-13-2012
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/TODO 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,5 @@
+Swift in PATH
+
+swift module
+
+account to use - pi_gavoth
\ No newline at end of file
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,40 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my $rmsdmin = 123456789.0; # Set large number to find min RMSD
+my $b1rmsdmin=0.0;
+my $b2rmsdmin=0.0;
+my $b1name;
+my $b2name;
+
+for(my $i=0; $i<=$#ARGV; $i++) {
+
+ my $filename = $ARGV[$i];
+ my $basename = basename($filename,".dat");
+ my @params = split(/_/,$basename);
+
+ $b1name = $params[0];
+ my $b1 = $params[1];
+ $b2name = $params[2];
+ my $b2 = $params[3];
+
+ open(INPUT, "<", $filename);
+ my $_ = <INPUT>;
+ my @data = split(/ +/,$_);
+ my $rmsd=$data[2]*1.0;
+
+ # Find Minimum
+ if ($rmsd<$rmsdmin) {
+ $rmsdmin=$rmsd;
+ $b1rmsdmin=$b1;
+ $b2rmsdmin=$b2;
+ }
+
+ printf "%0.3f %0.3f %0.9f\n", $b1, $b2, $rmsd;
+ close(INPUT);
+}
+
+printf "\nMinimum Values: RMSD=%0.9f eps_$b1name=%0.3f eps_$b2name=%0.3f\n", $rmsdmin, $b1rmsdmin, $b2rmsdmin;
Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/analyze_pd.pl
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cf 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,7 @@
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=false
+status.mode=provider
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.pdb 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,470 @@
+REMARK original generated coordinate pdb file
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Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.psf 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,1078 @@
+PSF
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+ 461 462 463 464 465 456 457 458
+ 465 456 461 462 465 466 467 468
+
+ 0 !NDON: donors
+
+
+ 0 !NACC: acceptors
+
+
+ 0 !NNB
+
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0
+
+ 1 0 !NGRP
+ 0 0 0
+
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/cg_clath_cage.temp.conf 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,90 @@
+# NAMD Config file - autogenerated by NAMDgui plugin
+# Author: Jan Saam, saam at charite.de
+
+#set DIR /lustre/beagle/fxv/CLATH/CG_MODEL/OPT/CAGE/PSWEEP
+
+set id FILEID
+# input
+coordinates ../cg_clath_cage.pdb
+structure ../cg_clath_cage.psf
+parameters ../PAR/${id}.inp
+paratypecharmm on
+
+# output
+#set output cg_clath_cage.BLAB1_BLAB2
+outputname ../OUT/$id
+dcdfile ../OUT/${id}.dcd
+xstFile ../OUT/${id}.xst
+dcdfreq 1000
+xstFreq 1000
+
+binaryoutput yes
+binaryrestart yes
+outputEnergies 1000
+restartfreq 1000
+
+fixedAtoms off
+
+# Basic dynamics
+exclude scaled1-4
+1-4scaling 1
+COMmotion no
+dielectric 1.0
+
+
+# Simulation space partitioning
+cutoff 630
+switching on
+switchdist 629
+pairlistdist 640
+
+# Multiple timestepping
+firsttimestep 0
+timestep 1
+stepspercycle 20
+nonbondedFreq 1
+fullElectFrequency 1
+rigidBonds all
+
+# Temperature control
+
+set temperature 310
+set tempini 0
+temperature $temperature; # initial temperature
+
+# Langevin Dynamics
+langevin on; # do langevin dynamics
+langevinDamping 0.5 # damping coefficient (gamma) of 1/ps
+langevinTemp $temperature; # bath temperature
+langevinHydrogen no; # don't couple langevin bath to hydrogens
+
+
+
+# Scripting
+
+# Simulated Annealing
+#reassignFreq 10000
+#reassignTemp 0
+#minimize 10000
+#for { set TEMP 0 } { $TEMP <= 310 } { incr TEMP 5 } {
+# run 10000
+# reassignTemp $TEMP
+# langevinTemp $TEMP
+#}
+
+#run 2500000
+#
+#for { set TEMP 650 } { $TEMP >= 0 } { incr TEMP -5 } {
+# reassignTemp $TEMP
+# langevinTemp $TEMP
+# run 10000
+#}
+
+#reassignTemp $temperature
+#langevinTemp $temperature
+
+
+minimize 10000
+#reinitvels $temperature
+#run 1000000 desired, 200000 min to get non-zero RMSDs
+run 20000
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+rm -rf *.log *stdout.txt *.rlog *.d *.kml _concurrent *.swiftx PAR/* RMSD/* VMD/* CONF/* OUT/*
Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/clean.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/par_cg_clath.temp.inp 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,79 @@
+* Charmm Parameter file
+* For 13 bead CG clathrin model
+* Handmade by FXV - 7-21-11
+* Initial guess (very rough)
+
+BONDS
+!
+
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb b0
+!
+
+HB PX 0.5 85.5
+PX DT 0.018 135.2
+DT AK 0.045 124.2
+AK LT 0.08 94.1
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!
+!atom types Ktheta Theta0
+!
+PX HB PX 70.0 120.00
+DT PX HB 50.0 144.3
+AK DT PX 35.0 132.6
+LT AK DT 150.0 141.5
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types Kchi n delta
+!
+X X X X 0.0 1 0.0 ! No dihedrals
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types Kpsi psi0
+!
+PX PX HB PX 200.00 0 161.17
+PX HB PX DT 10.0 0 -30.4
+HB PX DT AK 9.5 0 -16.1
+PX DT AK LT 45.0 0 26.1
+
+NONBONDED
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom ignored epsilon Rmin/2
+!
+HB 0.000000 HBEPS 43.075000
+PX 0.000000 PXEPS 18.425000
+DT 0.000000 DTEPS 10.455000
+AK 0.000000 AKEPS 25.975000
+LT 0.000000 LTEPS 36.905000
+
+
+END
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,74 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+# This code will run many short simulations in order to
+# sweep the nonbonded parameter space
+
+# File names
+open (OFILE, ">", "rmsd_pd.dat");
+
+# Bead names
+my $b1name = "PX";
+my $b2name = "DT";
+
+# Bead ranges
+my $b1min=0.0;
+my $b1max=10.0;
+
+my $b2min=0.0;
+my $b2max=10.0;
+
+my $del=0.50;
+
+# Set large number to find RMSD min
+my $rmsdmin = 123456789.0;
+my $b1rmsdmin=0.0;
+my $b2rmsdmin=0.0;
+
+
+my $b1=$b1min;
+
+while ($b1<=$b1max)
+{
+ my $b2=$b2min;
+
+ while ($b2<=$b2max)
+ {
+
+
+
+ if (-s "RMSD/rmsd.$b1name${b1}_$b2name${b2}.dat")
+ {
+ open(INPUT, "<", "RMSD/rmsd.$b1name${b1}_$b2name${b2}.dat");
+ my $_ = <INPUT>;
+
+ my @data = split(/ +/,$_);
+ my $rmsd=$data[2]*1.0;
+
+ # Find Minimum
+ if ($rmsd<$rmsdmin)
+ {
+ $rmsdmin=$rmsd;
+ $b1rmsdmin=$b1;
+ $b2rmsdmin=$b2;
+ }
+
+ print OFILE "$b1 $b2 $rmsd\n";
+ close(INPUT);
+ }
+
+ $b2 = $b2+$del;
+
+ }
+
+ print OFILE " \n";
+ $b1 = $b1+$del;
+
+}
+
+close(OFILE);
+
+print "Minimum Values\n";
+print "RMSD = $rmsdmin, eps_$b1name = $b1rmsdmin, eps_$b2name = $b2rmsdmin\n" ;
Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/plot_pd.pl
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,11 @@
+#! /bin/sh
+
+id=$1
+
+module load namd
+module load vmd
+
+ mpiexec namd2 CONF/$id.conf > OUT/$id.log 2>&1
+# mpiexec -n 8 namd2 CONF/$id.conf > OUT/$id.log 2>&1
+
+vmd -dispdev text -e VMD/$id.tcl >> OUT/$id.log 2>&1
Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.swift 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,44 @@
+type file;
+
+global string cwd = @arg("cwd",".");
+
+app (file blist) genConfigs (string max, string delta)
+{
+ gensweep cwd max delta stdout=@blist;
+}
+
+app (file rmsdout, file rmsd) rmsd (file i[], string id)
+{
+ rmsd id;
+}
+
+app (file plot_data) analyze (file[] rmsdfiles)
+{
+ analyze @filenames(rmsdfiles) stdout=@plot_data;
+}
+
+file pdb <"cg_clath_cage.pdb">;
+file psf <"cg_clath_cage.psf">;
+
+file rmsds[];
+
+string sweepMax=@arg("max","0.6"), sweepDelta=@arg("delta","0.5");
+
+string beadids[] = readData(genConfigs(sweepMax, sweepDelta));
+
+trace("Processing these bead IDs:", beadids);
+
+foreach beadid, i in beadids {
+ file conf <single_file_mapper; file=@strcat("CONF/",beadid,".conf")>;
+ file inp <single_file_mapper; file=@strcat("PAR/", beadid,".inp")>;
+ file vmdtcl <single_file_mapper; file=@strcat("VMD/", beadid,".tcl")>;
+
+ file log <single_file_mapper; file=@strcat("OUT/", beadid,".log")>;
+ file dat <single_file_mapper; file=@strcat("RMSD/",beadid,".dat")>;
+
+ (log,dat) = rmsd([conf,pdb,psf,inp,vmdtcl], beadid);
+ rmsds[i] = dat;
+}
+
+file plot_out <"OUT/plot_pd.txt">;
+plot_out = analyze(rmsds);
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/rmsd.temp.tcl 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,56 @@
+#====================================
+# THis script will measure the
+# the average angles, bond lengths
+# and dihedral angles.
+#
+# -FXV Oct, 2011
+#===================================
+
+mol delete all
+
+# set atom selection
+set seltext "type HB AK"
+
+# Set the initial frame
+set inifrm 200
+
+set psf cg_clath_cage.psf
+set pdb cg_clath_cage.pdb
+set dcd OUT/FILEID.dcd
+
+# Load input files
+mol load psf $psf
+# Load trajectory
+mol addfile $pdb type pdb
+mol addfile $dcd type dcd first $inifrm last -1 waitfor all
+
+# Get molecule information
+set mol [molinfo top]
+
+# Get the number of frames
+set nmfrm [molinfo $mol get numframes]
+puts "number of frames $nmfrm"
+
+# open rmsd file
+set frmsd [open RMSD/FILEID.dat w]
+
+# Select atoms
+set ref [atomselect top $seltext frame 0]
+
+# Loop over the number of frames
+for {set ifrm 0} {$ifrm <= $nmfrm} {incr ifrm} {
+
+ set sel [atomselect top $seltext frame $ifrm]
+
+ set irmsd [measure rmsd $ref $sel]
+
+ lappend rmsdlist $irmsd
+
+
+}
+
+# Analysis
+puts $frmsd "B1 B2 [vecmean $rmsdlist]"
+
+exit
+
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,7 @@
+PATH=$PATH:$PWD
+
+# export SBATCH_RESERVATION=swift_test
+
+mkdir -p CONF PAR VMD RMSD OUT
+
+swift -sites.file sites.xml -tc.file tc -config cf rmsd.swift -cwd=$PWD -max=${1:-0.0} -delta=${2:-0.5}
Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/run.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,10 @@
+#!/bin/bash
+
+mkdir -p saved/run000
+rundir=saved/run$(cd saved; /bin/ls -1 | tail -1 | sed -e 's/run//' | awk '{printf("%03d",$1+1)}')
+mkdir $rundir
+rmdir saved/run000
+
+echo Saving run in $rundir
+
+mv *.log *.rlog *.d *.kml _concurrent *.swiftx CONF PAR VMD RMSD OUT $rundir 2>/dev/null
Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/save.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sites.xml 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,104 @@
+<config>
+
+ <pool handle="local">
+ <execution provider="local"/>
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ </pool>
+
+ <pool handle="westmere">
+ <execution provider="coaster" jobmanager="local:slurm"/>
+
+ <!-- Set partition and account here: -->
+ <profile namespace="globus" key="queue">westmere</profile>
+ <profile namespace="globus" key="ppn">12</profile>
+ <profile namespace="globus" key="project">pi-gavoth</profile>
+
+ <!-- Set number of jobs and nodes per job here: -->
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxnodes">2</profile>
+ <profile namespace="globus" key="nodegranularity">2</profile>
+ <profile namespace="karajan" key="jobThrottle">.03</profile>
+
+ <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+ <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+ <profile namespace="globus" key="maxtime">1800</profile>
+
+ <!-- Typically leave these constant: -->
+ <profile namespace="globus" key="slurm.exclusive">true</profile>
+ <profile namespace="globus" key="jobtype">single</profile>
+ <profile namespace="globus" key="jobsPerNode">1</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+
+ <!-- Set data staging model and work dir here: -->
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ </pool>
+
+ <pool handle="sandyb">
+ <execution provider="coaster" jobmanager="local:slurm"/>
+
+ <!-- Set partition and account here: -->
+ <profile namespace="globus" key="queue">sandyb</profile>
+ <profile namespace="globus" key="ppn">12</profile>
+ <profile namespace="globus" key="project">pi-gavoth</profile>
+
+ <!-- Set number of jobs and nodes per job here: -->
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxnodes">1</profile>
+ <profile namespace="globus" key="nodegranularity">1</profile>
+ <profile namespace="karajan" key="jobThrottle">.03</profile>
+
+ <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+ <profile namespace="globus" key="maxWalltime">00:15:00</profile>
+ <profile namespace="globus" key="maxtime">1800</profile>
+
+ <!-- Typically leave these constant: -->
+ <profile namespace="globus" key="slurm.exclusive">false</profile>
+ <profile namespace="globus" key="jobtype">single</profile>
+ <profile namespace="globus" key="jobsPerNode">1</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <!-- <profile namespace="globus" key="slurm.qos">ht</profile> -->
+
+ <!-- Set data staging model and work dir here: -->
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ </pool>
+
+ <pool handle="bigmem">
+ <execution provider="coaster" jobmanager="local:slurm"/>
+
+ <!-- Set partition and account here: -->
+ <profile namespace="globus" key="queue">bigmem</profile>
+ <profile namespace="globus" key="ppn">16</profile>
+ <profile namespace="globus" key="project">pi-gavoth</profile>
+
+ <!-- Set number of jobs and nodes per job here: -->
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="maxnodes">1</profile>
+ <profile namespace="globus" key="nodegranularity">1</profile>
+ <profile namespace="karajan" key="jobThrottle">.03</profile>
+
+ <!-- Set estimated app time (maxwalltime) and requested job time (maxtime) here: -->
+ <profile namespace="globus" key="maxWalltime">00:05:00</profile>
+ <profile namespace="globus" key="maxtime">1800</profile>
+
+ <!-- Typically leave these constant: -->
+ <profile namespace="globus" key="slurm.exclusive">false</profile>
+ <profile namespace="globus" key="jobtype">single</profile>
+ <profile namespace="globus" key="jobsPerNode">1</profile>
+ <profile namespace="globus" key="highOverAllocation">100</profile>
+ <profile namespace="globus" key="lowOverAllocation">100</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <!-- <profile namespace="globus" key="slurm.qos">ht</profile> -->
+
+ <!-- Set data staging model and work dir here: -->
+ <filesystem provider="local"/>
+ <workdirectory>/scratch/midway/{env.USER}/swiftwork</workdirectory>
+ </pool>
+
+</config>
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,45 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+# Create NAMD input file for short simulations
+# to sweep the nonbonded parameter space
+#
+# ARGS: dir max delta # FIXME: add bead names and epsilon
+
+chdir($ARGV[0]);
+
+# Bead names
+
+my $b1name = "PX";
+my $b2name = "DT";
+
+# Bead ranges
+
+my $b1min=0.0;
+my $b2min=0.0;
+
+my $b1max = $ARGV[1];
+my $b2max = $ARGV[1];
+my $del = $ARGV[2];
+my $eps = "-0.01";
+
+my $b1=$b1min;
+while ($b1<=$b1max) {
+ my $b2=$b2min;
+ while ($b2<=$b2max) {
+
+ my $s1=sprintf("%05.2f",$b1);
+ my $s2=sprintf("%05.2f",$b2);
+ my $fileid="${b1name}_${s1}_${b2name}_${s2}";
+
+ print("$fileid\n");
+ system("sed -e s/FILEID/${fileid}/g cg_clath_cage.temp.conf > CONF/$fileid.conf");
+ system("sed -e s/FILEID/${fileid}/g -e s/B1/$s1/ -e s/B2/$s2/ rmsd.temp.tcl > VMD/$fileid.tcl");
+ system("sed -e s/HBEPS/$eps/ -e s/PXEPS/-$s1/ -e s/DTEPS/-$s2/ -e s/AKEPS/$eps/ -e s/LTEPS/$eps/ par_cg_clath.temp.inp > PAR/$fileid.inp");
+
+ $b2 = $b2+$del;
+ }
+ $b1 = $b1+$del;
+}
Property changes on: SwiftTutorials/CMTS_2013-06-17/namd_sweep/sweep_pd.pl
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/namd_sweep/tc 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,8 @@
+
+local gensweep sweep_pd.pl null null null
+local analyze analyze_pd.pl null null null
+
+#bigmem rmsd rmsd.sh null null null
+#sandyb rmsd rmsd.sh null null null
+#trestles rmsd rmsd.sh null null null
+westmere rmsd rmsd.sh null null null
Added: SwiftTutorials/CMTS_2013-06-17/setup.csh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/setup.csh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/setup.csh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,35 @@
+
+module load swift
+
+setenv SBATCH_RESERVATION swift
+
+set DIR=`dirname ${0}`
+cd $DIR
+set DIR=`pwd`
+
+echo Adding $DIR/bin to PATH:
+setenv PATH $DIR/bin:$PATH
+
+mkdir -p $HOME/.swift
+
+if ( -f $HOME/.swift/swift.properties ) then
+ echo Adding properties to end of $HOME/.swift/swift.properties
+else
+ echo creating $HOME/.swift/swift.properties
+endif
+
+cat >>$HOME/.swift/swift.properties <<END
+
+# Properties for Swift Tutorial
+
+status.mode=provider
+use.provider.staging=false
+use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+file.gc.enabled=false
+tcp.port.range=50000,51000
+END
Added: SwiftTutorials/CMTS_2013-06-17/setup.sh
===================================================================
--- SwiftTutorials/CMTS_2013-06-17/setup.sh (rev 0)
+++ SwiftTutorials/CMTS_2013-06-17/setup.sh 2013-06-16 13:30:27 UTC (rev 6559)
@@ -0,0 +1,50 @@
+
+echo -e "\nNOTE: This command must be run as \"source setup.sh\", not directly! \n"
+echo -e "Initializing Swift tutorial environment\n"
+
+module load swift
+
+# export SBATCH_RESERVATION=swift
+
+DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+echo -e "Adding $DIR/bin to PATH\n"
+
+PATH=$DIR/bin:$PATH
+
+# echo -e "PATH=$PATH\n"
+
+mkdir -p $HOME/.swift
+
+if [ -f $HOME/.swift/swift.properties ]; then
+ echo -e "Adding properties to end of $HOME/.swift/swift.properties\n"
+else
+ echo -e "creating $HOME/.swift/swift.properties\n"
+fi
+
+cat >>$HOME/.swift/swift.properties <<END
+
+# Swift runtime properties for CMTS Cyber Tutorial
+
+# Get sites and apps lists from these files in cwd:
+
+sites.file=sites.xml
+tc.file=apps
+
+# Data and status staging modes:
+
+use.provider.staging=false
+provider.staging.pin.swiftfiles=false
+use.wrapper.staging=false
+status.mode=provider
+
+# For better debugging:
+
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+sitedir.keep=true
+file.gc.enabled=false
+file.gc.enabled=false
+
+END
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