[Swift-commit] r8180 - SwiftTutorials/ATPESC_2014-08-14/swift-t

[wozniak at ci.uchicago.edu]

Author: wozniak
Date: 2014-08-14 11:22:06 -0500 (Thu, 14 Aug 2014)
New Revision: 8180

Modified:
   SwiftTutorials/ATPESC_2014-08-14/swift-t/tutorial.txt
Log:
Doc 05


Modified: SwiftTutorials/ATPESC_2014-08-14/swift-t/tutorial.txt
===================================================================
--- SwiftTutorials/ATPESC_2014-08-14/swift-t/tutorial.txt	2014-08-14 15:50:58 UTC (rev 8179)
+++ SwiftTutorials/ATPESC_2014-08-14/swift-t/tutorial.txt	2014-08-14 16:22:06 UTC (rev 8180)
@@ -22,7 +22,7 @@
 Configuration files are in +cfg/+.  These refer to public
 installations of Swift/T on Cetus/Mira.
 
-Each example contains a +*.swift+ Swift script that is the Swift
+Each example contains a +*.swift+ Swift script that is the Swift
 program.  The Swift/T compiler +stc+ translates the Swift script into
 an MPI program encoded in a +*.tcl+ file.  This is launched by using
 the +turbine+ program or a scheduler-specific script, such as the
@@ -121,7 +121,7 @@
 NOTE: Ease of calling to Tcl makes for ease of calling to native code,
 as shown in the next example.
 
-== 03 BLAS
+=== 03 BLAS
 
 In this example, we use Swift to call a BLAS routine for dot product.
 
@@ -182,5 +182,32 @@
 http://swig.org[SWIG], Fortran code with SciPy's
 http://wiki.scipy.org/Cookbook/F2Py[F2PY].
 
-Thus, a variety of scripts and libraries can be easily integrated with
-Swift/T and run concurrently on massive computers like the Blue Gene/Q!
+[red]*★* Thus, a variety of scripts and
+libraries can be easily integrated with Swift/T and run concurrently
+on massive computers like the Blue Gene/Q!
+
+=== 05 Molecular dynamics
+
+In our most realistic example, we bundle a small molecular dynamics
+simulator http://people.sc.fsu.edu/~jburkardt/c_src/md/md.html[MD] for
+Swift/T and call it concurrently.
+
+1. +cd+ to +examples/md-src/+ and run:
++
+----
+make
+----
++
+This builds the Tcl package by:
++
+a. Running SWIG to expose the core +simulate()+ function to Tcl;
+b. Compiling the SWIG-generated wrapper code and linking it as a Tcl
+package.
+2. +cd+ back to +examples/05-md/+.
+3. The +md.swift+ library shows the calling sequence for MD.
+4. The +run-md.swift+ script shows how to call MD once.  The output
+files are indicated in the script, in addition to the usual
++output.txt+.  Run this with +./run-*-md.sh+.
+5. A concurrent ensemble of simulations is launched by
++run-mds.swift+.  This script accepts many arguments on the command
+line: see +run-*-mds.sh+.