[Swift-commit] r2418 - text/hpdc09submission

[noreply at svn.ci.uchicago.edu]

Author: benc
Date: 2009-01-09 09:25:24 -0600 (Fri, 09 Jan 2009)
New Revision: 2418

Modified:
   text/hpdc09submission/paper.latex
Log:
remove XDTM present-tense references; LONI GUI note; correct an identifier

Modified: text/hpdc09submission/paper.latex
===================================================================
--- text/hpdc09submission/paper.latex	2009-01-09 15:15:37 UTC (rev 2417)
+++ text/hpdc09submission/paper.latex	2009-01-09 15:25:24 UTC (rev 2418)
@@ -924,16 +924,15 @@
 represented by an Image (voxels) and a Header (scanner metadata). An
 Air is a parameter file for spatial adjustment, and an AirVector is a
 set of such parameter files.  Datasets are operated on by procedures,
-which take typed data described by XDTM as input, perform computations
-on those data, and produce data described by XDTM as output. The
-procedure reslice\_wf defines a compound procedure, which may comprise
-a series of procedure calls, using variables or datasets to establish
-data dependencies. Such procedures can themselves be called by other
-procedures, thus defining a potentially large and complex execution
-graph.
+which take typed data described by a mapper, perform computations
+on those data, and produce data to be stored in locations specified
+by a mapper. The
+procedure reslice\_wf defines a compound procedure, which comprises
+a series of procedure calls, using variables to establish
+data dependencies. 
 
-In the example, reslice\_wf essentially defines a simple four-step
-pipeline computation, using variables and/or datasets to establish
+In the example, reslice\_wf defines a four-step
+pipeline computation, using variables to establish
 data dependencies. It applies reorientRun to a run first in the x axis
 and then in the y axis, and then aligns each image in the resulting
 run with the first image. The program alignlinear determines how to
@@ -941,25 +940,22 @@
 air parameter file. The actual alignment is done by the program
 reslice. Note that variable yR, being the output of the first step and
 the input of the second step, defines the data dependencies between
-the two steps. The pipeline is illustrated in the center of Figure 2,
-while on the right we show the expanded graph for a 20-volume
+the two steps. The pipeline is illustrated in the center of figure \ref{FMRIFigure2}, while in figure \ref{FMRIgraph} we show the expanded graph for a 20-volume
 run. Each volume comprises an image file and a header file, so there
 are a total of 40 input files and 40 output files. We can also apply
 the same procedure to a run containing hundreds or thousands of
 volumes.
 
 In this example we show the details of the procedure reorientRun,
-which is also a compound procedure. Note the typed input arguments (to
-the right of the procedure name) and output argument (to the
-left). The foreach statement defines an iteration over the input run
+which is also a compound procedure. 
+The foreach statement defines an iteration over the input run
 ir and applies the procedure reorient (which rotates a brain image
 along a certain axis) to each volume in the run to produces a
 reoriented run or. Because the multiple calls to reorient operate on
 independent data elements, they can proceed in parallel.  The
-procedure reorient in this example is an atomic procedure, which
-specifies the interface to calling an executable program. This
-procedure has typed input parameters iv, direction and overwrite and
-one output ov. The body of this particular procedure specifies that it
+procedure reorient in this example is an atomic procedure.
+This procedure has typed input parameters iv, direction and overwrite and
+one output ov. The body specifies that it
 invokes a program (conveniently, also called reorient) that will be
 dynamically mapped to a binary executable. (This executable will
 execute at an execution site chosen by the Swift runtime system.) The
@@ -995,7 +991,7 @@
 \includegraphics{omxFigure}
 
 \caption{Schematic of a single OpenMx model containing 4 regions of
-interest (I through K) with 5 regression starting values (asymmetric
+interest (I through L) with 5 regression starting values (asymmetric
 connections) of weight 0.75 and 4 residual variances (symmetric connections)
 of weight 1.0}
 \end{figure}
@@ -1093,7 +1089,7 @@
 
 TODO: what's the conclusion (if any) of this section?
 
-\section{Swift as a framework for ongoing and experimental work}
+\section{Future work}
 
 \subsection{Automatic characterisation of site and application behaviour}
 
@@ -1133,12 +1129,20 @@
 TODO write about the stuff on provenance db that I did before - that whole
 document of notes...
 
-\subsection{Workflow GUIs as generators of SwiftScript programs - LONI
-Pipeline}
+\subsection{GUI workflow design tools}
 
-\cite{LONIPIPELINE}
+In contrast to a text-oriented programming language like SwiftScript,
+some scientists prefer to design simple programs using GUI design tools.
+An example of this is the LONI Pipeline tool\cite{LONIPIPELINE}. Preliminary
+investigations suggest that scientific workflows designed with that tool
+can be straightforwardly compiled into SwiftScript and thus benefit from
+Swift's execution system.
+
 \subsection{The IBM BG/P}
 
+TODO: hopefully Ioan will write some section that is interesting in this
+area.
+
   TODO: interesting from Swift perspective:
 
   1. getting things running at all: use of BG/P for loosely coupled
@@ -1312,8 +1316,6 @@
 workflow restart, reliable execution over multiple Grid sites, and
 (via Falkon and CoG coasters) fast job execution.
 
-\section{Future Work}
-
 \section{Acknowledgements}
 
 TODO: authors beyond number 3 go here according to ACM style guide, rather