[Swift-commit] r3348 - text/parco10submission
noreply at svn.ci.uchicago.edu
noreply at svn.ci.uchicago.edu
Tue Jun 15 09:54:17 CDT 2010
Author: wozniak
Date: 2010-06-15 09:54:17 -0500 (Tue, 15 Jun 2010)
New Revision: 3348
Modified:
text/parco10submission/paper.bib
text/parco10submission/paper.tex
Log:
Fixes to get it to compile
Modified: text/parco10submission/paper.bib
===================================================================
--- text/parco10submission/paper.bib 2010-06-15 14:25:00 UTC (rev 3347)
+++ text/parco10submission/paper.bib 2010-06-15 14:54:17 UTC (rev 3348)
@@ -13,14 +13,12 @@
@incollection{GCRPNOVA,
author = {Yong Zhao and Ioan Raicu and Ian Foster an Mihael Hategan and Veronika Nefedova and Mike Wilde},
- title = {{Scalable and Reliable Scientific Computations in Grid Environments}}
+ title = {{Scalable and Reliable Scientific Computations in Grid Environments}},
booktitle = {Grid Computing Research Progress},
isbn = {978-1-60456-404-4},
- pages = {TODO},
publisher = {Nova Publisher},
year = 2008,
- editor = (TODO},
- url = {http://people.cs.uchicago.edu/~iraicu/publications/2008_NOVA08_book-chapter_Swift.pdf),
+ url = {http://people.cs.uchicago.edu/~iraicu/publications/2008_NOVA08_book-chapter_Swift.pdf},
}
@inproceedings{SWIFTIWSW2007,
@@ -183,7 +181,7 @@
@inproceedings{mds,
title = {{Grid Information Services for Distributed Resource Sharing}},
- author = {Czajkowski K and Fitzgerald S and Foster I and Kesselman C},
+ author = {Czajkowski K and Fitzgerald S and Foster I and Kesselman C},
booktitle = {Proceedings of the Tenth IEEE International Symposium on High-Performance Distributed Computing (HPDC-10), IEEE Press},
month = {August},
year = 2001
@@ -191,8 +189,8 @@
@inproceedings{rls,
title = {{Giggle: A Framework for Constructing Sclable Replica Location Services}},
- author = {Chervenak A and Deelman E and Foster I and Guy L and Hoschek W and Iamnitchi A and Kesselman C and
- Kunst P and Ripeanu M and Schwartzkopf B and Stockinger H and Stockinger K and Tierney B},
+ author = {Chervenak A and Deelman E and Foster I and Guy L and Hoschek W and Iamnitchi A and Kesselman C and
+ Kunst P and Ripeanu M and Schwartzkopf B and Stockinger H and Stockinger K and Tierney B},
booktitle = {Proceedings of Supercomputing 2002 (SC2002)},
month = {November},
year = 2002
Modified: text/parco10submission/paper.tex
===================================================================
--- text/parco10submission/paper.tex 2010-06-15 14:25:00 UTC (rev 3347)
+++ text/parco10submission/paper.tex 2010-06-15 14:54:17 UTC (rev 3348)
@@ -8,7 +8,7 @@
\bibliographystyle{abbrv} % for ACM SIGS style
\title{Swift - a language for distributed
-parallel scripting}
+ parallel scripting}
% draft - contact benc at ci.uchicago.edu
@@ -227,7 +227,7 @@
\subsection{Language basics}
A Swift script describes data, application components, invocations
-of applications components, and the inter-relations (data flow)
+of applications components, and the inter-relations (data flow)
between those invocations.
Data is represented in a script by strongly-typed single-assignment
@@ -237,7 +237,7 @@
type can be either a \emph{primitive type} or a \emph{mapped type}.
Swift provides a fixed set of primitive types, such as \emph{integer} or
\emph{string}. A mapped type indicates that the actual data does not
-reside in CPU addressable memory (as it would in conventional
+reside in CPU addressable memory (as it would in conventional
programming languages), but in POSIX-like files. Composite types are
further subdivided into \emph{structures} and \emph{arrays}. Structures
are similar in most respects to structure types in other languages. One
@@ -246,7 +246,7 @@
mapped types as \emph{datasets}.
Mapped type and composite type variable declarations can be annotated with a
-\emph{mapping} descriptor indicating the file(s) that make up that \emph{dataset}.
+\emph{mapping} descriptor indicating the file(s) that make up that \emph{dataset}.
For example, the following line declares a variable named \verb|photo| with
type \verb|image|. It additionally declares that the data for this
variable is stored in a single file named \verb|shane.jpeg|
@@ -256,8 +256,8 @@
\end{verbatim}
Conceptually, a parallel can be drawn between Swift \emph{mapped} variables
-and Java \emph{reference types}. In both cases there is no syntactic distinction
-between \emph{primitive types} and \emph{mapped} types or
+and Java \emph{reference types}. In both cases there is no syntactic distinction
+between \emph{primitive types} and \emph{mapped} types or
\emph{reference types} respectively. Additionally, the semantic distinction
is also kept to a minimum.
@@ -587,8 +587,8 @@
\label{LanguageEnvironment}
A SwiftScript \verb|app| declaration describes how a component
-program is invoked. In order to ensure the correctness of the
-Swift model, the environment in which programs are executed needs
+program is invoked. In order to ensure the correctness of the
+Swift model, the environment in which programs are executed needs
to be constrained.
A program is invoked in its own working directory; in that working
@@ -699,8 +699,8 @@
\begin{verbatim}
<pool handle="tguc">
<gridftp
- url="gsiftp://tg-gridftp.uc.teragrid.org" />
- <execution provider="gt4" jobmanager="PBS"
+ url="gsiftp://tg-gridftp.uc.teragrid.org" />
+ <execution provider="gt4" jobmanager="PBS"
url="tg-grid.uc.teragrid.org" />
<workdirectory>
/home/benc/swifttest
@@ -828,7 +828,7 @@
stats - the reliability of coasters vs clusters on a range of sites
(eg a bunch of osg engage and TG sites). also could do: diagram showing
clustering/coasters vs some plain gram submission - CNARI app with 3s
-jobs shows this in an extreme way. Either show such a graph here or in
+jobs shows this in an extreme way. Either show such a graph here or in
CNARI app section.
TODO: comment on how this relates to Falkon
@@ -890,7 +890,8 @@
(out,err) = blastall(i, pir);
\end{verbatim}
-The trick here is that blastall reads takes the prefix name of the database files that it will read (.phr, .seq and .pin files). So i made a dummy file called "UNIPROT_for_blast_14.0.seq" to satisfy the data dependency . So here is the final list of my files:
+The trick here is that blastall reads takes the prefix name of the database files that it will read (.phr, .seq and .pin files).
+So i made a dummy file called ``{\tt UNIPROT\_for\_blast\_14.0.seq}'' to satisfy the data dependency . So here is the final list of my files:
\begin{verbatim}
-rw-r--r-- 1 aespinosa ci-users 0 Nov 15 13:49 UNIPROT_for_blast_14.0.seq
@@ -908,7 +909,7 @@
I looked at the dock6 documentation for OSG. It looks that it recommends to transfer the datafiles to OSG sites manually via globus-url-copy. By my understanding of how swift works, it should be able to transfer my local files to the selected sites. I have yet to try this and will look more on examples in the data management side of Swift.
-Do you know other users who went in this approach? The documentation has only a few examples in managing data. I'll check the swift Wiki later and see what material we have and also post this email/ notes.
+Do you know other users who went in this approach? The documentation has only a few examples in managing data. I'll check the swift Wiki later and see what material we have and also post this email/ notes.
\subsection{fMRI Application Example}
@@ -918,7 +919,7 @@
\end{figure}
\begin{verbatim}
-type Study { Group g[]; }
+type Study { Group g[]; }
type Run { Volume v[]; }
type Volume {
Image img;
@@ -929,15 +930,15 @@
type Subject {
Volume anat;
Run run[];
-}
+}
(Run resliced) reslice_wf ( Run r) {
Run yR = reorientRun( r , "y", "n" );
Run roR = reorientRun( yR , "x", "n" );
Volume std = roR.v[1];
- AirVector roAirVec = alignlinearRun(std, roR,
+ AirVector roAirVec = alignlinearRun(std, roR,
12, 1000, 1000, "81 3 3");
- resliced = resliceRun( roR, roAirVec, "-o",
+ resliced = resliceRun( roR, roAirVec, "-o",
"-k");
}
@@ -949,7 +950,7 @@
}
-(Run or) reorientRun (Run ir, string direction,
+(Run or) reorientRun (Run ir, string direction,
string overwrite) {
foreach Volume iv, i in ir.v {
or.v[i] = reorient (iv, direction, overwrite);
@@ -972,7 +973,7 @@
by a mapper. The
procedure reslice\_wf defines a compound procedure, which comprises
a series of procedure calls, using variables to establish
-data dependencies.
+data dependencies.
In the example, reslice\_wf defines a four-step
pipeline computation, using variables to establish
@@ -990,7 +991,7 @@
volumes.
In this example we show the details of the procedure reorientRun,
-which is also a compound procedure.
+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
@@ -1067,36 +1068,36 @@
\subsection{Molecular Dynamics with DOCK}
\begin{verbatim}
-(file t,DockOut tarout) dockcompute (DockIn infile, string targetlist) {
- app {
- rundock @infile targetlist stdout=@filename(t) @tarout;
- }
-}
-
-type params {
- string ligandsfile;
- string targetlist;
-}
-
-#params pset[] <csv_mapper;file="paramslist.txt">;
-doall(params pset[])
-{
- foreach params,i in pset {
- DockIn infile < single_file_mapper; file=@strcat("/home/houzx/dock-
-run/databases/KEGG_and_Drugs/",pset[i].ligandsfile)>;
- file sout <single_file_mapper; file=@strcat("/home/houzx/dock-
-run/databases/results/stdout/",pset[i].targetlist,"-",i,"-stdout.txt")>;
- DockOut tout <single_file_mapper; file=@strcat(pset[i].ligandsfile,"-result.tar.gz")>;
-# DockOut tout <"result.tar.gz">;
-# sout = dockcompute(infile,pset[i].targetlist);
- (sout,tout) = dockcompute(infile,pset[i].targetlist);
-
- }
-}
-
-params p[];
-p = readdata("paramslist.txt");
-doall(p);
+(file t,DockOut tarout) dockcompute (DockIn infile, string targetlist) {
+ app {
+ rundock @infile targetlist stdout=@filename(t) @tarout;
+ }
+}
+
+type params {
+ string ligandsfile;
+ string targetlist;
+}
+
+#params pset[] <csv_mapper;file="paramslist.txt">;
+doall(params pset[])
+{
+ foreach params,i in pset {
+ DockIn infile < single_file_mapper; file=@strcat("/home/houzx/dock-
+run/databases/KEGG_and_Drugs/",pset[i].ligandsfile)>;
+ file sout <single_file_mapper; file=@strcat("/home/houzx/dock-
+run/databases/results/stdout/",pset[i].targetlist,"-",i,"-stdout.txt")>;
+ DockOut tout <single_file_mapper; file=@strcat(pset[i].ligandsfile,"-result.tar.gz")>;
+# DockOut tout <"result.tar.gz">;
+# sout = dockcompute(infile,pset[i].targetlist);
+ (sout,tout) = dockcompute(infile,pset[i].targetlist);
+
+ }
+}
+
+params p[];
+p = readdata("paramslist.txt");
+doall(p);
\end{verbatim}
\section{Usage Experience}
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