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<P><FONT SIZE=2>That was it!<BR>
<BR>
thank you,<BR>
e<BR>
<BR>
<BR>
Erin M. Hodgess, PhD<BR>
Associate Professor<BR>
Department of Computer and Mathematical Sciences<BR>
University of Houston - Downtown<BR>
mailto: hodgesse@uhd.edu<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: Michael Wilde [<A HREF="mailto:wilde@mcs.anl.gov">mailto:wilde@mcs.anl.gov</A>]<BR>
Sent: Wed 6/3/2009 11:03 PM<BR>
To: Hodgess, Erin<BR>
Cc: swift-user@ci.uchicago.edu<BR>
Subject: Re: [Swift-user] doesn't create output file<BR>
<BR>
Erin,<BR>
<BR>
Looking at your R script, it seems like it ran OK (from e1.in.Rout) but<BR>
there is no R statement in the R input that writes the output object xz<BR>
to the data file xy.out where your swift scriptis expecting to find it.<BR>
<BR>
Also, in future email questions, send the name of the directory that you<BR>
ran from - I had to hunt around a bit in /home/erin to find it.<BR>
<BR>
- Mike<BR>
<BR>
R output was:<BR>
<BR>
more e1.in.Rout<BR>
<BR>
R version 2.5.1 (2007-06-27)<BR>
Copyright (C) 2007 The R Foundation for Statistical Computing<BR>
ISBN 3-900051-07-0<BR>
<BR>
R is free software and comes with ABSOLUTELY NO WARRANTY.<BR>
You are welcome to redistribute it under certain conditions.<BR>
Type 'license()' or 'licence()' for distribution details.<BR>
<BR>
Natural language support but running in an English locale<BR>
<BR>
R is a collaborative project with many contributors.<BR>
Type 'contributors()' for more information and<BR>
'citation()' on how to cite R or R packages in publications.<BR>
<BR>
Type 'demo()' for some demos, 'help()' for on-line help, or<BR>
'help.start()' for an HTML browser interface to help.<BR>
Type 'q()' to quit R.<BR>
<BR>
> allinputs <- Sys.getenv("R_SWIFT_ARGS")<BR>
> print(allinputs)<BR>
R_SWIFT_ARGS<BR>
"xx.dat 25 4"<BR>
> inputfilename <- noquote(strsplit(allinputs," ")[[1]][1])<BR>
> start_num <- as.numeric(noquote(strsplit(allinputs," ")[[1]][2]))<BR>
> n1 <- as.numeric(noquote(strsplit(allinputs," ")[[1]][3]))<BR>
> print(n1)<BR>
[1] 4<BR>
> xy <- matrix(scan(inputfilename),byrow=TRUE,ncol=5)<BR>
Read 50 items<BR>
> xz <- apply(xy,2,mean)<BR>
> xz<BR>
[1] 0.2526954 -0.7243118 0.2969102 -0.2283567 -0.2468762<BR>
><BR>
> proc.time()<BR>
user system elapsed<BR>
0.775 0.033 0.797<BR>
<BR>
<BR>
^^^^ No statement to write xy into xy.out (or to write out any other<BR>
result, like xz).<BR>
<BR>
<BR>
<BR>
On 6/3/09 10:03 PM, Hodgess, Erin wrote:<BR>
> Hi again!<BR>
><BR>
> I'm looking at some of Sarah's really cool stuff and trying to reproduce<BR>
> test versions.<BR>
><BR>
> Here is the swift file:<BR>
> [erin@tp-login2 bin]$ cat test1.swift<BR>
> type file{}<BR>
> #--- trying to learn from Sarah's cool stuff<BR>
><BR>
><BR>
> [erin@tp-login2 bin]$ cat test1.swift<BR>
> type file{}<BR>
> #--- trying to learn from Sarah's cool stuff<BR>
><BR>
><BR>
> <BR>
> app (file simResult) simScript (file scriptFile, file inputFile,<BR>
> int iter,int tval){<BR>
> RInvoke @filename(scriptFile) @filename(inputFile) iter tval;<BR>
> }<BR>
> <BR>
> <BR>
> file script<"e1.in">;<BR>
> file inputData<"xx.dat">;<BR>
> file simResult<"xy.out">;<BR>
> int iter = 25;<BR>
> int tval = 4;<BR>
> simResult=simScript(script,inputData,iter,tval); <BR>
><BR>
> [erin@tp-login2 bin]$<BR>
><BR>
><BR>
> And here is the result:<BR>
> [erin@tp-login2 bin]$ swift -tc.file tc.data test1.swift<BR>
> Swift svn swift-r2950 cog-r2406<BR>
><BR>
> RunID: 20090603-2200-krmao849<BR>
> Progress:<BR>
> Progress: Checking status:1<BR>
> Progress: Checking status:1<BR>
> Progress: Checking status:1<BR>
> Execution failed:<BR>
> Exception in RInvoke:<BR>
> Arguments: [e1.in, xx.dat, 25, 4]<BR>
> Host: localhost<BR>
> Directory: test1-20090603-2200-krmao849/jobs/k/RInvoke-k4l6zqbj<BR>
> stderr.txt:<BR>
> stdout.txt:<BR>
> ----<BR>
><BR>
> Caused by:<BR>
> The following output files were not created by the application:<BR>
> xy.out<BR>
> [erin@tp-login2 bin]$<BR>
><BR>
><BR>
> The tc.data is here:<BR>
> [erin@tp-login2 bin]$ cat tc.data<BR>
> #NOTE WELL: fields in this file must be separated by tabs, not spaces<BR>
> # and there must be no trailing whitespace at the end of each<BR>
> line.<BR>
> #<BR>
> # sitename app pathname (ignored) (ignored) <BR>
> profiles<BR>
> localhost echo /bin/echo INSTALLED INTEL32::LINUX null<BR>
> teraport echo /bin/echo INSTALLED INTEL32::LINUX null<BR>
> localhost translate /usr/bin/tr INSTALLED <BR>
> INTEL32::LINUX null<BR>
> localhost R /home/erin/R-2.9.0/bin/R INSTALLED <BR>
> INTEL32::LINUX null<BR>
> localhost wc /usr/bin/wc INSTALLED INTEL32::LINUX null<BR>
> localhost convert /usr/bin/convert INSTALLED <BR>
> INTEL32::LINUX null<BR>
> localhost RInvoke /home/erin/R-2.9.0/bin/RInvoke.sh <BR>
> INSTALLED INTEL32::LINUX null<BR>
><BR>
> Any suggestions most appreciated.<BR>
><BR>
> Erin<BR>
><BR>
><BR>
> Erin M. Hodgess, PhD<BR>
> Associate Professor<BR>
> Department of Computer and Mathematical Sciences<BR>
> University of Houston - Downtown<BR>
> mailto: hodgesse@uhd.edu<BR>
><BR>
><BR>
> ------------------------------------------------------------------------<BR>
><BR>
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