[Swift-user] still having problems

[Hodgess, Erin]

it works fine from command line.  The echo $? gives a zero, the correct file is produced.


It just seems to be the jump from command line to swift that is the snag.



Erin M. Hodgess, PhD
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: hodgesse at uhd.edu



-----Original Message-----
From: Ben Clifford [mailto:benc at hawaga.org.uk]
Sent: Mon 6/15/2009 11:57 AM
To: Hodgess, Erin
Cc: swift-user at ci.uchicago.edu
Subject: Re: [Swift-user] still having problems 
 

based on previous messages, its still unclear to me that you have the 
program working outside of Swift.

Pretty much you need to be able to run rInvoke perm.short.R 0 from the 
commandline successfully before attempting to run that command inside 
Swift.

On Mon, 15 Jun 2009, Hodgess, Erin wrote:

> Hi again!
> 
> I have brought things down to the bones here.  Still no luck.
> 
> The files are /home/erin/R-2.9.0/bin/perm.short.R and /home/erin/R-2.9.0/bin/perm4.swift
> 
> 
> [erin at tp-login2 bin]$ swift -tc.file tc.data perm4.swift
> Swift svn swift-r2950 cog-r2406
> 
> RunID: 20090615-1137-nbfujhb2
> Progress:
> Progress:  Checking status:1
> Progress:  Stage in:1
> Execution failed:
> 	Exception in RInvoke:
> Arguments: [perm.short.R, 0]
> Host: localhost
> Directory: perm4-20090615-1137-nbfujhb2/jobs/v/RInvoke-vti60bcj
> stderr.txt: 
> stdout.txt: 
> ----
> 
> Caused by:
> 	Exit code 1
> [erin at tp-login2 bin]$ cat perm4.swift
> type file{}
> 
> (file procOut) permScript (file script, int batchSize){
> 	        app{
> 	                RInvoke @filename(script) batchSize ;
> 	        }
> 	}
> 
> 
> 
> 
> 
> 
> 
> 	        int batchSize=0;
> 		        file script<"perm.short.R">;
> 	                file procOut<"a.txt">;
> 	                procOut=permScript(script, batchSize);
> 
> [erin at tp-login2 bin]$ cat perm.short.R
> 	# -- read data files that are hardcoded per analysis and get
> 	vox_speech_vec <- as.matrix(read.table("origccf.txt"))
> 	pm <- as.matrix(read.table("corr.perm.matrix.txt"))
> 	allinputs <- Sys.getenv("R_SWIFT_ARGS")
> 	print(allinputs)
> 	permlength <-  as.numeric(noquote(strsplit(allinputs," ")[[1]][1]))
> #	startrpermrow <- as.numeric(noquote(strsplit(allinputs," ")[[1]][1]))
> 	startrpermrow <- 1
> 	endpermrow <- permlength + startrpermrow
> 	debug = 1
> 	if (debug == 1) {
> 	        print(paste("start", startrpermrow, "end", endpermrow, sep=","))
> 	}
> 	 # rotate across specified rows in permutation matrix
> 	for (rr in startrpermrow:endpermrow){
> 	        permvec = pm[rr,]
> 	        # initialize a 'ccf' matrix for each permutation
> 	        ccf <- matrix(nrow=200, ncol=1)
> 	        mat_row = 0
> 	        for (vox in 1:200) {
> 	                mat_row = mat_row + 1
> 	                speechperm_ccf <- ccf(vox_speech_vec[vox,], permvec, lag.max = 6, type = c("correlation"), na.action=na.pass, plot = FALSE)
> 	                if (any(speechperm_ccf$acf[1:13] == "NaN")) {
> #	                        speechperm_ccf$acf[1:13] = 0
> 				speechperm_ccf$acf[1:13] <- rep(0,13)
> 	                        } else {
> 	                        speechperm_ccf$acf[1:13] = speechperm_ccf$acf[1:13]
> 	                }
> 	        speechperm_ccf <- as.matrix(data.frame(speechperm_ccf$acf, speechperm_ccf$lag))[7:13,]
> 	        speechperm_cor <- speechperm_ccf[which.max(speechperm_ccf[,1]),]
> 	        ccf[mat_row, ] <- c(speechperm_cor[[1]])
> 	        }
> 	        write.table (ccf, file=paste("a.txt",sep=""), row.names=FALSE, col.names=FALSE)
> 	        if (debug == 1) {
> 	                print(paste("permrow finished", rr, sep=","))
> 	                print(date())
> 	        }
> 	        rm(ccf)
> 	}
> [erin at tp-login2 bin]$ 
> 
> Any help appreciated.
> 
> 
> 
> 
> Erin M. Hodgess, PhD
> Associate Professor
> Department of Computer and Mathematical Sciences
> University of Houston - Downtown
> mailto: hodgesse at uhd.edu
> 
> 

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