[Swift-user] still having problems

[Hodgess, Erin]

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/swift-user/attachments/20090615/29cfa644/attachment.html>