[Swift-user] still having problems

[Zhao Zhang]

Hi, Erin

Could you try to run it without swift? Without swift, what does the 
command look like if you invoke "RInvoke" under shell?
By your swift script, I am assuming RInvoke requires 2 input parameters, 
one for input file, the other one is a Integer parameter.
What does the output look like? does RInvoke write output to standard 
output, or write to a output file? How do we define the
output file name before we invoke the script?

zhao

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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>
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