runPoped_matlab <- function(remote=remote, name=name, sh.script="run.sh",cluster=T){
print('- Running POPED')
# remove old output.log
unlink("output.log")
# run optimization / call PopED
#com="/usr/local/MATLAB/R2011b/bin/matlab -nosplash -nodisplay -nodesktop -r \"poped(function_input()); quit\" -logfile output.log"
if(remote == TRUE) com <- paste("ssh andy@doris.biof.uu.se 'cd AOD/coen/",name,"; bash ",sh.script,"'", sep="")
if(remote == FALSE) com <- paste("bash ", sh.script, sep="")
if(Sys.which("execute")=="") com <- paste("source ~/.bashrc;",com,sep="")
print(com);
# run poped
if(!cluster){
system(com)
} else {
system(com, wait=TRUE)
# check if run is already finished
run <- TRUE
cat("Running")
while(run == TRUE){
#if(remote == TRUE) state <- system("ssh doris.biof.uu.se qstat", intern=TRUE)
#if(remote == FALSE) state <- system("qstat", intern=TRUE)
#if(length(state) > 0) { Sys.sleep(4)}
#if(length(state) == 0) { print('finished poped'); run=FALSE}
# read output file
if(file.exists("output.log")){
o<-file("output.log")
f<-readLines(o)
close(o)
finished <- " strengine: 'MATLAB 7.9.0.529 (R2009b)'"
tail <- tail(f,2)[1]
if( !is.na(tail) ) {
if( is.logical(tail == finished) ){
if( tail == finished ){
print('Finished poped');
run=FALSE;
} else {
cat('.'); Sys.sleep(3)
}
} else {
cat('.'); Sys.sleep(3)
}
} else {
cat('.'); Sys.sleep(3)
}
}
}
}
}
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