[R] R gets slow

[Peter Dalgaard]

"pau carre" <pau.carre at gmail.com> writes:

> Hello, I finally solved the problem. The solution was just remove the
> attach operations. When attach is called a copy of the data is
> generated and since I know it is not possible to delete it with rm as
> it is not associated to any object.

You can detach() it though...
 
> Pau
> 
> 2006/3/26, pau carre <pau.carre at gmail.com>:
> > Hello, I am still having the same problem, even removing the objects
> > (with rm()).
> > I checked the memory allocated by R and it is constant (about 4.5%),
> > so I have no idea of what is happening...
> > Moreover in few minutes (15) the models are generated 5 times
> > slower... restarting the server is the only (but not acceptable)
> > solution I have.
> > (I do not generate any graph and/or extra object)
> > Pau
> >
> >
> > 2006/3/25, pau carre <pau.carre at gmail.com>:
> > > Hello, I have R as a socket server that computes R code sent by some
> > > scripts (the clients). These scrips send R code to generate models
> > > (SVM). The problem is that first models are generated in less than one
> > > second and one hour later, the same models are generated in more than
> > > ten seconds (even training with same data). If I restart the server ,
> > > then it works well (fast). I don't know if I have to free the memory
> > > or something.
> > >
> > > Here you have the code:
> > > R server:
> > > FSsocket <- function(){
> > >     continue = TRUE;
> > >     while(continue){
> > >         conn <- try(socketConnection(server = TRUE, port = 7890, blocking =
> > > TRUE, open = "ab"), silent = FALSE);
> > >         isOpened = !inherits(conn, "try-error");
> > >         isOpened = isOpened && isOpen(conn);
> > >         while(!isOpened){
> > >             Sys.sleep(1);
> > >             conn <- try(socketConnection(server = TRUE, port = 7890, blocking
> > > = TRUE, open = "ab"), silent = FALSE);
> > >             isOpened = !inherits(conn, "try-error");
> > >             isOpened = isOpened && isOpen(conn);
> > >         }
> > >         print("Waitting for source");
> > >         srcFile = readLines(conn, n = 1)
> > >         print(srcFile)
> > >         continue = srcFile != "--close"
> > >         if(continue){
> > >             print("Executing source");
> > >             error <- try(source(srcFile), silent = FALSE);
> > >             if(inherits(error, "try-error")){
> > >                 writeLines("ERROR", conn)
> > >             }
> > >             print("Sending confirmation")
> > >             writeLines("DONE", conn)
> > >             print("Closing connection")
> > >         }
> > >         close(conn)
> > >     }
> > > }
> > > FSsocket();
> > >
> > > Model generator example:
> > > library("class");
> > > library("e1071");
> > > dd = read.table("sampling/adapteddataSet");
> > > attach(dd);
> > > ddv = read.table("sampling/adaptedvalidationDataSet");
> > > attach(ddv);
> > > dd[,1] = factor(dd[,1]);
> > > ddv[,1] = factor(ddv[,1]);
> > > attach(dd);
> > > tr_in = as.matrix(dd[,2:(1 + 1)]);
> > > tr_out = dd[,1];
> > > val_in = as.matrix(ddv[,2:(1 + 1)]);
> > > val_out = ddv[,1];
> > > t = tune(svm, kernel = "radial", train.x = tr_in, train.y = tr_out,
> > > validation.x = val_in, validation.y = val_out,
> > >           range = list( gamma = 2^(-1:1), cost = 2^(2:4) ), tunecontrol =
> > > tune.control(sampling = "fix") )
> > > z = t$best.model
> > > save(z, file = "./models/1/20", compress=FALSE);
> > >
> > > Thanks
> > > Pau.
> > >
> >
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
> 

-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)                  FAX: (+45) 35327907