RSperl & threads

[sperlyjinx]

Hi all, I'm trying to use the RSPerl module in a script that uses threads. I am able to call R functions without a problem when I don't use threads. However, using threads, I get varying errors depending on how I call the R functions. If I call the R::initR function in the "boss" thread and then try to call R functions from a "worker" thread, I get the following error: Error: C stack usage is too close to the limit Caught error in R::call() However, if I move the "use" declarations for R & RReferences to the worker thread, along with the initR call, I get this: Fatal error: R home directory is not defined I've attached some code for your reference. Is there any way to get this module working with Perl threads? Thanks in advance for your help. -Jay

#!/usr/bin/perl

use warnings;
use strict;

#use R;
#use RReferences;
#&R::initR("--silent");

use threads;
use threads::shared;
use Thread::Queue;

our $queue : shared = Thread::Queue->new;
our $hold : shared;

my $thr = threads->new (\&command_runner);

$hold =1;
$queue->enqueue("ls");
while ($hold) {
    sleep(1);
}
$queue->enqueue("end");

$thr->join();

# Thread for processing functions
sub command_runner {

    use R;
    use RReferences;
    &R::initR("--silent");

    my $run = 1;
    # run until return
    while ($run) {
        # This call will block until the main thread sends the job
        my $job = $queue->dequeue;

    print "j: $job\n";

    if ($job eq "ls"){
        R::ls();
        } elsif ($job eq "end") {
            $run = 0
        }
        { lock $hold; $hold = 0; }
    }
   
}

[renodino]

Caveat: I know nothing about RSPerl, other than it embeds one interpretter in the other.

Since each Perl thread starts a new interpretter, its unclear whether an R interpretter created in the main thread will get cloned into all the children, or each child will get a brand new R interpretter instance.

Assuming you revert to the original approach, you might try cranking up the per-thread stack size, and see if that corrects the error message. Note that doing so will reduce the number of threads you can start.

[zentara]

I couldn't find the R or the RReferences module on cpan. There probably is a way to make it work with threads, but reading the reviews of Statistics::R module, it is problem prone on it's own, even without threads.

Since it involves a "shell" you may need some kind of pty, or pipes, to run it from Perl thru IPC.

See if you can get it to work thru a forking mechanism first, until you get a handle on what is exactly happening, and then try to convert to threads.

[zentara]

I was just meditating last night, and thought about your problem. I had a thought( better duck :-) ). If the RSPerl is an interpreter, which you send commands to stdin and get results out of stdout, you probably should run it thru IPC::Open3. I have sample code below

#!/usr/bin/perl 
use warnings;
use strict;
use IPC::Open3;

$|=1;

#my $pid=open3(\*IN,\*OUT,\*ERR,'/bin/bash');
my $pid=open3(\*IN,\*OUT,0,'/bin/bash');
# set \*ERR to 0 to send STDERR to STDOUT
my $cmd = 'date';
#my $cmd = 'top';
#send cmd to bash
print IN "$cmd\n";

#getresult
my $result = <OUT>;
print $result;

Now you should be able to do a similar thing with the RSPerl interpreter. Of course, in a real script, you may want to separate stdout and stderr, and use IO::Select. Search for examples of IPC::Open3 for more detailed usage.

Now, once you get IPC::Open3 to run the interpreter, you can put the code into a thread, and pass in strings to be eval'd thru ther shared variable mechanism.

[sperlyjinx]

Thanks to everyone for your input. I've solved the problem a slightly different way. I was able to set up a socket connection between R & Perl. If anyone is interested in the Perl or R code that accomplishes this, please let me know.

[Anonymous Monk]

Hi, could you please share the code with us all? I am a biologist used to working in R environment for my statistical analysis. But, now I have to call my .R files from perl. I have tried using RSperl, but it doesn't seem to support source("filename.R") function. Any take on this? Your comments are highly appreciated.

[lsm]

Yes, I am interested in the Perl and the R code. Thank you very much.

[amesdaq]

i would be very interested in this code. can you post it up on here or send it to me directly?