snow, socket cluster: problem with path to rscript

Mon, Apr 20, 2009 5:34 AM

I solved the problem ;-)

I think that the issue come from that snow is expecting that the name of 
the master has been exported in /etc/hosts (typically by IP master_name) 
on the workers. In my case, it wasn't working before and since I've 
exported it it is working!

The error I did was to check with

#open from the master (212):
socketConnection(port = 10187, server = TRUE)

#and from the slave
socketConnection("192.100.100.212", port = 10187) #from 210

#Even if this works it is not a sufficient condition, for snow to work, 
indeed:
socketConnection("master_name", port = 10187) #from 210
has to be working also



Thanks a lot for the help of Dirk, Luke and Steve, who helped me a lot 
in finding this!!

Matthieu

luke at stat.uiowa.edu a ?crit :

On Fri, 17 Apr 2009, Matthieu Stigler wrote:

Steve Weston a ?crit :

I just noticed that you're running R 2.7.1 on your 192.100.100.212
machine.  I believe there are known socketConnection issues
with that version of R that Luke fixed as of R 2.7.2.  So I strongly
suggest that you upgrade your version of R.

I upgraded to R 2.8 but unfortunately this doesn't change, the port 
10187 is still said to be close...

I obviously have a problem in opening the port, maybe should I rather 
post on the debian list or on other forums? I use nc -l -p 10187, so 
that telnet

According to my man page that argument combination is not legal so I
don't know what you actually did.

xxx.212 10187 is working, did it on both machines, but still when 
running with makeCluster have that issue, also when running from worker:

socketConnection("ubuntu", port = 10187)
192.100.100.212:10187 cannot be opened


and with:

socketConnection(port = 10187, server = TRUE)

nothing happens, what is actually the expected output?

the server call waits until a connection occurs and then returns an R
connection object.  The clinet socketConnection call returns a socket
connection if curresful and gives an error message if not.

So on the master do

s <- socketConnection(port = 10187, server = TRUE)

and this will wait for a connection and return to the prompt when a
connectin occurs.  On the wroker machine

telnet master 10187

will either succeed and wait until the server socket is closed or fail
with an error message about not being able to open the port.  If I use

nc master 10187

then no an successful connection nc waits (for input) until the server
closes the socket with close(s) and then returns to the shell prompt.
Failure for me is an immediate resurn to the shell prompt, no error
message (and the server side continues to wait).

luke

Thanks a lot for your help and advices!!!

Mat

-- 
Steve Weston
REvolution Computing
One Century Tower | 265 Church Street, Suite 1006
New Haven, CT  06510
P: 203-777-7442 x266 | www.revolution-computing.com


On Thu, Apr 16, 2009 at 4:52 AM, Matthieu Stigler
<matthieu.stigler at gmail.com> wrote:

luke at stat.uiowa.edu a ?crit :

On Wed, 15 Apr 2009, Matthieu Stigler wrote:

Steve Weston a ?crit :

On Tue, Apr 14, 2009 at 5:29 AM, Matthieu Stigler
<matthieu.stigler at gmail.com> wrote:

So it is now working for the local computer with. However, when 
trying
to
use the external computer, it seems to be working but nothing 
happens
after
he asked for the last password...

This tells you is that "something went wrong".  The basic 
strategy in
this case
is to use the "outfile" option to hopefully capture an error 
message.
 You might
need to set outfile differently for different slaves, 
particularly if
you're starting
more than one on the same machine, but I suggest just starting 
one slave
on 210 to avoid the issue.  So do something like:

host210 <- list(host = "mat at 192.100.100.210", rscript =
"/usr/bin/Rscript",

+                       outfile="/tmp/log.txt")

cl2 <- makeCluster(list(host210), type = "SOCK")

Ok, thanks for pointing out this methid.

I tried it and got following error message. This does not seem 
not be
computer specific (tried to do it to other host 213, and from 
other host 213
to 212, always same error message):

starting worker for ubuntu:10187 Error in 
socketConnection(master, port =
port, blocking = TRUE, open = "a+b") : unable to open connection

Calls: local ... slaveLoop -> recvData -> makeSOCKmaster ->
socketConnection

In addition: Warning message:

In socketConnection(master, port = port, blocking = TRUE, open = 
"a+b") :

ubuntu:10187 cannot be opened

Execution halted


Is it related to ssh or snow? I did not find any reference to 
that prob
googling for it...

It is an issue with your ability to make a socket connection to the
master. Most likely the master computer has a firewall that is
blocking connections to the port snow uses.  Try turning the firewall
off or at least enabling the port in the error message.
A simple test is to do

   socketConnection(port = 10187, server = TRUE)

in an R session on the master and

   telnet ubuntu 10187

in a shell on your worker machine (assumign your master is called
ubuntu) (or you can use R and

   socketConnection("ubuntu", port = 10187)

in an R session on the worker).

luke

Thanks Luke and Dirk for your help!

I don't think it is a firewall error, as both machines have all 
port open
(as default with iptables as I understood), and the admin of the 
network
opened even port 10187.

I tried first the three solutions suggested, none of them seem to 
give good
results:

$telnet 192.100.100.212 10187

Trying 192.100.100.212...

telnet: Unable to connect to remote host: Connection refused

R>socketConnection(port = 10187, server=TRUE)

#nothing happens... is it right?


R > socketConnection("192.100.100.212", port = 10187)
Erreur dans socketConnection("192.100.100.212", port = 10187) :
 impossible d'ouvrir la connexion

De plus : Warning message:

In socketConnection("192.100.100.212", port = 10187) :

 192.100.100.212:10187 cannot be opened

Same error message when using "ubuntu"/ dsge at 192.100.100.212 etc..

Going to a ubuntu forum, someone told that one has to open a server 
on the
port (excuse, explanations are not good as I don't understand that 
much the
subject :-( ).
So launching in the master (212):

$nc -l -p 10187


then one is able to  have in 210:

$telnet 192.100.100.212 10187

Trying 192.100.100.212...

Connected to 192.100.100.212.

Escape character is '^]'.

So it seems that it is working, but there is then no effect on the 
previous
commands socketConnection, makeCluster, still claims that 10187 
can't be
open.

With those elements, do you guys see clearer or is it even darker? 
Thanks a
lot for your help!

Matthieu

Thanks a lot for your help!!

If it hangs, go to another terminal, ssh to 192.100.100.210, and 
look at
the contents of /tmp/log.txt, and hopefully that will provide a 
clue to
the problem.

Another approach is to use the "manual" option.  That will print 
the
command that you should use to manually start each of the slaves.
You just ssh to that machine from another terminal, and cut and 
paste
the printed command to start the slave.  If you set "outfile" to an
empty
string, then output messages will go right to that terminal.

-- 
Steve Weston
REvolution Computing
One Century Tower | 265 Church Street, Suite 1006
New Haven, CT  06510
P: 203-777-7442 x266 | www.revolution-computing.com

snow, socket cluster: problem with path to rscript

Thread (18 messages)