[R] R process gets killed spontaneously

[rmailbox at justemail.net]

Cedrick is correct. I was referring to the command invoked by entering the string "screen" at the shell prompt.


----- Original message -----
From: "Cedrick W. Johnson" <cedrick at cedrickjohnson.com>
To: "Peng Yu" <pengyu.ut at gmail.com>
Cc: r-help at r-project.org
Date: Tue, 10 Nov 2009 16:38:09 -0500
Subject: Re: [R] R process gets killed spontaneously

I think he was referring to the actual 'screen' command..

but, I digress... Is there any way you can put your commands in a script 
and execute them from the command line so that you see the actual memory 
and GC output from R in realtime? I use the following (in WinXP) to 
debug any faulty processes or detect if the job was actually completed 
successfully:

(adapted for Linux, *not* winxp)
R --verbose MorningStartup.r > morningsummary-log.txt

That should yield some more results which hopefully should help you 
investigate. The pertinent stuff is output to the console.

-cedrick


Peng Yu wrote:
> I run R in gnome-terminal. Is it what you referred as 'screen session'?
>
> On Tue, Nov 10, 2009 at 3:01 PM,  <rmailbox at justemail.net> wrote:
>   
>> This was happening to me on Red Hat Linux when I was running huge jobs within a screen session. By any chance are your R processes running within a screen session? (screen is a very nice program that will keep your sessions alive after you log out, but it was killing off my big memory jobs for unknown reasons.)
>>
>> Eric
>>
>>
>>
>> ----- Original message -----
>> From: "Peng Yu" <pengyu.ut at gmail.com>
>> To: r-help at stat.math.ethz.ch
>> Date: Tue, 10 Nov 2009 10:23:18 -0600
>> Subject: Re: [R] R process gets killed spontaneously
>>
>> 2009/11/10 Uwe Ligges <ligges at statistik.tu-dortmund.de>:
>>     
>>> Peng Yu wrote:
>>>       
>>>> My R process has been killed for a few times, although the system
>>>> administrator did not do so. It happened when R attempted to allocate
>>>> a lot of memory. I'm wondering whether R would spontaneously kill
>>>> itself if it can not allocate enough memory?
>>>>         
>>> It does not kill itself. If it was not some out-of-memory kill process of
>>> your OS, then you may have seen some segfault. We need reproducible code and
>>> all the details described in the posting guide.
>>>       
>> Please see this thread about the necessary information.
>>
>> http://www.mail-archive.com/r-help@r-project.org/msg74804.html
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>     
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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