Re: [R] R process gets killed spontaneously
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. Uwe Ligges __ R-help@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@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.
Re: [R] R process gets killed spontaneously
Hi Peng, in a very simplistic manner, what happens is that the Operating System thinks it is too dangerous to let the R process to use so much memory. So, to protect the whole system, it kills R, before the system becomes unstable. I've been looking at the problem you observed last week and, as I promised, I will come back to you with my findings sometime this week. I was already informed on how to reduce the memory footprint when creating the specific object you're interested in, but still need to run some tests. Will get back to you soon, b On Nov 10, 2009, at 2:23 PM, Peng Yu wrote: 2009/11/10 Uwe Ligges lig...@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@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@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.
Re: [R] R process gets killed spontaneously
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...@gmail.com To: r-h...@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 lig...@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@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@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.
Re: [R] R process gets killed spontaneously
I run R in gnome-terminal. Is it what you referred as 'screen session'? On Tue, Nov 10, 2009 at 3:01 PM, rmail...@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...@gmail.com To: r-h...@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 lig...@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@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@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.
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, rmail...@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...@gmail.com To: r-h...@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 lig...@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@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@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@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.
Re: [R] R process gets killed spontaneously
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 cedr...@cedrickjohnson.com To: Peng Yu pengyu...@gmail.com Cc: r-help@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, rmail...@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...@gmail.com To: r-h...@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 lig...@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@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@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@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@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] R process gets killed spontaneously
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? __ R-help@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.
