Re: [R] multiple R sessions from one working directory using GNU screen
Olga
There was a presentation at the London R user group about doing what you
ask using the bigmemory package
(http://www.londonr.org/LondonR-20090331/realtimeR.pdf). I believe you
can do the same thing with ff. This wouldn't share the whole workspace
but just the objects you choose.
Regards
David
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Steven McKinney
Sent: 03 August 2010 21:05
To: Olga Lyashevska; r-help@r-project.org
Subject: Re: [R] multiple R sessions from one working directory using
GNU screen
Dear Olga
An R session is conducted entirely in the RAM memory of your computer,
and each invocation of R will have its own memory space, not shared with
any other application, including another R session.
You will have to architect a scheme to allow one R session to find out
about events and objects in another R session. This might involve
writing files to disk from session R1, having session R2 check the
directory for new files every now and then, and so on. (save.image()
saves objects from one R session to a file on disk, but there can be
other items in the saved file such as environments that are not
straightforward to manipulate or investigate from another R session.)
Your situation is similar to cluster computing, where a task is broken
up into independent pieces and each piece is handled by a separate R
process.
Reading about cluster computing with R might help you figure out
strategies to share bits of data and information across multiple R
sessions.
HTH
Steven McKinney
From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On
Behalf Of Olga Lyashevska [o...@herenstraat.nl]
Sent: August 3, 2010 8:04 AM
To: r-help@r-project.org
Cc: Olga Lyashevska
Subject: [R] multiple R sessions from one working directory using GNU
screen
Dear all,
I am using GNU screen to run multiple R sessions from one working
directory in order to split task, however I noticed that dataset is not
synchronized e.g. if I have two sessions R1 and R2, and I remove an
object from R1, R2 doesn't change as expected or change at random.
I have tried to save.image(), q() and then restart both sessions, but it
does not help.
Any suggestions?
Many thanks
Olga
R version 2.11.1 (2010-05-31)
2010 x86_64 GNU/Linux
Ubuntu 10.04.1 LTS
Intel(R) Xeon(R) CPU X3220 @ 2.40GHz
MemTotal: 4050180 kB
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Re: [R] multiple R sessions from one working directory using GNU screen
Dear Steven, Thanks for your post. It explains a lot. The reason I wanted to use multiple sessions simultaneously is that because when I run something it usually takes quite a while (calculating distance matrices), meaning that I have to wait before R can handle the next task. Also RAM is reaching its limits quite often resulting in shutdown, so I wanted to split one task into pieces which indeed similar to cluster computing. I will check documentation on this topic. Kind regards, Olga On Tue, 2010-08-03 at 13:04 -0700, Steven McKinney wrote: Dear Olga An R session is conducted entirely in the RAM memory of your computer, and each invocation of R will have its own memory space, not shared with any other application, including another R session. You will have to architect a scheme to allow one R session to find out about events and objects in another R session. This might involve writing files to disk from session R1, having session R2 check the directory for new files every now and then, and so on. (save.image() saves objects from one R session to a file on disk, but there can be other items in the saved file such as environments that are not straightforward to manipulate or investigate from another R session.) Your situation is similar to cluster computing, where a task is broken up into independent pieces and each piece is handled by a separate R process. Reading about cluster computing with R might help you figure out strategies to share bits of data and information across multiple R sessions. HTH Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Olga Lyashevska [o...@herenstraat.nl] Sent: August 3, 2010 8:04 AM To: r-help@r-project.org Cc: Olga Lyashevska Subject: [R] multiple R sessions from one working directory using GNU screen Dear all, I am using GNU screen to run multiple R sessions from one working directory in order to split task, however I noticed that dataset is not synchronized e.g. if I have two sessions R1 and R2, and I remove an object from R1, R2 doesn't change as expected or change at random. I have tried to save.image(), q() and then restart both sessions, but it does not help. Any suggestions? Many thanks Olga R version 2.11.1 (2010-05-31) 2010 x86_64 GNU/Linux Ubuntu 10.04.1 LTS Intel(R) Xeon(R) CPU X3220 @ 2.40GHz MemTotal: 4050180 kB __ 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] multiple R sessions from one working directory using GNU screen
Thanks David, I looked briefly through the bigmemory package and it looks very promising. As I mentioned in my previous post to Steven I am calculating distance matrices, and if it is my bottleneck (I am nearly sure it is) I believe that the bigmemory will be particularly useful as it is designed to manage massive matrices with shared memory and memory-mapped files. Now I will try to see how it can be implemented in my code. Many thanks Olga On Wed, 2010-08-04 at 13:51 +0100, david.jes...@ubs.com wrote: Olga There was a presentation at the London R user group about doing what you ask using the bigmemory package (http://www.londonr.org/LondonR-20090331/realtimeR.pdf). I believe you can do the same thing with ff. This wouldn't share the whole workspace but just the objects you choose. Regards David -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Steven McKinney Sent: 03 August 2010 21:05 To: Olga Lyashevska; r-help@r-project.org Subject: Re: [R] multiple R sessions from one working directory using GNU screen Dear Olga An R session is conducted entirely in the RAM memory of your computer, and each invocation of R will have its own memory space, not shared with any other application, including another R session. You will have to architect a scheme to allow one R session to find out about events and objects in another R session. This might involve writing files to disk from session R1, having session R2 check the directory for new files every now and then, and so on. (save.image() saves objects from one R session to a file on disk, but there can be other items in the saved file such as environments that are not straightforward to manipulate or investigate from another R session.) Your situation is similar to cluster computing, where a task is broken up into independent pieces and each piece is handled by a separate R process. Reading about cluster computing with R might help you figure out strategies to share bits of data and information across multiple R sessions. HTH Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Olga Lyashevska [o...@herenstraat.nl] Sent: August 3, 2010 8:04 AM To: r-help@r-project.org Cc: Olga Lyashevska Subject: [R] multiple R sessions from one working directory using GNU screen Dear all, I am using GNU screen to run multiple R sessions from one working directory in order to split task, however I noticed that dataset is not synchronized e.g. if I have two sessions R1 and R2, and I remove an object from R1, R2 doesn't change as expected or change at random. I have tried to save.image(), q() and then restart both sessions, but it does not help. Any suggestions? Many thanks Olga R version 2.11.1 (2010-05-31) 2010 x86_64 GNU/Linux Ubuntu 10.04.1 LTS Intel(R) Xeon(R) CPU X3220 @ 2.40GHz MemTotal: 4050180 kB __ 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. Issued by UBS AG or affiliates to professional investors for information only and its accuracy/completeness is not guaranteed. All opinions may change without notice and may differ to opinions/recommendations expressed by other business areas of UBS. UBS may maintain long/short positions and trade in instruments referred to. Unless stated otherwise, this is not a personal recommendation, offer or solicitation to buy/sell and any prices/quotations are indicative only. UBS may provide investment banking and other services to, and/or its employees may be directors of, companies referred to. To the extent permitted by law, UBS does not accept any liability arising from the use of this communication. \251 UBS 2010. All rights reserved. Intended for recipient only and not for further distribution without the consent of UBS. UBS Limited is a company registered in England Wales under company number 2035362, whose registered office is at 1 Finsbury Avenue, London, EC2M 2PP, United Kingdom. UBS AG (London Branch) is registered as a branch of a foreign company under number BR004507, whose registered office is at 1 Finsbury Avenue, London, EC2M 2PP, United Kingdom. UBS Clearing and Execution Services Limited is a company registered in England Wales under company number 03123037, whose registered office is at 1 Finsbury Avenue, London, EC2M 2PP, United Kingdom. UBS
Re: [R] multiple R sessions from one working directory using GNU screen
I don't think one session can get information from another session, except use load. I simulate you situation within one session. Hope it helps. #Simulate the first session object1 - 1:10 save(object1,file=ob1) rm(object1) object1 #Simulate the second session object2 - (1:10)*2 save(object2,file=ob2) rm(object2) object2 #Simulate the third session load(file=ob1) load(file=ob2) object1 object2 - A R learner. -- View this message in context: http://r.789695.n4.nabble.com/multiple-R-sessions-from-one-working-directory-using-GNU-screen-tp2312037p2312461.html Sent from the R help mailing list archive at Nabble.com. __ 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] multiple R sessions from one working directory using GNU screen
Dear Olga An R session is conducted entirely in the RAM memory of your computer, and each invocation of R will have its own memory space, not shared with any other application, including another R session. You will have to architect a scheme to allow one R session to find out about events and objects in another R session. This might involve writing files to disk from session R1, having session R2 check the directory for new files every now and then, and so on. (save.image() saves objects from one R session to a file on disk, but there can be other items in the saved file such as environments that are not straightforward to manipulate or investigate from another R session.) Your situation is similar to cluster computing, where a task is broken up into independent pieces and each piece is handled by a separate R process. Reading about cluster computing with R might help you figure out strategies to share bits of data and information across multiple R sessions. HTH Steven McKinney From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Olga Lyashevska [o...@herenstraat.nl] Sent: August 3, 2010 8:04 AM To: r-help@r-project.org Cc: Olga Lyashevska Subject: [R] multiple R sessions from one working directory using GNU screen Dear all, I am using GNU screen to run multiple R sessions from one working directory in order to split task, however I noticed that dataset is not synchronized e.g. if I have two sessions R1 and R2, and I remove an object from R1, R2 doesn't change as expected or change at random. I have tried to save.image(), q() and then restart both sessions, but it does not help. Any suggestions? Many thanks Olga R version 2.11.1 (2010-05-31) 2010 x86_64 GNU/Linux Ubuntu 10.04.1 LTS Intel(R) Xeon(R) CPU X3220 @ 2.40GHz MemTotal: 4050180 kB __ 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.
