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From: John Hendy <jw.hendy@gmail.com>
To: nicholas.dokos@hp.com
Cc: cberry@tajo.ucsd.edu, emacs-orgmode@gnu.org
Subject: Re: Bug? R: Org babel block execution *drastically* slower than in ESS session directly
Date: Thu, 1 Nov 2012 13:18:58 -0500	[thread overview]
Message-ID: <CA+M2ft9-Ufrnf_uaTzsc2D5q3ZLOqaxK8FVZ_j14GPs1MC1NMw@mail.gmail.com> (raw)
In-Reply-To: <11876.1351784283@alphaville>

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On Thu, Nov 1, 2012 at 10:38 AM, Nick Dokos <nicholas.dokos@hp.com> wrote:

> John Hendy <jw.hendy@gmail.com> wrote:
>
> >     o run top (or whatever equivalent is available on your OS) and see
> >       whether the CPU (or one of the CPUs) gets pegged at 100%
> utilization
> >       and stays there. If yes, that's an indication of an infinite loop
> >       somewhere.
> >
> > - quit any other instances of emacs/R
> > - start `top` in terminal
> > - execute block
> > - Use '<' '>' to sort back and forth between cpu and ram
> >
> > Observations
> > - R is at 80-100% cpu for about 5sec
> > - Then emacs shifts to fairly constant ~100% cpu usage
> > - After about a minute, the minibuffer expands to ~1/3 of the window
> height and fills with the csv
> > data
> > - Finished after ~5min total time
> > - So, R took about 5sec, emacs took another 5min to finish
> >
> >
>
> So not an infinite loop. That's progress ;-)
>
> Perhaps emacs is thrashing? If you are on linux, use swapon -s
> or (perhaps better) iostat, or (perhaps even better, at least if
> you are on the Gnome 2.x desktop[fn:1]), run the system monitor
> applet, click Properties, enable all the monitored resources
> (cpu, mem, net, swap, load, disk) and watch it while you are
> running the test: in particular, check memory and swap. If you
> are swapping even a little bit, that's enough to cause severe
> performacne problems[fn:2], which can be cured by using less memory
> (so stop any memory hogs from running) or by adding memory.
>

Oh, and I'm conscious of R using RAM, so I tried to run this stuff without
browsers open, no other R sessions, etc. Prior to running R and without a
browser, I'm typically around 10-15% RAM utilized...

I have 4gb, so that should be enough to read this, especially per Chuck's
results! This is also an i7 work computer. It should fly (and in the ESS
session itself, it does).


John


>
> Top can also show you memory and swap so maybe that's the quickest
> way to check.
>
> Nick
>
> Footnotes:
>
> [fn:1] You can pobably do this in other desktops but I have no
>        experience with them, so no guidance to give.
>
> [fn:2] My old laptop with 1GB of memory would swap whenever I ran mairix
>        to index my mail: it would take 30 minutes or so to finish.  My
>        new(er) laptop has 4GB and finishes in 30 seconds: memory usage
>        peaks at about 2.5 GB.
>
>

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  parent reply	other threads:[~2012-11-01 18:19 UTC|newest]

Thread overview: 217+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2012-10-31  6:12 Bug? R: Org babel block execution *drastically* slower than in ESS session directly John Hendy
2012-10-31 16:41 ` cberry
2012-10-31 17:18   ` John Hendy
2012-10-31 20:12     ` cberry
2012-10-31 20:23       ` John Hendy
2012-10-31 20:56         ` Thomas S. Dye
2012-10-31 23:00           ` Nick Dokos
2012-10-31 22:53         ` Nick Dokos
2012-11-01 14:53           ` John Hendy
2012-11-01 15:38             ` Nick Dokos
2012-11-01 18:17               ` John Hendy
2012-11-01 18:18               ` John Hendy [this message]
2012-11-01 18:48                 ` Nick Dokos
2012-11-14  3:27                   ` Aaron Ecay
2012-11-14  4:52                     ` John Hendy
2012-11-14  6:32                       ` Aaron Ecay
2012-11-14  8:28                         ` Thomas S. Dye
2012-11-14  8:35                           ` Andreas Leha
2012-11-16 15:45                             ` Eric Schulte
2012-11-16 17:47                               ` Andreas Leha
2012-11-16 19:00                                 ` John Hendy
2012-11-16 20:25                                 ` Achim Gratz
2012-11-17 17:12                                   ` Eric Schulte
2012-11-18  0:41                               ` Aaron Ecay
2012-11-18  0:57                                 ` Eric Schulte
2012-11-18  1:41                                   ` Aaron Ecay
2012-11-19  1:18                                     ` Eric Schulte
2012-11-19  5:11                                       ` Eric Schulte
  -- strict thread matches above, loose matches on Subject: below --
2013-03-19 21:40 python sessions Gary Oberbrunner
2013-03-20  0:04 ` John Hendy
2013-03-20  3:07   ` Nick Dokos
2013-03-20  6:44     ` Andreas Röhler
2013-03-20 12:54       ` Ista Zahn
2013-03-20 14:08         ` Nick Dokos
2013-03-20 14:28           ` Gary Oberbrunner
2013-03-20 17:21         ` Andreas Röhler
2013-03-20  7:08   ` Andreas Röhler
2013-03-20 15:38     ` John Hendy
2013-03-20 15:42       ` John Hendy
2013-03-20 16:06       ` Nick Dokos
     [not found]         ` <CAFChFygsUeBejEY6m2bSU0C5cjLYz0nUADH=s+BYxajfZ2sKKQ@mail.gmail.com>
2013-03-20 16:12           ` Fwd: " Gary Oberbrunner
2013-03-20 17:08         ` Andreas Röhler
2013-03-20 17:25           ` Nick Dokos
2013-03-20 17:54             ` John Hendy
2013-03-20 18:15               ` Nick Dokos
2013-03-20 18:32                 ` Ista Zahn
2013-03-20 18:39                   ` Nick Dokos
2013-03-20 18:43                   ` Andreas Röhler
2013-03-20 19:42                     ` Ista Zahn
2013-03-20 19:53                       ` Andreas Röhler
2013-03-20 20:12                         ` Ista Zahn
2013-03-20 20:25                           ` Gary Oberbrunner
2013-03-20 22:06                             ` Ista Zahn
2013-03-20 18:42                 ` Andreas Röhler
2013-03-20 19:01             ` Andreas Röhler
     [not found]       ` <CAFChFygPrhuHHyMo2Vk2_OdksWVB=oACA7jnOXN+itUNqh-nqw@mail.gmail.com>
     [not found]         ` <CA+M2ft9bO7DU61vVeYrhduVvkg1V6PMuiyvsOy5tNWuXcSUEpw@mail.gmail.com>
     [not found]           ` <CAFChFyhbeXE4HNLKA6Ubii+MtQwD7=4khAypa+--coZrQiJekA@mail.gmail.com>
2013-03-21  1:22             ` Gary Oberbrunner
2013-03-21  1:54               ` John Hendy
2013-03-21  1:56                 ` Gary Oberbrunner
2013-03-21  7:42                   ` Andreas Röhler
2013-03-21  7:43                     ` Bastien
2013-03-21  8:13                       ` Andreas Röhler
2013-03-23 22:07                         ` Eric Schulte
2013-03-24  1:29                           ` John Hendy
2013-03-24 22:59                             ` Eric Schulte
2013-03-25  2:38                               ` Nick Dokos
2013-03-25  2:59                                 ` John Hendy
2013-03-25  6:34                                   ` Andreas Röhler
2013-03-25 15:40                                   ` Eric Schulte
2013-03-25 15:55                                     ` John Hendy
2013-03-25 16:07                                       ` Eric Schulte
2013-03-25 16:41                                         ` Nick Dokos
2013-03-25 16:01                                     ` Ista Zahn
2013-03-25 16:23                                       ` John Hendy
2013-03-25 16:43                                         ` Eric Schulte
2013-03-25 17:27                                           ` Andreas Röhler
2013-03-25 17:41                                             ` John Hendy
2013-03-25 18:16                                               ` Ista Zahn
2013-03-25 19:30                                             ` Ivan Andrus
2013-03-24  7:47                           ` Andreas Röhler
2013-03-24 14:47                             ` John Hendy
2013-03-24 15:30                               ` Andreas Röhler
2013-03-24 16:58                               ` Nick Dokos
2013-03-24 16:59                                 ` John Hendy
2013-03-24 18:41                                   ` Nick Dokos
2013-03-25 20:46                                     ` Andreas Röhler
2013-03-25 21:37                                       ` Eric Schulte
2013-03-26  6:29                                         ` Andreas Röhler
2013-03-26 12:32                                           ` Eric Schulte
2013-03-26 21:41                                             ` Gary Oberbrunner
2013-03-26 21:47                                               ` John Hendy
2013-03-27  6:19                                               ` Andreas Röhler
2013-03-30  7:19                                                 ` Andreas Röhler
2012-08-26 20:11 Alternate format for datetree c b
2012-08-27  1:16 ` John Hendy
2012-08-27  4:04   ` Nick Dokos
2012-08-27  6:08     ` John Hendy
2012-08-28  8:49       ` Ian Barton
2012-08-28 12:49         ` Nick Dokos
2012-08-28 12:50         ` Nick Dokos
2012-08-29  7:49           ` Ian Barton
     [not found]             ` <lists@manor-farm.org>
2012-08-29 14:17               ` Nick Dokos
2012-08-29 14:25             ` John Hendy
2012-08-29 20:01               ` Ian Barton
2012-09-06  7:46                 ` Ian Barton
2012-09-06  5:42       ` c b
2012-09-06  6:26         ` Nick Dokos
2012-09-06  7:00         ` Jambunathan K
2012-09-06 15:33         ` John Hendy
2012-09-06 16:08           ` Jonathan Leech-Pepin
2011-11-02  2:22 Pass LaTeX exporter option prior to \documentclass John Hendy
2011-11-02  2:43 ` suvayu ali
2011-11-02 10:30   ` suvayu ali
2011-11-03 17:48     ` John Hendy
2011-11-03 17:55       ` suvayu ali
2011-11-03 18:07         ` John Hendy
2011-11-04 17:29           ` Nick Dokos
2011-11-04 19:29             ` suvayu ali
2011-10-19 14:54 Prompt for time when clocking in? Nathan Neff
2011-10-19 15:12 ` John Hendy
2011-10-19 15:35   ` Nick Dokos
2011-10-20 16:15     ` Nathan Neff
2011-10-20 17:09       ` Nick Dokos
2011-10-20 17:44         ` Nathan Neff
2011-10-19 16:37 ` Bernt Hansen
2011-08-05 22:15 Handling errors in command line exporting of agenda? John Hendy
2011-08-05 23:34 ` suvayu ali
2011-08-05 23:35   ` suvayu ali
2011-08-08 18:12   ` John Hendy
2011-08-08 18:28     ` suvayu ali
2011-08-08 18:53       ` John Hendy
2011-08-08 18:59         ` suvayu ali
2011-08-08 19:48           ` John Hendy
2011-08-08 20:22             ` suvayu ali
2011-08-08 20:31               ` John Hendy
2011-08-08 20:33               ` Nick Dokos
2011-08-08 20:37             ` Nick Dokos
2011-08-08 20:54               ` John Hendy
2011-08-08 21:09                 ` Nick Dokos
2011-08-08 21:27                   ` John Hendy
2011-08-08 21:30               ` suvayu ali
2011-08-08 22:17                 ` Nick Dokos
2011-08-08 21:46             ` suvayu ali
2011-06-15 10:29 BUG: Newest org-mode interferes with desktop save Rainer M Krug
2011-06-15 16:49 ` Eric Schulte
2011-06-15 17:35   ` Nick Dokos
2011-06-15 18:23     ` Rainer M Krug
2011-06-15 18:21   ` Rainer M Krug
2011-06-15 18:31     ` Eric Schulte
2011-06-15 18:59       ` Rainer M Krug
2011-06-15 22:40         ` Nick Dokos
2011-06-16  7:15           ` Rainer M Krug
2011-06-16  7:29             ` Jambunathan K
2011-06-16  8:22               ` Rainer M Krug
2011-05-24 15:54 Passing font size to exported LaTeX table John Hendy
2011-05-24 16:44 ` Sebastien Vauban
2011-05-24 18:57   ` John Hendy
2011-05-24 19:25     ` Nick Dokos
2011-05-24 19:31       ` John Hendy
2011-05-24 19:58         ` Thomas S. Dye
2011-05-24 20:42           ` Nick Dokos
2011-05-24 21:12             ` Nick Dokos
2011-05-24 21:19               ` Nick Dokos
2011-05-25  7:22                 ` Thomas S. Dye
2011-05-27  0:58                   ` suvayu ali
2011-05-27  6:46                     ` Thomas S. Dye
2011-05-27  7:07                       ` suvayu ali
2011-05-27 16:17                         ` Thomas S. Dye
2011-05-27 16:50                           ` Suvayu Ali
2011-05-27 17:37                             ` Thomas S. Dye
2011-05-27 18:30                               ` Suvayu Ali
2011-05-27 21:25                                 ` Thomas S. Dye
2011-05-28  7:17                                   ` Sebastien Vauban
2011-05-28 10:14                                     ` Suvayu Ali
2011-05-28 15:21                                       ` Nick Dokos
2011-05-28 18:10                                         ` Suvayu Ali
2011-06-01 18:50                                   ` Nick Dokos
2011-06-01 19:08                                     ` Suvayu Ali
2011-06-10 22:31                                       ` Suvayu Ali
2011-06-13  1:38                                         ` suvayu ali
2011-06-13  1:52                                         ` Nick Dokos
2011-06-13  2:40                                           ` Suvayu Ali
2011-06-13  3:29                                             ` Nick Dokos
2011-06-13  3:45                                           ` Thomas S. Dye
2011-06-13  4:27                                             ` Nick Dokos
2011-06-13  4:56                                               ` Suvayu Ali
2011-06-13  5:29                                                 ` Nick Dokos
2011-06-13  6:42                                                   ` Suvayu Ali
2011-05-24 20:06         ` Nick Dokos
2011-05-24 19:42       ` Sebastien Vauban
2010-08-21 19:30 Gnuplot unevenly spaced non-numeric data plot? John Hendy
2010-08-21 20:35 ` Eric S Fraga
2010-08-21 20:41 ` Nick Dokos
2010-08-21 21:11   ` John Hendy
2010-08-21 22:41     ` John Hendy
2010-08-21 23:17       ` Nick Dokos
2010-08-23 14:22         ` John Hendy
2010-08-23 15:16           ` Nick Dokos
     [not found]             ` <AANLkTi=WTLBL1Giq0GTrjCo-A1s=iP4u1Qxn57cH-xnB@mail.gmail.com>
     [not found]               ` <AANLkTimSVm=-2o39CQ9wSMT276Dee4Tuj9jLKJH-c+cd@mail.gmail.com>
2010-08-24  2:44                 ` [For Worg?] " John Hendy
2010-08-24  5:25                   ` suvayu ali
2010-08-24  5:56               ` Nick Dokos
2010-08-25  0:32                 ` Eric Schulte
2010-08-25  1:06                   ` John Hendy
2010-08-25  1:35                     ` Eric Schulte
2010-08-25 18:38                       ` John Hendy
2010-08-25 18:52                         ` Eric Schulte
     [not found]         ` <jw.hendy@gmail.com>
2012-03-12 21:13           ` Beamer specific setupfile? John Hendy
2012-03-12 21:48             ` Nick Dokos
2012-03-12 22:09               ` John Hendy
2012-03-12 22:30                 ` Nick Dokos
2012-03-12 22:44                   ` Nick Dokos
2012-03-13  5:02                     ` John Hendy
2012-03-13  5:46                       ` Nick Dokos
2012-04-25  8:16                         ` Eric Fraga
2012-04-25  8:59                           ` Eric Fraga
2012-03-12 23:01                 ` Nick Dokos
2012-03-12 21:51             ` Nick Dokos
2012-03-12 22:05             ` Nick Dokos

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