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Re: [O] Bug? R: Org babel block execution *drastically* slower than in E
From: |
Nick Dokos |
Subject: |
Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly |
Date: |
Thu, 01 Nov 2012 14:48:02 -0400 |
John Hendy <address@hidden> wrote:
> On Thu, Nov 1, 2012 at 10:38 AM, Nick Dokos <address@hidden> wrote:
>
> John Hendy <address@hidden> 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).
>
Check /var/log/syslog (or thereabouts) to see if the kernel is seeing errors
with
some blocks on the disk and keeps retrying. Assuming SMART is enabled, run
smartctl -a
as well and look for problems.
Nick
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, John Hendy, 2012/11/01
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Nick Dokos, 2012/11/01
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, John Hendy, 2012/11/01
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, John Hendy, 2012/11/01
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly,
Nick Dokos <=
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Aaron Ecay, 2012/11/13
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, John Hendy, 2012/11/13
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Aaron Ecay, 2012/11/14
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Thomas S. Dye, 2012/11/14
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Andreas Leha, 2012/11/14
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Eric Schulte, 2012/11/16
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Andreas Leha, 2012/11/16
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, John Hendy, 2012/11/16
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Achim Gratz, 2012/11/16
- Re: [O] Bug? R: Org babel block execution *drastically* slower than in ESS session directly, Eric Schulte, 2012/11/17