From mboxrd@z Thu Jan 1 00:00:00 1970 From: John Hendy Subject: Re: Bug? R: Org babel block execution *drastically* slower than in ESS session directly Date: Thu, 1 Nov 2012 13:18:58 -0500 Message-ID: References: <874nlappb1.fsf@tajo.ucsd.edu> <878vam1jvh.fsf@tajo.ucsd.edu> <3477.1351723988@alphaville> <11876.1351784283@alphaville> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=f46d04478add86673804cd730dfd Return-path: Received: from eggs.gnu.org ([208.118.235.92]:60477) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1TTzM6-0000Ka-Cs for emacs-orgmode@gnu.org; Thu, 01 Nov 2012 14:19:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1TTzM3-0002xQ-Jl for emacs-orgmode@gnu.org; Thu, 01 Nov 2012 14:19:02 -0400 Received: from mail-ob0-f169.google.com ([209.85.214.169]:34977) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1TTzM3-0002xB-A9 for emacs-orgmode@gnu.org; Thu, 01 Nov 2012 14:18:59 -0400 Received: by mail-ob0-f169.google.com with SMTP id va7so3152708obc.0 for ; Thu, 01 Nov 2012 11:18:58 -0700 (PDT) In-Reply-To: <11876.1351784283@alphaville> List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: nicholas.dokos@hp.com Cc: cberry@tajo.ucsd.edu, emacs-orgmode@gnu.org --f46d04478add86673804cd730dfd Content-Type: text/plain; charset=UTF-8 On Thu, Nov 1, 2012 at 10:38 AM, Nick Dokos wrote: > John Hendy 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. > > --f46d04478add86673804cd730dfd Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

On Thu, Nov 1, 2012 at 10:38 AM, Nick Do= kos <nicholas.dokos@hp.com> wrote:
John Hendy <jw.h= endy@gmail.com> wrote:

> =C2=A0 =C2=A0 o run top (or whatever equivalent is available on your O= S) and see
> =C2=A0 =C2=A0 =C2=A0 whether the CPU (or one of the CPUs) gets pegged = at 100% utilization
> =C2=A0 =C2=A0 =C2=A0 and stays there. If yes, that's an indication= of an infinite loop
> =C2=A0 =C2=A0 =C2=A0 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=C2=A0
> - After about a minute, the minibuffer expands to ~1/3 of the window h= eight and fills with the csv
> data
> - Finished after ~5min total time
> - So, R took about 5sec, emacs took another 5min to finish
> =C2=A0
>

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 t= o 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 utiliz= ed...

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


John
=C2=A0

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
=C2=A0 =C2=A0 =C2=A0 =C2=A0experience with them, so no guidance to give.
[fn:2] My old laptop with 1GB of memory would swap whenever I ran mairix =C2=A0 =C2=A0 =C2=A0 =C2=A0to index my mail: it would take 30 minutes or so= to finish. =C2=A0My
=C2=A0 =C2=A0 =C2=A0 =C2=A0new(er) laptop has 4GB and finishes in 30 second= s: memory usage
=C2=A0 =C2=A0 =C2=A0 =C2=A0peaks at about 2.5 GB.


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