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MathGroup Archive 2006

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Re: Re: "No more memory available" -- a recurring problem

  • To: mathgroup at smc.vnet.net
  • Subject: [mg68423] Re: [mg68388] Re: [mg68356] "No more memory available" -- a recurring problem
  • From: "Charlie Brummitt" <cbrummitt at wisc.edu>
  • Date: Fri, 4 Aug 2006 03:59:54 -0400 (EDT)
  • References: <200608020924.FAA28575@smc.vnet.net> <D6C89613-F0EB-4D7E-9E29-2FFAA6FB40D4@yale.edu> <321730f50608021216o11d69435g5d278a6b7d06dfa5@mail.gmail.com> <200608031007.GAA15786@smc.vnet.net>
  • Sender: owner-wri-mathgroup at wolfram.com

I took my MacBook Pro into the university computer support & repair
office, and they concluded that the RAM is fine and that it probably
is not a hardware problem. I ran memtest (www.memtestosx.org/) on the
new memory stick alone (it's from OMNI Technology) and found no
errors.

That leaves me with three possibilities:
1) my code can simply be too difficult for a personal computer and
some sort of grid or supercomputer is required
2) there is a bug in Mathematica, in the act of porting Mathematica to
Intel (i.e. to being universal), or in OSX which causes memory
failures even when there is plenty of memory and virtual memory
available
3) my code is poorly written and needs radical change. To answer Bill
Rowe's question, I would consider myself an intermediate Mathematica
user, and I think I'm fairly well-versed in the area of Mathematica in
which I'm working (namely, solving and analyzing differential
equations).

Basically, my calculation consists of using NDSolve thousands of times
to solve and evaluate PDE's in order to find ones that are chaotic.

I'm not sure what else to do. Contact Wolfram maybe?

I guess this ends my research project.

Thanks to János and Bill for their helpful comments.

Charlie

On 8/3/06, János <janos.lobb at yale.edu> wrote:
> Charlie,
>
> Your MacBook Pro has an Intel  core duo processor and looks to me
> that Mathematica is using just one of the cores.  I do not know what
> You can do about it.  Probably nothing.  If you can put your hand on
> a Personal Grid edition that would engage the second core more
> vigorously.
>
> I do not see that you have a memory problem as regarding the usage of
> the memory reported by top.
>
> You might  have a bad memory chip and that is crashing your
> program.   Unfortunately we see bad memory coming even from Apple
> these days with newer Macs.  There is a service CD that came with
> your MacBook Pro.  Try to run the memory test from it all night in a
> loop and see if it is caching anything.
>
> You might also want to do a hard drive check with Diskwarrior.  Wooly
> disks can lead to wooly virtual memory and causing crashes.
>
> Look if you have anything in ~/Library/Logs/Crashreporter regarding
> Mathematica.crash.log or Mathkernel.cash.log.   /I have plenty in
> mine for both :)/  If you find any, send them to support at wolfram.com
> and ask their opinion.
>
> I also recommend to do additional exhausting tests for the
> motherboard and other elements of the machine by using the service CD.
>
> In summary it looks like a hardware problem - unless you have other
> long running Mathematica programs which run just fine.
>
> With the best,
>
> János
>
> On Aug 2, 2006, at 3:16 PM, Charlie Brummitt wrote:
>
> > János,
> >
> > Thanks for the advice. I'm not really sure how to interpret the
> > information in the terminal window, so I have attached screenshots of
> > it at various stages (see the names of the images). I have attached
> > them in chronological order.
> >
> > It seems to me that Mathematica is only being allocated 50% of the CPU
> > and 100 megabytes of RAM! When I did the "top" on my 12" PowerBook,
> > 93% of the CPU was being used while Mathematica was running my code.
> > How do I change this on my 15" MacBook Pro?
> >
> > My 12" PowerBook is able to run this code overnight and very rarely
> > gives the "ran out of memory" error message. I would like to be able
> > to run my code overnight on my MacBook Pro, but it can only run for 5
> > to 10 minutes before it runs out of memory and completely halts. Thus
> > I can't "set it and leave it"; instead, I must always be at my
> > computer to restart the calculation every 5 to 10 minutes. Any
> > suggestions?
> >
> >
> > Thanks for all your help, János.
> >
> > Charlie
> >
> > On 8/2/06, János <janos.lobb at yale.edu> wrote:
> >>
> >> On Aug 2, 2006, at 5:24 AM, Charlie Brummitt wrote:
> >>
> >> > I keep getting the following error message while running a search
> >> > of many PDE's:
> >> >
> >> > "No more memory available.
> >> > Mathematica kernel has shut down.
> >> > Try quitting other applications and then retry."
> >> >
> >> > This message is becoming so common that it is crippling my research
> >> > project, which is to find the simplest PDE with one quadratic
> >> > nonlinearity that is chaotic.
> >> >
> >> > I have Googled and searched the Mathgroup archives for help, and I
> >> > employed the following fixes:
> >> >
> >> > --CODE & SOFTWARE--
> >> > 1) Share[] -- does not help because my code rarely has common
> >> elements
> >> > that Share[] could consolidate.
> >> >
> >> > 2) I used Module[] and made as many variables local as possible. I
> >> > eliminated extra variables and functions in addition to adding
> >> Clear[]
> >> > in several places in the code to clear variables that are no longer
> >> > needed.
> >> >
> >> > 3) I streamlined and optimized the code in general, and I made the
> >> > routines as simple and least data-intensive as possible.
> >> >
> >> > 4) I never have any other applications open when running
> >> Mathematica.
> >> > (Unfortunately, closing other applications is the only
> >> suggestion that
> >> > Mathematica provides in the "out of memory" error message.)
> >> >
> >> > 5) I should note that I run the latest version of Mathematica
> >> > (5.2.2.0).
> >> >
> >> > --HARDWARE--
> >> > 1) I upgraded from a 12" PowerBook to a 15" MacBook Pro. This
> >> computer
> >> > has an 2.16 GHz Intel Core Duo processor.
> >> >
> >> > 2) I upgraded the RAM on this new computer from 1 GB to 2 GB.
> >> >
> >> > 3) I now have much more free hard drive space (20 GB) in case
> >> > Mathematica needs to use virtual memory. In addition, this hard
> >> drive
> >> > is 7200 rpm versus the standard 5400 rpm.
> >> >
> >> >
> >> > I have been using functions like MemoryInUse[] and On
> >> [MemoryConserve]
> >> > to monitor the use of memory. I almost always find that I am only
> >> > using a few megabytes at a time (usually 5-10 MB, sometimes as
> >> high as
> >> > 100 or once 1000 after a large computation). However, despite
> >> finding
> >> > that I usually use only a few megabytes during my computations, I
> >> > often get the above "out of memory" error message, and I can never
> >> > figure out why and how much memory was needed in that particular
> >> > computation.
> >> >
> >> >
> >> > Some questions:
> >> > 1) How can I tell whether Mathematica is using virtual memory or
> >> not?
> >> > It seems to me that it is not. I have 20 GB of hard drive space
> >> free
> >> > and it never seems to use it. Why should I ever run out of
> >> memory if I
> >> > have 20 GB free in case it needs more memory than my RAM provides?
> >> >
> >> > 2) Is there a way to determine how much of my 2 GB of RAM are
> >> > allocated to Mathematica? Can I increase how much RAM
> >> Mathematica can
> >> > access?
> >> >
> >> > Thanks in advance for any help you may be able to provide! I
> >> greatly
> >> > appreciate it. If you need more information on my code or the
> >> > computations I am doing, I would be happy to provide it.
> >> >
> >> > Regards,
> >> > Charlie
> >>
> >> If you open a Terminal window on the side and type "top" and hit
> >> return and start up your application, what do You see for real memory
> >> usage for the kernel and the front end from top?
> >>
> >> János
> >> <before mathematica.jpeg>
> >> <mma loaded, code loaded, pre-execution.jpeg>
> >> <running1.jpeg>
> >> <running2.jpeg>
> >> <running3.jpeg>
> >> <running4.jpeg>
> >> <ran out of memory.jpeg>
>
>


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