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MathGroup Archive 2006

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

  • To: mathgroup at smc.vnet.net
  • Subject: [mg68446] Re: Re: [mg68423] Re: [mg68388] Re: [mg68356] "No more memory available" -- a recurring problem
  • From: "Charlie Brummitt" <cbrummitt at wisc.edu>
  • Date: Sat, 5 Aug 2006 03:46:48 -0400 (EDT)
  • References: <200608020924.FAA28575@smc.vnet.net> <D6C89613-F0EB-4D7E-9E29-2FFAA6FB40D4@yale.edu> <321730f50608021216o11d69435g5d278a6b7d06dfa5@mail.gmail.com> <200608031007.GAA15786@smc.vnet.net> <200608040759.DAA01108@smc.vnet.net> <4035DD91-055A-434E-A2F4-AC6F14A296CB@yale.edu>
  • Sender: owner-wri-mathgroup at wolfram.com

János,

Below are my responses.

> Do you have any Mathematica.crash.log or Mathkernel.crash.log file in
> your ~Library/Logs/Crashreporter folder ?
> If yes, does the datetime entries coincide with the kernel crashes ?

I don't see any Mathematica crash logs in my
~Library/Logs/Crashreporter folder (only one file called
mds.crash.log, which I doubt is Mathematica-related).

> Did you try to eliminate or cut back on History /$HistoryLength /?

I had set $HistoryLength to 5 all along. Since learning that
$HistoryLength can take up a lot of memory, I set it to zero, but I
still get the "No more memory available" message often.

> Did you set any iteration related env variables Wolfram provide to
> Infinity like $IterationLimit and $RecusionLimit, etc....

No, I did not change any of those from the default. I rarely, if ever,
get other error messages, such as "reached the recursion limit,"
preceding the "No more memory available" message.

Thanks again for all your help, János.

Charlie


> On Aug 4, 2006, at 3:59 AM, Charlie Brummitt wrote:
>
> > 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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