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MathGroup Archive 2006

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


Charlie

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 ?

If you find any of the two files, send them to support at wolfram.com.

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

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

With the best,

János

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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