Re: computer memory and Octave

[Paul Roberts]

Hi Tracy,

There are a couple options. You could save the result from each
replicate in a separate file (5000 files total) or you could append
each replicate to one file yielding one very large file. I have
attached a code snippet for the first case:


% The prefix for the file name
fprefix = 'a_file_name_';

% The postfix for the file name
fpostfix = '.oct';

% Set the default file mode
default_save_format='binary';

for i=1:100

 %make some data
 data = randn(1,100);

 % Make the name for the file using 3 spaces for the file number.
 fname = [fprefix,sprintf('%03d',i),fpostfix];

 % Save the data
 save(fname,'data');

end

Hope that helps.

Paul

On 7/11/06, Tracy Feldman <address@hidden> wrote:
> Dear Dr. Roberts,
>
> Thank you so much for your response to my query.  Might I ask for some
> clarification?  I am not sure how to store information to a disk during each
> of several bootstrap replicates without overwriting this information after
> the next replicate.  In addition, the program should then be able use that
> stored information from all replicates to do some calculations (I guess I
> can do the calculations in a separate program later on).
>
> I appreciate your help.
>
> Take care,
> Tracy
>
>
> Paul Roberts <address@hidden> wrote:
>
> It looks like an out of memory issue to me. It would be good to check
> the memory requirements for your program and compare that to the
> available physical memory. For instance, check the size in bytes of
> arrays that are persistent throughout all the replicates. Since you
> are able to get 180 replicates, is it possible that the results are
> being kept in memory rather than stored to disk and thus filling up
> memory as more replicates are computed? One fix would be to store the
> data on disk after each replicate.
>
> Paul
>
> On 7/11/06, Tracy Feldman wrote:
> >
> > To whom it may concern:
> >
> > I am running Octave on a laptop with windows XP. I have been trying to run
> > a relatively complicated bootstrap program, and I hope to run 5000
> bootstrap
> > replicates. Octave is crashing before 180 replicates have finished, and on
> > the screen it gives the error messages listed below the text of this
> message
> > (I do not understand the message except for the first line).
> >
> > I wondered if anyone can discern from the error messages below if this
> issue
> > is caused by problems with the program itself (too much information stored
> > at once), by limitations of my computer, or by limitations of Octave. When
> > I installed Octave (April 2006), my computer had only 512 megabytes of
> RAM,
> > but we have since upgraded to 768 megabytes (my computer has a maximum
> > capacity of 1024 megabytes). Could this affect how Octave is running? I
> > have not been using the computer actively for any other processes while
> > running Octave.
> >
> > I would appreciate any help you might offer. I hope I have given enough
> > information. Please reply to me directly, as I am not currently subscribed
> > to this list.
> >
> > Sincerely,
> >
> > Tracy S. Feldman
> > Postdoctoral Associate at the Noble Foundation, in Ardmore, OK
> >
> > Here are the error messages I receive:
> >
> > error: memory exhausted - trying to return prompt
> >
> > 7 [main] octave-2.1.73 3512
> > fhandler_dev_zero::fixup_mmap_after_fork: requested
> > 0x20B30000 !=3D 0x0
> > mem alloc base 0x0, state 0x10000, size 1062010880, Win32 error 1455
> >
> > 2129613 [main] octave-2.1.73 3512 C:\Program
> > Files\Octave\bin\octave-2.1.73.exe: *** fatal error -
> > recreate_mmaps_after_fork_failed
> >
> > 12 [main] octave 3056 child_copy: stack write copy failed,
> > 0x22C1E0..0x230000, done 0, windows pid 2277652, Win32 error 5
> >
> > warning: in fopen near line 23, column 14:
> > warning: fopen: default open mode is now binary
> >
> >
> >
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