Memory error

Respected Collegues,
I am a project trainee in Bioinformatics.
For storing the details of 8000 sequences,i declared a two dimensional array as
double[][] seqArray=new double[8000][8000];
But while running the program i encountered with a run time error as
java.lang.OutOfMemoryError
I searched the NET and got the information that
the default memory space which JVM takes is 16MB and we can make the JVM to take more space by giving as
java -mx64M <application_name> ,
since somewhat 40MB of RAM space is always left unused.
But by giving this also I encountered the same problem
So is there any way of overcoming this run-time error?
If any ,please sent the reply to [email protected]
Thank you

Let's see how much memory you need to store a doubles[8000][8000]...
Storing one double requires 8 bytes so for the numbers alone the virtual machine should allocate 8*8000*8000 = 512000000 bytes of memory, that is over 488 MB (*way* more than I have in my computer) so no wonder 64 wasn't enough.
To solve the you should consider if you really need to hold all those values in memory at the same time. Can a part of the data be written on a temporary file on disk and be loaded when you need it? Do you really need double precision floating point numbers?

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On 9/7/2011 2:16 AM, pdjongh wrote:
>
> Hi,
>
> We recently have memory error messages on the POA and on the Client.
> The error seemed to follow several C042 errors:
> -The database function 53 reported error [C042] on user4mn.db
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>
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>
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>
>
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