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Blast2Go Memory Allocation

I'm running BLAST2GO on a Linux (Ubuntu 10.04 32 bit) machine with 24 GB RAM (8 processors). No matter what I specify for the maximum memory, it only allocates 455 MB RAM, which is not enough for the data I am working with. I've tried increasing and decreasing the maximum memory, but this doesn't change how much is allocated. Any ideas?

java blast memory
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updated by Stefan • Stefan • written by Daniel Standage Daniel Standage

did you know that with a 32 bit operating system, you can only use up to 4 GB of RAM? You should re-install a 64-bit version of your operating system.

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

well, if you are using a PAE kernel, you should be able to use all the RAM as well. check the contents of your /proc/meminfo file , and also type "uname -a"

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written by Giovanni M Dall'Olio Giovanni M Dall'Olio

3 answers

Turns out it was a Java implementation issue. Ubuntu ships with OpenJDK. When I downloaded, unpacked, and used Sun's Java implementation, I got helpful error messages and finally the amount of memory I asked for.

For the boring details, check out this thread on StackOverflow.

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written by Daniel Standage Daniel Standage

Daniel, you can approve your own answer as final answer.

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written by Egon Willighagen Egon Willighagen

Hi, to run Blast2GO with more than 1500MB (win) or more than 1800MB (Linux) you have to have a 64bit system architecture, a 64bit java version from SUN/Oracle and a 64bit operation system. Information is from: http://www.blast2go.com/b2gsupport/faqs

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written by Stefan • Stefan

Check whether you are using a PAE kernel; otherwise your system will only recognize up to 4 GB of RAM.

You can do it by executing this at the command line:

less /proc/meminfo
uname -a

or now Ubuntu is quite easy to use, you can see your kernel and memory by simply looking at System->Administration->System Monitor->System tab

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updated by Ram Ram • written by Giovanni M Dall'Olio Giovanni M Dall'Olio

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