Question: Blast2Go Memory Allocation
2
gravatar for Daniel Standage
8.0 years ago by
Daniel Standage3.8k
Davis, California, USA
Daniel Standage3.8k wrote:

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 memory blast • 2.9k views
ADD COMMENTlink modified 7.9 years ago by Stefan30 • written 8.0 years ago by Daniel Standage3.8k

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.

ADD REPLYlink written 8.0 years ago by Giovanni M Dall'Olio26k

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"

ADD REPLYlink written 8.0 years ago by Giovanni M Dall'Olio26k
2
gravatar for Daniel Standage
8.0 years ago by
Daniel Standage3.8k
Davis, California, USA
Daniel Standage3.8k wrote:

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.

ADD COMMENTlink written 8.0 years ago by Daniel Standage3.8k

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

ADD REPLYlink written 8.0 years ago by Egon Willighagen5.2k
1
gravatar for Stefan
7.2 years ago by
Stefan30
Spain
Stefan30 wrote:

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

ADD COMMENTlink written 7.2 years ago by Stefan30
0
gravatar for Giovanni M Dall'Olio
8.0 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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

ADD COMMENTlink written 8.0 years ago by Giovanni M Dall'Olio26k
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