[Biojava-l] Multithreads on a multiprocessor machine

Matthew Pocock matthew_pocock@yahoo.co.uk
Tue, 27 Aug 2002 15:14:21 +0100

Hi everyone,

We seem to have solved this by running sgi java with -hotspot.


ZHOU, YIHUA [AG/1000] wrote:
> All,
> My problem may be not directly related to Biojava, but the anwser may help
> Biojava users. Thanks for your help in advance.
> I am trying to run external programs (such blast and estwise) within a
> multi-thread Java program in an attempt to run the programs concurrently. It
> worked very well with NCBI blast. Each thread started a separate blast
> process on a different processor and run concurrently. However, it failed
> with estwise and fgenesh. With these programs, the threads could start the
> external processes, however it seemed that all of the processes were running
> on the same processor and competing for that processor (the same process
> that Java runs on), resulting in a much slower performance than expected.
> The tests were done on a 32-processor SGI machine that runs IRIX64 6.5 and
> JavaVM-1.3. Does anyone get any idea about this?? Your help is greatly
> appreciated. 
> Yihua
> ---
> Bioinformatics, Monsanto Company
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