[Biojava-l] Multithreads on a multiprocessor machine

Schreiber, Mark mark.schreiber@agresearch.co.nz
Tue, 27 Aug 2002 10:02:18 +1200

Hi -

I know that some JVMs need a hint by putting each Process in its own
thread. Beyond that I don't know of a way to force a JVM to
multiprocess. Could be worth contacting the makers of your JVM for their

- Mark

> -----Original Message-----
> From: ZHOU, YIHUA [AG/1000] [mailto:yihua.zhou@monsanto.com] 
> Sent: Tuesday, 27 August 2002 6:43 a.m.
> To: 'biojava-l@biojava.org'
> Subject: [Biojava-l] Multithreads on a multiprocessor machine
> 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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