[Biojava-l] Multithreads on a multiprocessor machine

[ZHOU, YIHUA [AG/1000]]

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

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Bioinformatics, Monsanto Company