Hi everyone, We seem to have solved this by running sgi java with -hotspot.
Matthew 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 > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > -- BioJava Consulting LTD - Support and training for BioJava http://www.biojava.co.uk __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
