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Subjectthreading question

I am a summer student implementing a multi-threaded version of a very
popular bioinformatics tool. So far it compiles and runs without problems
(as far as I can tell ;) on Linux 2.2.x, Sun Solaris, SGI IRIX and Compaq
OSF/1 running on Alpha. I have ran a lot of timing tests compared to the
sequential version of the tool on all of these machines (most of them are
dual-CPU, although I am also running tests on 12-CPU Solaris and 108 CPU
SGI IRIX). On dual-CPU machines the speedups are as follows: my version
is 1.88 faster than the sequential one on IRIX, 1.81 times on Solaris,
1.8 times on OSF/1, 1.43 times on Linux 2.2.x and 1.52 times on Linux 2.4
kernel. Why are the numbers on Linux machines so much lower? It is the
same multi-threaded code, I am not using any tricks, the code basically
size is set to 8K (but the numbers are the same with larger/smaller stack

Is there anything I am missing? Is this to be expected due to Linux way of
handling threads (clone call)? I am just trying to explain the numbers and
nothing else comes to mind....

Best regards,
Ognen Duzlevski
Plant Biotechnology Institute
National Research Council of Canada
Bioinformatics team

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