[Biojava-dev] [Bug 2164] Restriction Mapper - Thread (or dual core cpu) problem

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2164





------- Comment #10 from mark.schreiber at novartis.com  2008-01-20 03:28 EST -------
As suggested I have added back the synchronized blockas as they are certainly
needed even though this doesn't fully solve the problem.  Interestingly on
windows vista on a dual core CPU a race condition develops and never seems to
resolve (not even a stack trace)!  Notably this was on a short sequence not one
likely to be a PackedSymbolList as mentioned below.

I wonder if there is a problem with the SimpleThreadPool. Maybe a switch to a
normal Java thread pool might be better?


(In reply to comment #9)
> Here are the comments at the top of org.biojava.bio.symbol.PackedSymbolList,
> and I quote:
> "WARNING: these variables constitute an opportunity
> for things to go wrong when doing multithreaded access
> via symbolAt().  Keep SymbolAt() synchronized so they
> don't get changed during a lookup! Naaasssty."


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