Okay. Looking at the code I see nothing -- other than perhaps the implementation of logmsg which you haven't supplied -- to suggest that it is your code that is preventing concurrency.

Having scanned a little of the information I can find about the blast program, I strongly suspect that it is serialising access to it database file -- probably through file locking. So the problem would also exist if you were using fork.

The solution I would try is to use different databases for the concurrent runs. If the nature of your workload means that you only want to use a single database, then you could make N (where N is the number of cores) copies of that db file and have each thread operate against a different copy. I am assuming that the blast program is using the db for reference only, not updating it.

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?

In reply to Re^3: Multithreads with an executable in the worker subroutine (fork (probably) won't help) by BrowserUk
in thread Multithreads with an executable in the worker subroutine by lskatz

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