ViennaRNA-extras-0.0.0.1: ViennaRNA v2 extensions

BioInf.ViennaRNA.Internal

Description

Internal mutex system to be used as long as the ViennaRNA package is not thread-safe.

Synopsis

# Documentation

The mutex guarding single-threaded access to the ViennaRNA bindings as long as the C library is not multi-threaded.

withMutex :: IO a -> IO a Source #

Work with the ViennaRNA mutex.

This version seems strict enough to not block indefinitely.

unsafePerformIO :: IO a -> a #

This is the "back door" into the IO monad, allowing IO computation to be performed at any time. For this to be safe, the IO computation should be free of side effects and independent of its environment.

If the I/O computation wrapped in unsafePerformIO performs side effects, then the relative order in which those side effects take place (relative to the main I/O trunk, or other calls to unsafePerformIO) is indeterminate. Furthermore, when using unsafePerformIO to cause side-effects, you should take the following precautions to ensure the side effects are performed as many times as you expect them to be. Note that these precautions are necessary for GHC, but may not be sufficient, and other compilers may require different precautions:

• Use {-# NOINLINE foo #-} as a pragma on any function foo that calls unsafePerformIO. If the call is inlined, the I/O may be performed more than once.
• Use the compiler flag -fno-cse to prevent common sub-expression elimination being performed on the module, which might combine two side effects that were meant to be separate. A good example is using multiple global variables (like test in the example below).
• Make sure that the either you switch off let-floating (-fno-full-laziness), or that the call to unsafePerformIO cannot float outside a lambda. For example, if you say:  f x = unsafePerformIO (newIORef [])  you may get only one reference cell shared between all calls to f. Better would be  f x = unsafePerformIO (newIORef [x])  because now it can't float outside the lambda.

It is less well known that unsafePerformIO is not type safe. For example:

    test :: IORef [a]
test = unsafePerformIO \$ newIORef []

main = do
writeIORef test [42]
print (bang :: [Char])
This program will core dump. This problem with polymorphic references is well known in the ML community, and does not arise with normal monadic use of references. There is no easy way to make it impossible once you use unsafePerformIO. Indeed, it is possible to write coerce :: a -> b with the help of unsafePerformIO. So be careful!