Re: [Seqan-dev] FaiIndex + getIdByName/readRegion not threads-safe

[Johannes Dröge <johdro@mpi-inf.mpg.de>]

Hi David,

thanks for the detailed explanation but I haven't understood all of it. I should probably look at the code. So:

1) I suppose you cannot just make the private mutable a local variable?

2) Sometimes I found it to be useful to work with sets of memory addresses/pointers when it comes to string comparisons or lookups. Not sure if this is applicable here.

3) As far as I understand getIdByName it the evil part, here, so instead of locking its access I could also keep a global read-only lookup map outside your container?

Gruß Johannes


Am 25.09.2013 10:48, schrieb Weese, David:
> Hi Johannes,
>
> there is a mutable private string inside the NameCache that is not thread-safe. So although getIdByName is used with a constant name store cache, there will be some concurrent write accesses if you use it with multiple threads. Internally a name store cache is a set of ids (unsigned ints) that are sorted lexicographically with respect to the corresponding names in the name store (a StringSet).
> The std::set::find() only supports to search for keys of the set, i.e. ids. That means if a random string needs to be looked up we first store it temporarily in a private mutable string inside the less operator and search for the id -1 to signal the less operator that this string should be compared with the strings inside the name store. If the std::set would be more generic in the types that find and the less operator would accept we wouldn't need to do it this way.
>
> So right now, you should put your lookups inside an critical section until we found a better solution.
>
> Cheers,
> David