I've just realised that David Koes has already fixed this, by providing just such an interface, a Match function where you pass in the vector for storing the matches. I owe you a pint or two, David.
Note to self: as part of the API cleanup, we should remove the other functions. - Noel On 19 February 2017 at 10:21, Noel O'Boyle <baoille...@gmail.com> wrote: > I've made progress, but my current problem is that it's not possible > to match the same SmartsPattern on different threads (as required, for > example, by the typers, where sets of smarts patterns are initialised > once and then reused). The matchers store the results as part of the > pattern instead of returning it directly, so two simultaneous matches > against the same pattern will confuse things. I'm not sure of the > exact details of a solution until I study the existing code, but it > will involve separating the parsed smarts pattern data structure from > any match results and I'm guessing this will need an API change. > > - Noel > > On 12 February 2017 at 20:18, Noel O'Boyle <baoille...@gmail.com> wrote: >> ...googling through the mailing list, I see that David Lonie mentions >> that OBErrorLog has problems, and Tim that all formats are singletons. >> I need to think some more about this latter. >> >> - Noel >> >> On 12 February 2017 at 16:45, Noel O'Boyle <baoille...@gmail.com> wrote: >>> Classes or variables with a global instance are susceptible to >>> multithreading problems. It turns out that these are listed in the >>> Python bindings. >>> >>> Classes: OBElementTable, OBTypeTable, OBIsotopeTable, OBAromaticTyper, >>> OBAtomTyper, OBChainsParser, OBResidueData, OBPhModel, OBErrorLog >>> Variables: Residue, ElemDesc, ResNo, ElemNo (these all from the bottom >>> of residue.h) >>> >>> The following don't appear to be a problem: >>> OBElementTable, OBTypeTable, OBIsotopeTable >>> >>> On my branch (https://github.com/baoilleach/openbabel/tree/fixglobalstate) >>> I think I've fixed the following: >>> OBAromaticTyper, OBAtomTyper, OBPhModel >>> >>> Roger didn't anticipate multi-processor architectures and it looks >>> like OBChainsParser and OBResidueData as well as those variables >>> listed above do have a problem. It should be possible to fix, but >>> perceiving residues (or reading PDB and also I guess MOL2) will cause >>> problems right now. >>> >>> I haven't really looked at OBErrorLog, and my time is up right now. >>> Have I missed any classes that you know of? >>> >>> David, do you have any test code that reads an SDF multithreadedly, >>> that could be used to force segfaults? >>> >>> Regards, >>> - Noel >>> >>> On 11 February 2017 at 21:08, Noel O'Boyle <baoille...@gmail.com> wrote: >>>> Here's of what I was thinking: >>>> https://github.com/baoilleach/openbabel/commit/697b92180f9f61f738ef3e5c04d30340b9f8ee8e >>>> >>>> If it looks okay, I can make a similar change to other classes that >>>> have the same problem (assuming one size fits all). >>>> >>>> - Noel >>>> >>>> >>>> On 8 February 2017 at 09:32, Noel O'Boyle <baoille...@gmail.com> wrote: >>>>> There's no memory overhead on the molecule class - it's unchanged. Let >>>>> me make the change on a branch for one of the classes, and we can chew >>>>> it over. >>>>> >>>>> - Noel >>>>> >>>>> On 7 February 2017 at 13:35, Koes, David <dk...@pitt.edu> wrote: >>>>>> I think this is most definitely the way to go if you can tolerate the >>>>>> API changes. The main drawback is potentially each molecule class >>>>>> taking up more memory. I would welcome any changes that push openbabel >>>>>> closer to thread safety.. >>>>>> >>>>>> David Koes >>>>>> >>>>>> Assistant Professor >>>>>> Computational & Systems Biology >>>>>> University of Pittsburgh >>>>>> >>>>>> >>>>>>> On Feb 7, 2017, at 5:20 AM, Noel O'Boyle <baoille...@gmail.com> wrote: >>>>>>> >>>>>>> Hi there, >>>>>>> >>>>>>> Wouldn't a better solution to the race conditions that David Koes is >>>>>>> experiencing with global state be to remove the global state? For the >>>>>>> cases he mentioned, e.g. the OBAromTyper, the global state relating to >>>>>>> a single molecule can easily be moved to a OBAromTyperPrivate class >>>>>>> instantiated by a TypeThisMolecule() function in the global class. >>>>>>> >>>>>>> This is an API breakage, but only because these internal >>>>>>> implementation functions were exposed. I think the time might be ripe >>>>>>> for a couple of API cleanups, not for the sake of it, but where they >>>>>>> limit or affect the toolkit's usage. >>>>>>> >>>>>>> Regards, >>>>>>> - Noel >>>>>> ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
