Given the fun that threading is, this isn't necessarily conclusive, but I just created a small C++ multi-threading test for the morgan fingerprinting code and everything looks fine. That remains true when the code is run under valgrind (which is quite good at picking up the usual types of memory corruption that cause threading issues).
-greg On Wed, Feb 3, 2021 at 1:36 PM Greg Landrum <greg.land...@gmail.com> wrote: > Hi Tim, > > I haven't seen this particular problem myself, nor have we gotten any > reports of crashes from the Morgan fingerprinting code. > Comparing the fingerprinting code itself across the 2019.09 and 2020.09 > branches I also don't see anything which is likely to cause problems, but > one never knows. > > One thing that might help to know is how you construct the molecule's > you're generating fingerprints for: are these from one of the RDKit file > parsers? Have they been sanitized? > > Another thing you might have already tried, but it's worth checking > anyway: can you force your web app to only run a single thread at a time? > That shouldn't be a problem with the morgan fingerprinting code, but it's > still worth the experiment. > > -greg > > > On Tue, Feb 2, 2021 at 7:14 PM Tim Dudgeon <tdudgeon...@gmail.com> wrote: > >> Wondering if anyone had any thoughts on this core dump from Java. >> What other info would be useful? >> >> Tim >> >> On Tue, Jan 12, 2021 at 12:55 PM Tim Dudgeon <tdudgeon...@gmail.com> >> wrote: >> >>> I'm struggling to work out a stange core dump I'm getting when >>> calculating Morgan fingerprints from Java. This seems to happen with the >>> Release_2020_09 releases but not with the Release_2019_09 ones. It does not >>> happen when calculating RDKit fingerprints. The exact Java code involved is: >>> >>> RDKFuncs.MorganFingerprintMol(mol, 2); >>> >>> More precisely this is happening when running inside a Docker container >>> which is running the code as a Tomcat webapp, but a simple test of running >>> that same function inside the container directly from Java (e.g. not when >>> running in tomcat) works OK and does not core dump. >>> Building an otherwise identical container with the Release_2019_09 code >>> does not core dump from Tomcat. >>> >>> The core dump looks like this: >>> >>> # A fatal error has been detected by the Java Runtime Environment: >>> # >>> # SIGSEGV (0xb) at pc=0x00007ff9edc00518, pid=1, tid=111 >>> # >>> # JRE version: OpenJDK Runtime Environment (11.0.9.1+1) (build >>> 11.0.9.1+1-post-Debian-1deb10u2) >>> # Java VM: OpenJDK 64-Bit Server VM (11.0.9.1+1-post-Debian-1deb10u2, >>> mixed mode, sharing, tiered, compressed oops, g1 gc, linux-amd64) >>> # Problematic frame: >>> # [thread 145 also had an error] >>> [thread 149 also had an error] >>> [thread 113 also had an error] >>> [thread 117 also had an error] >>> C [libGraphMolWrap.so+0xa20518] void >>> RDKit::MorganFingerprints::calcFingerprint<RDKit::SparseIntVect<unsigned >>> int> >(RDKit::ROMol const&, unsigned int, std::vector<unsigned int, >>> std::allocator<unsigned int> >*, std::vector<unsigned int, >>> std::allocator<unsigned int> > const*, bool, bool, bool, bool, >>> std::map<unsigned int, std::vector<std::pair<unsigned int, unsigned int>, >>> std::allocator<std::pair<unsigned int, unsigned int> > >, >>> std::less<unsigned int>, std::allocator<std::pair<unsigned int const, >>> std::vector<std::pair<unsigned int, unsigned int>, >>> std::allocator<std::pair<unsigned int, unsigned int> > > > > >*, bool, >>> RDKit::SparseIntVect<unsigned int>&)+0x148 >>> >>> It's difficult to know what's wrong, but thought it might be worth >>> asking if anything in the Morgan fingerprint code has changed over that >>> timeframe? >>> It might be related to threading as the fingerprint generation is being >>> done inside Java streams. >>> >>> Tim >>> >>> >>> >>> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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