Hi Greg, The problem seems to happen whether running in a single thread or not. It does not seem to depend on the molecule. Seems to always happen AFAICT. The molecules are created from SMILES using RWMol.MolFromSmiles(smiles), which I believe sanatizes by default.
Tim On Wed, Feb 3, 2021 at 12:36 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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