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 > > > >
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