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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