after upgrading to 2.9 I get a strange behaviour from the substructure counter node. it's unusual because it does not seem to be consistent i.e. not every time I run the node with the same smarts and molecules I get the error. I am pasting below the text that I get in the shell (I am running linux on a 64 bit machine by the way)
I am also attaching a workflow that I used to reproduce this error: I had to use the loop in order to get the error because it doesn't show up everytime I run it. the last two times that I ran it, the first one went all the way through the 100 loops and the second one it crashed after few cycles giving me the text below
I should mention also that I get the same error (and same inconsistency) from the fingerprint calculator if I use the MACCS fingerprints.
has anyone seen something like this before?
thanks a lot in advance
# A fatal error has been detected by the Java Runtime Environment:
# SIGSEGV (0xb) at pc=0x00007f0b918a7f34, pid=41147, tid=139686072264448
# JRE version: 7.0_07-b10
# Java VM: Java HotSpot(TM) 64-Bit Server VM (23.3-b01 mixed mode linux-amd64 compressed oops)
# Problematic frame:
# C [libstdc++.so.6+0x69f34] std::_Rb_tree_rotate_left(std::_Rb_tree_node_base*, std::_Rb_tree_node_base*&)+0x4
# Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
# An error report file with more information is saved as:
# If you would like to submit a bug report, please visit:
# The crash happened outside the Java Virtual Machine in native code.
# See problematic frame for where to report the bug.