How to Debug JNI C++ multi threaded code in unix

I have a huge C++ code base and on top of it is a java/JNI wrapper. So now somehow my program is causing issues in multithreaded run on unix but is fine in windows. I want to find out the best way to debug this issue. I know I can use GDB but apart from it I can use intellij Idea or Eclipse to do remote debugging from windows? Actually I am preferring to debug from windows where I am proficient. Please suggest the best approach for this scenario as the issues are very random.