How to Fix Symbol Lookup Error: Undefined Symbol Errors in a Cluster Environment

How to fix symbol lookup error: undefined symbol errors in a cluster environment

After two dozens of comments to understand the situation, it was found that the libhdf5.so.7 was actually a symlink (with several levels of indirection) to a file that was not shared between the queued processes and the interactive processes. This means even though the symlink itself lies on a shared filesystem, the contents of the file do not and as a result the process was seeing different versions of the library.

For future reference: other than checking LD_LIBRARY_PATH, it's always a good idea to check a library with nm -D to see if the symbols actually exist. In this case it was found that they do exist in interactive mode but not when run in the queue. A quick md5sum revealed that the files were actually different.

undefined symbol: __cxa_pure_virtual error when loading library from java

After rechecking all the answers related to my question on stackoverflow, I found out the answer by
Mark Seaborn to question: What is the purpose of __cxa_pure_virtual? fixed my problem.

As my jni library is managed by autotools, after adding "-Wl,--gc-sections -fPIC -shared -lstdc++" to AM_LDFLAGS of Makefile.am problems solved. libstdc++ might not necessary if code is compiled by a c++ compiler (e.g. g++).

Hope this could help others who have the same problem.

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