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

Question

I\'m working on some python code that extracts some image data from an ECW file using GDAL (http://www.gdal.org/) and its python bindings. GDAL was built from source to have ECW

Answer 1

yum update

helped me out. After I had

wget: symbol lookup error: wget: undefined symbol: psl_latest

Answer 2

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.