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The fix is to enable the 'Large File Support' by compiling libsaproc.so with -D_FILE_OFFSET_BITS=64. This is added to both agent/src/os/linux/Makefile (which builds SA from agent/make/) and make/linux/makefiles/saproc.make (which builds SA with Hotspot build).
There is one more change with which SA should first load libraries from the path specified with SA_ALTROOT rather than loading from the paths embedded in the core file.