I had the same problem. This helped me on Ubuntu:
1) Indicate the location of your own jpl jar library in the folder where you keep your "libswipl.so" (I do this using the settings of the "Java Build Path" project). For me it:
/usr/lib/swipl-6.2.6/lib/x86_64-linux
2) Add the folder in which you keep your "libjava.so" in your LD_LIBRARY_PATH variable (I do this in my runtime configuration on the "Environment" tab). For me it:
/ USR / Library / JVM / Java-6-OpenJDK / JRE / Library / amd64
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