You can use Matlab to communicate with GPIB instruments. You will require GPIB ENET/100 driver for Linux and you can get it from www.ni.com/linux
The driver comes with two libraries. The shared library is libgpibenet.and it gets stored by default at /usr/local/lib
You can link the shared library to your application to communicate with gpib instruments and using a shared library will ease the transition between different driver version and it won't increase the file size of executable. But if you don't want to use the shared library then a statically linked cib.o file is also available.