Steps to Build AliRoot with CMake : 1. Define environment variable ALICE_INSTALL export ALICE_INSTALL=$ALICE/AliRootInstall 2. Set Path to point to binaries and libraries that will be built in ALICE_INSTALL export PATH=$PATH:$ALICE_INSTALL/bin/tgt_${ALICE_TARGET} export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$ALICE_INSTALL/lib/tgt_${ALICE_TARGET} 3. Execute the following commands to build AliRoot cd $ALICE_INSTALL cmake make 4. In order to build addtional targets like TFluka, THydjet and SHUTTLE add the following options to the cmake command cmake -DTFLUKA=ON -DTHYDJET=ON -DSHUTTLE=ON !IMPORTANT! : Make sure you delete all the files in your ALICE_INSTALL directory before you generate the Makefile again to clear the CMakeCache or the generated build system may not function properly.