Writing a host application that does not need to reprogram the FPGA

Since you are using a pre-Intel version of the compiler, just run "export CL_CONTEXT_COMPILER_MODE_ALTERA=3" from command line. Note that you must configure the FPGA manually using "aocl program" first.

When you are done, you should run "unset CL_CONTEXT_COMPILER_MODE_ALTERA" from command line if you want to go back to the default method of run-time reconfiguration by the host code.

In my main program I run a kernel many times inside a loop and then I need to reprogram other kernels because all the logic doesn't fit inside a single kernel.

There is a command in c to export this variable within my main.c program and return this variable to normal after the for command? Thanks

Then I don't think you need to use that environmental variable at all. By default, the FPGA will be reconfigured only once when you call clBuildProgram() (or maybe clCreateProgramWithBinary(), I don't remember exactly). After that, the FPGA will not be reconfigured again no matter how many times you call the kernel using clEnqueueNDRangeKernel() or clEnqueueTask(). When you want to switch to the second bitstream, you are going to have to call clBuildProgram() again which will reconfigure the FPGA again.