Change linux kernel timer

Don't edit .config directly, unless you're a Kbuild expert (and if you're asking this, you're not a Kbuild expert). Instead run make menuconfig or make xconfig to load the menu-based configuration system. Alternately, make config will do a line-based configuration process (where it asks you several hundred questions about what to configure - not recommended). The relevant option is under "Processor type and features" as "Timer frequency".

That said, this may not be necessary. Modern Linux can use high-resolution event timers (CONFIG_HIGH_RES_TIMERS) to acheive low-latency timers even without increasing the timer frequency. With a tickless system (CONFIG_NO_HZ) , the timer frequency has little effect at all.

On the other hand, I'm not sure what timer support Geode CPUs have. You may want to run cyclictest with various kernel configurations to see what you need to get low latency performance. The test you ran tests maximum dispatch frequency, not dispatch latency, so comparing with cyclictest results would be interesting. If you need really low latency, the CONFIG_PREEMPT_RT patchset may also be of interest.

To change the timer setting you need to recompile the kernel. Change the option in some standard menu configuration tool, rather than the text file.

/boot/config... files only tell you what is installed in the specific kernel binary. This is not a configuration file you can change.