Add clock cycle to ptlcall_log output.
Added new machine configuration files for a 32 MB shared_l3 cache.
Add -checkpoint-after-run to simconfig options.

If the -checkpoint-after-run simconfig option is set, ptlsim will generate
a QEMU snapshot at the very end of the run. This feature was added to
allow for more precise warmup of the hybrid memory cache, since the
snapshot will correspond exactly to the saved hybrid memory state.
Fix bug in memoryController.cpp for HybridSim usage.

Do not treat MEMORY_OP_WRITE as writes to HybridSim. Only
MEMORY_OP_UPDATE should be considered writes. This fix was ported
over from marss.dramsim.