OK. So, I figured out the execution flow of the scripts. It goes like the following:
$GEMS/results/script/my_script.sh => $GEMS/gen-scripts/go.simics => $GEMS/gen-scripts/mfacet.py
Then, I modified the de-queue.simics now it works with one checkpoint that we could copy the benchmark into the checkpoint on the fly rather than taking a checkpoint for each benchmark. To do that, we need to have the new microbench.py from the gems mailing list.
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