Not sure if this is relevant these days, but the Emscripten FAQ mentions the need to use "-s ASM_JS=1" as an argument to emcc in order for it to actually output asm.js style code. See "Q. How fast will the compiled code be?" from: https://github.com/kripken/emscripten/wiki/FAQ
emcc -O2 nsieve.cpp
for example.
Yes, I also had to increase the runtime, they were quite short on a laptop - they were meant for a phone I think.