I have to point out the slowness of JavaScript is real in this case. PBKDF2-HMAC-SHA256 with 5000 iterations (and scrypt uses PBKDF2 on input and output of a me

I have to point out the slowness of JavaScript is real in this case. PBKDF2-HMAC-SHA256 with 5000 iterations (and scrypt uses PBKDF2 on input and output of a memory-hard function) takes ~2 sec. on my machine in Chrome. Even new typed arrays are not very helpful. This means that you essentially have to make your KDF's workload much weaker than if you used C implementation to get an acceptable performance.