android-decodeencodetest | convert ExtractDecodeEditEncodeMuxTest to asynchronous mode

Efficiency wise, this drawing of the input frame probably is as efficient as it will get. Each time you submit a frame to the encoder, you can't really assume anything about the input surface buffer content (I think), so you need to copy the content to be encoded into it somehow, and this does pretty much it.

If you skip drawing, you need to keep in mind that the surface you're drawing into isn't just a single buffer, but a set of a number of buffers (usually 4-10 buffers or so). When using the direct buffer access mode of the encoder, the encoder will tell you exactly which one of the buffers out of the pool it gave you to fill, and in such cases, you might have better luck with skipping drawing in the case if you've already filled the buffer before (and hoping that the encoder hasn't invalidated the contents).

With surface input, you don't get to know which buffer you got to write into. In that case, you could e.g. try just doing the drawing the first N times. I don't think you can get the actual number of buffers though - you could try calling the deprecated getInputBuffers() method, but I don't think it's possible to use it in combination with surface input.

However, about performance, the absolutely biggest issue and reason for your (lack of) performance is that you're doing everything synchronously. You said

At the start of the processing, and then every time I successfully mux a frame thereafter, I call

Hardware encoders generally have a bit of latency, and the time it takes to encode a single frame from start to finish is longer than the average time per frame, if you start encoding more than one at a time.

Assuming you're using MediaCodec in async mode, I would suggest to just serially do the encoding of all the 90 frames in one thread, and write output packets to the muxer when you get them in the callback. That should keep the encoder pipeline busy. (Once the input buffers to the encoder are exhausted, the inputSurface methods will block until the encoder has completed a frame and freed up another one of the input buffers.) You might also want to buffer the output packets in a queue and write them asynchronously to the muxer (I remember reading about cases where MediaMuxer occasionally can block longer than you'd like).