The server will limit the response (batch) to the min(batchSize,
maxResponseBytes).
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That is a server limit and nothing you can change with the batchsize
from the client, unfortunately.
Unless your network latency is very high then a few batches shouldn't
make too big a deal, nor would it reduce the total time to process all
the docs. How long does it take to process all those docs?
If it is very slow it could be that the issue isn't with the
client/server interaction but with finding or retrieving the
documents. Can you compare the performance from the mongo javascript
shell with java
to see if one is very different from the other?