To write into more than one table in map-reduce job, you have to specify that in job configuration. You are right this can be done using MultiTableOutputFormat.
Normally for a single table you use like:
TableMapReduceUtil.initTableReducerJob("tableName", MyReducer.class, job);
Instead of this write:
job.setOutputFormatClass(MultiTableOutputFormat.class);
job.setMapperClass(MyMapper.class);
job.setReducerClass(MyReducer.class);
job.setNumReduceTasks(2);
TableMapReduceUtil.addDependencyJars(job);
TableMapReduceUtil.addDependencyJars(job.getConfiguration());
Now at the time of writing data in table write as:
context.write(new ImmutableBytesWritable(Bytes.toBytes("tableName1")),put1);
context.write(new ImmutableBytesWritable(Bytes.toBytes("tableName2")),put2);
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