So usually for 20 node cluster submitting job to process 3GB(200 splits) of data takes about 30sec and actual execution about 1m. I want to understand what is the bottleneck
I have seen similar issue and I can state the solution to be broken in following steps :
Try with the data nodes and name nodes:
Try installing lower version of hadoop (hadoop 2.5.2) which worked in two cases and it worked in hit and trial.