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To use gprof and gcov, add the appropriate flags to the Makefile. I'll run a single test job to get both profile and coverage data at once by using -pg for gprof and "-ftest-coverage -fprofile-arcs" for gcov (-g is included so that we have source code line numbering available): . Do a project>refresh and note the additional files created for use by gcov after compiling with "-ftest-coverage -fprofile-arcs". 
Setup the MPI run configuration with the Environment variable GMON_OUT_PREFIX defined with a name for your individual MPI rank gmon outputs. By default gmon.out is used but MPI doesn't do that well and you end up with a profile that's missing most of the information, so by using GMON_OUT_PREFIX, each MPI rank adds its process id to its gmon output filename.
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