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Cart3D is a computational fluid dynamics (CFD) application aimed at conceptual and preliminary design of aerospace vehicles with complex geometries. It is widely used by design engineers at NASA, Department of Defense and aerospace companies in the USA. We present detailed performance analysis of Cart3D using two tools SGI MPInside and op_scope that collects hardware counter data from Intel Performance Monitoring Unit (PMU) on supercomputers based on Nehalem micro-architecture. Using these tools, we have done dynamic profiling of Cart3D (compute time, communication time and I/O time), along with dynamic profiling of MPI functions (MPI_Sendrecv, MPI_Bcast, MPI_Isend, MPI_Irecv, MPI_Allreduce, MPI_Barrier, etc.) with respect to message size of each rank and time consumed by each function. MPI communication is further analyzed by studying the performance of MPI functions used in this application as a function of message size and number of cores. Using these tools we have also studied efficiency of the processor to measure its effective utilization, efficiency of the floating-point units, percentage of vectorization and percentage of data coming from L2 cache, L3 cache, and main memory. This study was performed on two computing sub-systems based on quad-core Nehalem-EP and hex-core West mere-EP processors that are part of Pleiades an SGI Altix ICE at NASA Ames Research Center.