# Application Case Studies

NERSC staff along with engineers have worked with NESAP applications to prepare for the Cori-Phase 2 system based on the Xeon Phi "Knights Landing" processor. We document the several optimization case studies below.

Our presentations at ISC 16 IXPUG Workshop can all be found: https://www.ixpug.org/events/ixpug-isc-2016

Other pages of interest for those wishing to learn optimization strategies of Cori Phase 2 (Knights Landing):

## EMGEO Case Study

Early experiences working with the EMGeo geophysical imaging applications. Read More »

## BerkeleyGW Case Study

Code Description and Science Problem BerkeleyGW is a Materials Science application for calculating the excited state properties of materials such as band gaps, band structures, absoprtion spectroscopy, photoemission spectroscopy and more. It requires as input the Kohn-Sham orbitals and energies from a DFT code like Quantum ESPRESSO, PARATEC, PARSEC etc. Like such DFT codes, it is heavily depedent on FFTs, Dense Linear algebra and tensor contraction type operations similar in nature to those… Read More »

## QPhiX Case Study

Background QPhiX [1,2,3] is a library optimized for Intel(R) manycore architectures and provides sparse solvers and slash kernels for Lattice QCD calculations.It supports the Wilson dslash operator with and without clover term as well as Conjugate Gradient [4] and BiCGStab [5] solvers. The main task for QPhiX is to solve the sparse linear system where the Dslash kernel is defined by Here, U are complex, special unitary, 3x3 matrices (the so-called gauge links) which depend on lattice site x… Read More »

## WARP Case Study

Update A more complete summary is now available at https://picsar.net/ Background WARP is an accelerator code that is used to conduct detailed simulations of particle accelerators, among other high energy physics applications. It is a so-called Particle-In-Cell (PIC) code that solves for the motion of charged particles acted upon by electric and magnetic forces. The particle motion is computed in a Lagrangian sense, following individual particles. The electric and magnetic fields acting on the… Read More »

## MFDn Case Study

Description of MFDn Many-Fermion Dynamics---nuclear, or MFDn, is a configuration interaction (CI) code for nuclear structure calculations. It is a platform independent Fortran 90 code using a hybrid MPI/ OpenMP programming model,and is being used on current supercomputers, such as Edison at NERSC, for ab initio calculations of atomic nuclei using realistic nucleon-nucleons and three-nucleon forces. A calculation consists of generating a many-body basis space, constructing the many-body… Read More »

## BoxLib/AMReX Case Study

Background AMReX is a publicly available software framework for building massively parallel block-structured AMR applications. It combines elements of both the BoxLib and Chombo AMR frameworks. Key features of AMReX include Support for block-structured AMR with optional subcycling in time Support for cell-centered, face-centered and node-centered data Support for hyperbolic, parabolic, and elliptic solves on hierarchical grid structure C++ and Fortran90 versions Support for hybrid… Read More »

## VASP Case Study

Code description and computational problem The Vienna Ab-initio Simulation Package (VASP) [1-2] is a widely used materials science application for performing ab-initio electronic structure calculations and quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. VASP computes an approximate solution to the many-body Schrödinger equation, either within the Density Functional Theory (DFT) to solve the… Read More »

## CESM Case Study

CESM MG2 Kernel Code Description The Community Earth System Model (CESM) is a coupled multi-physics code which consists of multiple model components: Atmosphere, Ocean, Sea-ice, Land-ice, Land, River Runoff, and Coupler. During the course of a CESM run, the model components integrate forward in time, periodically stopping to exchange information with the coupler. The active (dynamical) components are generally fully prognostic, and they are state-of-the-art climate prediction and analysis… Read More »

## Chombo-Crunch Case Study

Background Chombo-Crunch is a high-performance software package which has been developed jointly by research scientists from Applied Numerical Algorithms Group, Computational Research Division (PI: David Trebotich) and Earth Sciences Division at LBNL for large-scale numerical simulations of complex fluid flows with particular interest in modeling of subsurface flows. One important application example of subsurface flow is a carbon sequestration - the process of capturing carbon dioxide… Read More »

## HMMER3 Case Study

Background HMMER3 [1] is a bioinformatics application used to quickly identify protein sequences which are statistically similar to a desired pattern. This functionality is used at scale in genome sequencing pipelines to annotate the content of new genomes; the Joint Genome Institute uses 7 million CPU hours annually to run HMMER3 applications. Under the hood, HMMER3 uses dynamic programming to solve a sequence alignment problem in a similar manner to the Smith-Waterman algorithm. A Hidden… Read More »

## Early application case studies

The Babbage test system was used to study representative applications and kernels in various scientific fields to gain experience with the challenges and strategies needed to optimize code performance on the MIC architecture. Below we highlight a few examples: BerkeleyGW The BerkeleyGW package is a materials science application that calculates electronic and optical properties with quantitative accuracy, a critical need in materials design for more efficient and cost-effective solar… Read More »

## ISC16 IXPUG Performance Workshop

Materials from NERSC presentations at the ISC Workshop "Application Performance on Intel Xeon Phi –Being Prepared for KNL and Beyond" presented by the Intel Xeon Phi Users… Read More »

## Quantum ESPRESSO Exact Exchange Case Study

Background Quantum ESPRESSO is an OpenSource density functional theory (DFT) code and widely used in Materials Science and Quantum Chemistry to compute states of complex systems. It can be used for numerous purposes, including calculating the adsorption properties of porous materials, computing the thermodynamic and optical properties of existing and new materials, and simulating X-ray absorption spectra.This article focuses on calculations involving hybrid functionals, which differ from local… Read More »

## XGC1 Case Study

Background XGC1 is a gyrokinetic Particle-In-Cell code for simulating plasma turbulence in magnetic confinement fusion devices. It self-consistently solves the kinetic evolution of the charged particle distribution and the electromagnetic fields. Lagrangian equation of motion is used for time advancing the particles, while conserving the mass, canonical angular momentum, and energy. The usual gyrokinetic Poisson equation is solved with the four-point averaging technique. In order to simulate… Read More »