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HIGH-PERFORMANCE COMPUTINGEnergy, structureSelf-consistent field (SCF) energy, gradientGeneric tasks (first tier)theories defined by the input. Each module in this layer usestoolkits and routines that reside in the lower layers of thearchitecture to accomplish its tasks. These NWChem modulesRuntime databaseDFT energy, gradientMolecular dynamics (MD), nuclear magneticresonance (NMR), solvationIntegral APIOptimize, dynamicsGeometry objectBasis set objectParallel EigensolverSystem (PeIGS)Molecular calculationmodules (second tier)Molecular modelingtools (third tier)are independent and share data only through a disk-residentdatabase, which allows modules to share data or shareaccess to files containing data.• Molecular modeling tools: The third tier contains tools thatprovide a basic functionality common to many of the algorithmsused in the field of chemistry. These include symmetry,basis sets, grids, geometry, and integrals.• Molecular software development toolkit: This fourth-tiertoolkit makes up the foundation level of the five-tieredstructure of the NWChem code, and enables the developmentof an object-oriented code that is constructed mainlyChemIO APIMemory allocator toolGlobal arrays toolMolecular softwaredevelopment toolkit(fourth tier)in Fortran77.• Utilities: At the lowest level of the NWChem architecture,the fifth tier contains several basic, odds-and-ends functions,including utility routines that most of the higher tiers require.Examples include the timing routines, the input parser, andRuntime databasethe print routines.UtilitiesFigure 1. Five-tier NWChem architectureUnderstanding the architecture of NWChemMolecular dynamics simulations such as NWChem are an importanttool in the study and rational design of molecular systems andmaterials, providing information about the behavior of chemicalsystems that can be difficult to obtain by other means. Considerablecomputational resources are required even for small molecular systems,which have tens of thousands of atoms and short simulationperiods in the range of nanoseconds.Utilities (fifth tier)NWChem has a five-tier, modular architecture (see Figure 1).The application incorporates several existing modules and toolkits atvarious levels in the architecture because of its adherence to objectorientedprogramming concepts. The five tiers are as follows:• Generic tasks: At the first tier, the NWChem interface processesthe input, sets up the parallel environment, and performsany initialization needed for the desired calculations.This tier basically serves as the mechanism that transferscontrol to the different modules in the second tier.• Molecular calculation modules: At the second tier, thesehigh-level programming modules accomplish computationaltasks, performing particular operations using the specifiedTo enable all aspects of the hardware—such as CPU, disk,and memory—to scale to a massively parallel computing architecture,NWChem uses NUMA to distribute the data across allnodes. Memory access is achieved through explicit message passingusing the TCGMSG interface.2 TCGMSG is a toolkitfor writing portable parallelprograms using the MessagePassing Interface (MPI), amessage-passing model.Designed for chemical applications,TCGMSG is relativelysimple, having limitedfunctionality that includespoint-to-point communication,global operations, anda simple load-balancingfacility. This simplicity contributesto the robustness ofHPC clusters built fromindustry-standard componentsare tolerant to componentfailures because they haveno single point of failure,thus enhancing systemavailability and reliability.TCGMSG and its exemplary portability, as well as its high performancein a wide range of problem sizes.Applications written using TCGMSG can be ported betweenenvironments without changes to the parallel code. The memoryallocator (MA) tool is used to allocate memory that is local to thecalling process. The global arrays (GA) tool is used to share arraysbetween processors as if the memory were physically shared. This2For more information about the TCGMSG message-passing library, visit www.emsl.pnl.gov/docs/parsoft/tcgmsg/tcgmsg.html.138POWER SOLUTIONS Reprinted from Dell Power Solutions, February 2005. Copyright © 2005 Dell Inc. All rights reserved. February 2005
HIGH-PERFORMANCE COMPUTINGprovides sufficient transparency to the programmer and is compatiblewith the message-passing model.The complex I/O patterns required to accomplish efficientmemory management are handled using the abstract programminginterface ChemIO. ChemIO is a high-performance I/O applicationprogramming interface (API) designed to meet the requirements oflarge-scale computational chemistry problems. It allows the programmerto create I/O files that may be local or distributed.Like TCGMSG, the runtime database is a component of thefourth tier. The runtime database is a persistent data storage mechanismdesigned to hold calculation-specific information for all theupper-level programming modules. Because it is not destroyed atthe end of a calculation unless the user specifically requests itsdestruction, a given runtime database can be used in several independentcalculations.Examining the performance characteristics of NWChemEvery application behaves differently and has distinctive characteristics.For the study described in this article, which was conducted inNovember 2003, baseline performance was measured when runningNWChem on a single Intel Itanium processor–based Dell PowerEdge3250 server at various processor speeds and cache sizes; speedupwas evaluated when running the application on multiple nodes in aDell HPC cluster. The study also addressed the performance impact ofrunning applications like NWChem on various configurations of IntelItanium processor–based systems to obtain a better understanding ofNWChem’s dependencies on processor features such as cache sizeand clock frequency. Understanding the behavior and patterns of theNWChem application can help organizations identify how to designand allocate appropriate resources using standard data sets. This in turnhelps to identify bottlenecks while running NWChem on a cluster.All tests for this study were conducted using NWChem 4.5. Theinput file used for this study was siosi3.nw, a density functionaltheory (DFT) benchmark that calculates the DFT function on thesiosi3 molecule and provides as output the various atomic energiesrelated to the DFT function. This input file is publicly available anddownloadable from the NWChem home page (www.emsl.pnl.gov/docs/nwchem/nwchem.html). For comparison purposes, the inputfile was kept constant throughout this study. Wall-clock time—thatis, the real running time of the program from start to finish (inseconds)—was used to measure performance.Test configuration L3 cache Processor clock frequency1 4MB 1.4 GHz2 1.5 MB 1.4 GHz3 1.5 MB 1.0 GHzFigure 2. Test configurations comprising variable clock speeds and cache sizesPerformance improvement (percent)1401301201101009080BaselineCacheCPU frequencyPowerEdge 3250(1.4 GHz, 1.5 MB L3)Measuring the effect of Itanium 2 processor featuresTo understand the sensitivity of the NWChem application to cachesize and processor frequency, the Dell High-Performance ComputingCluster team conducted tests using the default data set (siosi3.nw).The team conducted multiple tests for various configurations suchas constant processor clock frequency and different cache size versusconstant cache size and different clock frequency.Three configurations using 64-bit Intel Itanium processors weretested as follows: The first two test configurations represented thesame clock speed but different level 3 (L3) cache sizes, while thesecond two test configurations represented the same cache size butdifferent clock speeds (see Figure 2).The results in Figure 3 were obtained on a single processorusing the Red Hat ® Enterprise Linux ® AS 2.1 operating system withkernel 2.4.18-e31smp. For this particular test, Dell engineers usedthe precompiled binaries with default optimization that are availablefrom the Red Hat Web site.PowerEdge 3250(1.4 GHz, 4 MB L3)Figure 3. Impact of cache size and processor speed on NWChem performanceFigure 3 shows that when the clock speed was kept at 1.4 GHzand the L3 cache size increased from 1.5 MB to 4 MB, performanceincreased approximately 11 percent. Thus, a larger cache size helpedachieve a performance improvement in this study when runningNWChem’s siosi3.nw benchmark. When running other data sets,the performance benefits from large caches will likely depend onthe size of the data set. Larger data sets typically benefit more thansmaller data sets from larger caches.PowerEdge 3250(1.0 GHz, 1.5 MB L3)Figure 3 also shows performance benefits when the L3 cachesize was kept constant at 1.5 MB and the CPU frequency wasincreased from 1.0 GHz to 1.4 GHz (a 40 percent increase in processorclock speed). The percentage performance gain for movingfrom the slower clock frequency to the higher clock frequency wasapproximately 35 percent. Thus, the results from this study signifythat the NWChem application is highly compute intensive and canbenefit from increasing processor clock speed because NWChemperformance scaled well with CPU frequency.PowerEdge 3250(1.4 GHz, 1.5 MB L3)www.dell.com/powersolutions Reprinted from Dell Power Solutions, February 2005. Copyright © 2005 Dell Inc. All rights reserved. POWER SOLUTIONS 139
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