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At least 73 records · Page 4

Enhancing Application Performance Using Mini-Apps: Comparison of Hybrid Parallel Programming Paradigms

In this work, several mini-apps have been created to enhance a real-world application performance, namely the VULCAN code for complex flow analysis developed at the NASA Langley Research Center. These mini-apps explore hybrid parallel programming paradigms with Message Passing Interface (MPI) for distributed memory access and either Shared MPI (SMPI) or OpenMP for shared memory accesses. Performance testing shows that MPI+SMPI yields the best execution performance, while requiring the largest number of code changes. A maximum speedup of 23X was measured for MPI+SMPI, but only 10X was measured for MPI+OpenMP.

Lawson, Gary

Enhancing Application Performance Using Mini-Apps: Comparison of Hybrid Parallel Programming Paradigms

In many fields, real-world applications for High Performance Computing have already been developed. For these applications to stay up-to-date, new parallel strategies must be explored to yield the best performance; however, restructuring or modifying a real-world application may be daunting depending on the size of the code. In this case, a mini-app may be employed to quickly explore such options without modifying the entire code. In this work, several mini-apps have been created to enhance a real-world application performance, namely the VULCAN code for complex flow analysis developed at the NASA Langley Research Center. These mini-apps explore hybrid parallel programming paradigms with Message Passing Interface (MPI) for distributed memory access and either Shared MPI (SMPI) or OpenMP for shared memory accesses. Performance testing shows that MPI+SMPI yields the best execution performance, while requiring the largest number of code changes. A maximum speedup of 23 was measured for MPI+SMPI, but only 11 was measured for MPI+OpenMP.

Lawson, Gary

Optimization of KINETICS Chemical Computation Code

NASA JPL has been creating a code in FORTRAN called KINETICS to model the chemistry of planetary atmospheres. Recently there has been an effort to introduce Message Passing Interface (MPI) into the code so as to cut down the run time of the program. There has been some implementation of MPI into KINETICS; however, the code could still be more efficient than it currently is. One way to increase efficiency is to send only certain variables to all the processes when an MPI subroutine is called and to gather only certain variables when the subroutine is finished. Therefore, all the variables that are used in three of the main subroutines needed to be investigated. Because of the sheer amount of code that there is to comb through this task was given as a ten-week project. I have been able to create flowcharts outlining the subroutines, common blocks, and functions used within the three main subroutines. From these flowcharts I created tables outlining the variables used in each block and important information about each. All this information will be used to determine how to run MPI in KINETICS in the most efficient way possible.

planetary atmospheres

Distributed Order Recording Techniques for Efficient Record-and-Replay of Multi-threaded Programs

After all these years and all these other shared memory programming frameworks, OpenMP is still the most popular one. However, its greater levels of non-deterministic execution makes debugging and testing more challenging. The ability to record and deterministically replay the program execution is key to address this challenge. However, scalably replaying OpenMP programs is still an unresolved problem. In this paper, we propose two novel techniques that use Distributed Clock (DC) and Distributed Epoch (DE) recording schemes to eliminate excessive thread synchronization for OpenMP record and replay. Our evaluation on representative HPC applications with ReOMP, which we used to realize DC and DE recording, shows that our approach is 2-5x more efficient than traditional approaches that synchronize on every shared-memory access. Furthermore, we demonstrate that our approach can be easily combined with MPI-level replay tools to replay non-trivial MPI+OpenMP applications. We achieve this by integrating ReOMP into ReMPI, an existing scalable MPI record-and-replay tool, with only a small MPI-scale-independent runtime overhead.

Fu, Xiang

Parallel Programming in MCNP6

Monte Carlo N-Particle (MCNP)1 is a general-purpose Monte Carlo particle transport code developed by Los Alamos National Laboratory (LANL). To efficiently handle long simulations, MCNP version 6 (MCNP6) supports parallel execution using two primary programming models: • Shared-memory task-based threading using OpenMP (Open Multi-Processing), and • Distributed-memory calculations using MPI (Message Passing Interface). The OpenMP and MPI programming models enable MCNP6 to scale from desktop systems to high-performance computing (HPC) clusters, allowing users to run MCNP in one of three parallel modes: • OpenMP-only, • MPI-only, and • Hybrid (MPI + OpenMP). The choice of parallelization mode depends on the underlying computer architecture and the characteristics of the simulation problem.

97 MATHEMATICS AND COMPUTING

I/O Parallelization for the Goddard Earth Observing System Data Assimilation System (GEOS DAS)

The National Aeronautics and Space Administration (NASA) Data Assimilation Office (DAO) at the Goddard Space Flight Center (GSFC) has developed the GEOS DAS, a data assimilation system that provides production support for NASA missions and will support NASA's Earth Observing System (EOS) in the coming years. The DAO's support of the EOS project along with the requirement of producing long-term reanalysis datasets with an unvarying system levy a large I/O burden on the future system. The DAO has been involved in prototyping parallel implementations of the GEOS DAS for a number of years and is now converting the production version from shared-memory parallelism to distributed-memory parallelism using the portable Message-Passing Interface (MPI). If the MPI-based GEOS DAS is to meet these production requirements, we must make I/O from the parallel system efficient. We have designed a scheme that allows efficient I/O processing while retaining portability, reducing the need for post-processing, and producing data formats that are required by our users, both internal and external. The first phase of the GEOS DAS Parallel I/O System (GPIOS) will expand upon the common method of gathering global data to a Single PE for output. Instead of using a PE also tasked with primary computation, a number of PEs will be dedicated to I/O and its related tasks. This allows the data transformations and formatting required prior to output to take place asynchronously with respect to the GEOS DAS assimilation cycle, improving performance and generating output data sets in a format convenient for our users. I/O PEs can be added as needed to handle larger data volumes or to meet user file specifications. We will show I/O performance results from a prototype MPI GCM integrated with GPIOS. Phase two of GPIOS development will examine ways of integrating new software technologies to further improve performance and build scalability into the system. The maturing of MPI-IO implementations and other supporting libraries such as parallel HDF should provide performance gains while retaining portability.

Lucchesi, R.

Testing New Programming Paradigms with NAS Parallel Benchmarks

Over the past decade, high performance computing has evolved rapidly, not only in hardware architectures but also with increasing complexity of real applications. Technologies have been developing to aim at scaling up to thousands of processors on both distributed and shared memory systems. Development of parallel programs on these computers is always a challenging task. Today, writing parallel programs with message passing (e.g. MPI) is the most popular way of achieving scalability and high performance. However, writing message passing programs is difficult and error prone. Recent years new effort has been made in defining new parallel programming paradigms. The best examples are: HPF (based on data parallelism) and OpenMP (based on shared memory parallelism). Both provide simple and clear extensions to sequential programs, thus greatly simplify the tedious tasks encountered in writing message passing programs. HPF is independent of memory hierarchy, however, due to the immaturity of compiler technology its performance is still questionable. Although use of parallel compiler directives is not new, OpenMP offers a portable solution in the shared-memory domain. Another important development involves the tremendous progress in the internet and its associated technology. Although still in its infancy, Java promisses portability in a heterogeneous environment and offers possibility to "compile once and run anywhere." In light of testing these new technologies, we implemented new parallel versions of the NAS Parallel Benchmarks (NPBs) with HPF and OpenMP directives, and extended the work with Java and Java-threads. The purpose of this study is to examine the effectiveness of alternative programming paradigms. NPBs consist of five kernels and three simulated applications that mimic the computation and data movement of large scale computational fluid dynamics (CFD) applications. We started with the serial version included in NPB2.3. Optimization of memory and cache usage was applied to several benchmarks, noticeably BT and SP, resulting in better sequential performance. In order to overcome the lack of an HPF performance model and guide the development of the HPF codes, we employed an empirical performance model for several primitives found in the benchmarks. We encountered a few limitations of HPF, such as lack of supporting the "REDISTRIBUTION" directive and no easy way to handle irregular computation. The parallelization with OpenMP directives was done at the outer-most loop level to achieve the largest granularity. The performance of six HPF and OpenMP benchmarks is compared with their MPI counterparts for the Class-A problem size in the figure in next page. These results were obtained on an SGI Origin2000 (195MHz) with MIPSpro-f77 compiler 7.2.1 for OpenMP and MPI codes and PGI pghpf-2.4.3 compiler with MPI interface for HPF programs.

Jin, H.

Use Computer-Aided Tools to Parallelize Large CFD Applications

Porting applications to high performance parallel computers is always a challenging task. It is time consuming and costly. With rapid progressing in hardware architectures and increasing complexity of real applications in recent years, the problem becomes even more sever. Today, scalability and high performance are mostly involving handwritten parallel programs using message-passing libraries (e.g. MPI). However, this process is very difficult and often error-prone. The recent reemergence of shared memory parallel (SMP) architectures, such as the cache coherent Non-Uniform Memory Access (ccNUMA) architecture used in the SGI Origin 2000, show good prospects for scaling beyond hundreds of processors. Programming on an SMP is simplified by working in a globally accessible address space. The user can supply compiler directives, such as OpenMP, to parallelize the code. As an industry standard for portable implementation of parallel programs for SMPs, OpenMP is a set of compiler directives and callable runtime library routines that extend Fortran, C and C++ to express shared memory parallelism. It promises an incremental path for parallel conversion of existing software, as well as scalability and performance for a complete rewrite or an entirely new development. Perhaps the main disadvantage of programming with directives is that inserted directives may not necessarily enhance performance. In the worst cases, it can create erroneous results. While vendors have provided tools to perform error-checking and profiling, automation in directive insertion is very limited and often failed on large programs, primarily due to the lack of a thorough enough data dependence analysis. To overcome the deficiency, we have developed a toolkit, CAPO, to automatically insert OpenMP directives in Fortran programs and apply certain degrees of optimization. CAPO is aimed at taking advantage of detailed inter-procedural dependence analysis provided by CAPTools, developed by the University of Greenwich, to reduce potential errors made by users. Earlier tests on NAS Benchmarks and ARC3D have demonstrated good success of this tool. In this study, we have applied CAPO to parallelize three large applications in the area of computational fluid dynamics (CFD): OVERFLOW, TLNS3D and INS3D. These codes are widely used for solving Navier-Stokes equations with complicated boundary conditions and turbulence model in multiple zones. Each one comprises of from 50K to 1,00k lines of FORTRAN77. As an example, CAPO took 77 hours to complete the data dependence analysis of OVERFLOW on a workstation (SGI, 175MHz, R10K processor). A fair amount of effort was spent on correcting false dependencies due to lack of necessary knowledge during the analysis. Even so, CAPO provides an easy way for user to interact with the parallelization process. The OpenMP version was generated within a day after the analysis was completed. Due to sequential algorithms involved, code sections in TLNS3D and INS3D need to be restructured by hand to produce more efficient parallel codes. An included figure shows preliminary test results of the generated OVERFLOW with several test cases in single zone. The MPI data points for the small test case were taken from a handcoded MPI version. As we can see, CAPO's version has achieved 18 fold speed up on 32 nodes of the SGI O2K. For the small test case, it outperformed the MPI version. These results are very encouraging, but further work is needed. For example, although CAPO attempts to place directives on the outer- most parallel loops in an interprocedural framework, it does not insert directives based on the best manual strategy. In particular, it lacks the support of parallelization at the multi-zone level. Future work will emphasize on the development of methodology to work in a multi-zone level and with a hybrid approach. Development of tools to perform more complicated code transformation is also needed.

Jin, H.

Message Passing vs. Shared Address Space on a Cluster of SMPs

The convergence of scalable computer architectures using clusters of PCs (or PC-SMPs) with commodity networking has become an attractive platform for high end scientific computing. Currently, message-passing and shared address space (SAS) are the two leading programming paradigms for these systems. Message-passing has been standardized with MPI, and is the most common and mature programming approach. However message-passing code development can be extremely difficult, especially for irregular structured computations. SAS offers substantial ease of programming, but may suffer from performance limitations due to poor spatial locality, and high protocol overhead. In this paper, we compare the performance of and programming effort, required for six applications under both programming models on a 32 CPU PC-SMP cluster. Our application suite consists of codes that typically do not exhibit high efficiency under shared memory programming. due to their high communication to computation ratios and complex communication patterns. Results indicate that SAS can achieve about half the parallel efficiency of MPI for most of our applications: however, on certain classes of problems SAS performance is competitive with MPI. We also present new algorithms for improving the PC cluster performance of MPI collective operations.

Shan, Hongzhang

MPIRUN: A Portable Loader for Multidisciplinary and Multi-Zonal Applications

Multidisciplinary and multi-zonal applications are an important class of applications in the area of Computational Aerosciences. In these codes, two or more distinct parallel programs or copies of a single program are utilized to model a single problem. To support such applications, it is common to use a programming model where a program is divided into several single program multiple data stream (SPMD) applications, each of which solves the equations for a single physical discipline or grid zone. These SPMD applications are then bound together to form a single multidisciplinary or multi-zonal program in which the constituent parts communicate via point-to-point message passing routines. One method for implementing the message passing portion of these codes is with the new Message Passing Interface (MPI) standard. Unfortunately, this standard only specifies the message passing portion of an application, but does not specify any portable mechanisms for loading an application. MPIRUN was developed to provide a portable means for loading MPI programs, and was specifically targeted at multidisciplinary and multi-zonal applications. Programs using MPIRUN for loading and MPI for message passing are then portable between all machines supported by MPIRUN. MPIRUN is currently implemented for the Intel iPSC/860, TMC CM5, IBM SP-1 and SP-2, Intel Paragon, and workstation clusters. Further, MPIRUN is designed to be simple enough to port easily to any system supporting MPI.

Fineberg, Samuel A.

Using Modules with MPICH-G2 (and "Loose Ends")

A new approach to running complex, distributed MPI jobs using the MPICH-G2 library is described. This approach allows the user to switch between different versions of compilers, system libraries, MPI libraries, etc. via the "module" command. The key idea is a departure from the prescribed "(jobtype=mpi)" approach to running distributed MPI jobs. The new method requires the user to provide a script that will be run as the "executable" with the "(jobtype=single)" RSL attribute. The major advantage of the proposed method is to enable users to decide in their own script what modules, environment, etc. they would like to have in running their job.

Chang, Johnny

What Multilevel Parallel Programs do when you are not Watching: A Performance Analysis Case Study Comparing MPI/OpenMP, MLP, and Nested OpenMP

With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors, parallel programming techniques have evolved that support parallelism beyond a single level. When comparing the performance of applications based on different programming paradigms, it is important to differentiate between the influence of the programming model itself and other factors, such as implementation specific behavior of the operating system (OS) or architectural issues. Rewriting-a large scientific application in order to employ a new programming paradigms is usually a time consuming and error prone task. Before embarking on such an endeavor it is important to determine that there is really a gain that would not be possible with the current implementation. A detailed performance analysis is crucial to clarify these issues. The multilevel programming paradigms considered in this study are hybrid MPI/OpenMP, MLP, and nested OpenMP. The hybrid MPI/OpenMP approach is based on using MPI [7] for the coarse grained parallelization and OpenMP [9] for fine grained loop level parallelism. The MPI programming paradigm assumes a private address space for each process. Data is transferred by explicitly exchanging messages via calls to the MPI library. This model was originally designed for distributed memory architectures but is also suitable for shared memory systems. The second paradigm under consideration is MLP which was developed by Taft. The approach is similar to MPi/OpenMP, using a mix of coarse grain process level parallelization and loop level OpenMP parallelization. As it is the case with MPI, a private address space is assumed for each process. The MLP approach was developed for ccNUMA architectures and explicitly takes advantage of the availability of shared memory. A shared memory arena which is accessible by all processes is required. Communication is done by reading from and writing to the shared memory.

Jost, Gabriele

Implementation of a Message Passing Interface into a Cloud-Resolving Model for Massively Parallel Computing

The capability for massively parallel programming (MPP) using a message passing interface (MPI) has been implemented into a three-dimensional version of the Goddard Cumulus Ensemble (GCE) model. The design for the MPP with MPI uses the concept of maintaining similar code structure between the whole domain as well as the portions after decomposition. Hence the model follows the same integration for single and multiple tasks (CPUs). Also, it provides for minimal changes to the original code, so it is easily modified and/or managed by the model developers and users who have little knowledge of MPP. The entire model domain could be sliced into one- or two-dimensional decomposition with a halo regime, which is overlaid on partial domains. The halo regime requires that no data be fetched across tasks during the computational stage, but it must be updated before the next computational stage through data exchange via MPI. For reproducible purposes, transposing data among tasks is required for spectral transform (Fast Fourier Transform, FFT), which is used in the anelastic version of the model for solving the pressure equation. The performance of the MPI-implemented codes (i.e., the compressible and anelastic versions) was tested on three different computing platforms. The major results are: 1) both versions have speedups of about 99% up to 256 tasks but not for 512 tasks; 2) the anelastic version has better speedup and efficiency because it requires more computations than that of the compressible version; 3) equal or approximately-equal numbers of slices between the x- and y- directions provide the fastest integration due to fewer data exchanges; and 4) one-dimensional slices in the x-direction result in the slowest integration due to the need for more memory relocation for computation.

Juang, Hann-Ming Henry

High frequency QRS ECG predicts ischemic defects during myocardial perfusion imaging

Background: Changes in high frequency QRS components of the electrocardiogram (HF QRS ECG) (150-250 Hz) are more sensitive than changes in conventional ST segments for detecting myocardial ischemia. We investigated the accuracy of 12-lead HF QRS ECG in detecting ischemia during adenosine tetrofosmin myocardial perfusion imaging (MPI). Methods and Results: 12-lead HF QRS ECG recordings were obtained from 45 patients before and during adenosine technetium-99 tetrofosmin MPI tests. Before the adenosine infusions, recordings of HF QRS were analyzed according to a morphological score that incorporated the number, type and location of reduced amplitude zones (RAZs) present in the 12 leads. During the adenosine infusions, recordings of HF QRS were analyzed according to the maximum percentage changes (in both the positive and negative directions) that occurred in root mean square (RMS) voltage amplitudes within the 12 leads. The best set of prospective HF QRS criteria had a sensitivity of 94% and a specificity of 83% for correctly identifying the MPI result. The sensitivity of simultaneous ST segment changes (18%) was significantly lower than that of any individual HF QRS criterion (P<0.001). Conclusions: Analysis of 12-lead HF QRS ECG is highly sensitive and specific for detecting ischemic perfusion defects during adenosine MPI stress tests and significantly more sensitive than analysis of conventional ST segments.

Rahman, Atiar

High frequency QRS ECG predicts ischemic defects during myocardial perfusion imaging

Changes in high frequency QRS components of the electrocardiogram (HF QRS ECG) (150-250 Hz) are more sensitive than changes in conventional ST segments for detecting myocardial ischemia. We investigated the accuracy of 12-lead HF QRS ECG in detecting ischemia during adenosine tetrofosmin myocardial perfusion imaging (MPI). 12-lead HF QRS ECG recordings were obtained from 45 patients before and during adenosine technetium-99 tetrofosmin MPI tests. Before the adenosine infusions, recordings of HF QRS were analyzed according to a morphological score that incorporated the number, type and location of reduced amplitude zones (RAZs) present in the 12 leads. During the adenosine infusions, recordings of HF QRS were analyzed according to the maximum percentage changes (in both the positive and negative directions) that occurred in root mean square (RMS) voltage amplitudes within the 12 leads. The best set of prospective HF QRS criteria had a sensitivity of 94% and a specificity of 83% for correctly identifying the MPI result. The sensitivity of simultaneous ST segment changes (18%) was significantly lower than that of any individual HF QRS criterion (P less than 0.00l). Analysis of 12-lead HF QRS ECG is highly sensitive and specific for detecting ischemic perfusion defects during adenosine MPI stress tests and significantly more sensitive than analysis of conventional ST segments.

Source record

GEOS Atmospheric Model: Challenges at Exascale

The Goddard Earth Observing System (GEOS) model at NASA's Global Modeling and Assimilation Office (GMAO) is used to simulate the multi-scale variability of the Earth's weather and climate, and is used primarily to assimilate conventional and satellite-based observations for weather forecasting and reanalysis. In addition, assimilations coupled to an ocean model are used for longer-term forecasting (e.g., El Nino) on seasonal to interannual times-scales. The GMAO's research activities, including system development, focus on numerous time and space scales, as detailed on the GMAO website, where they are tabbed under five major themes: Weather Analysis and Prediction; Seasonal-Decadal Analysis and Prediction; Reanalysis; Global Mesoscale Modeling, and Observing System Science. A brief description of the GEOS systems can also be found at the GMAO website. GEOS executes as a collection of earth system components connected through the Earth System Modeling Framework (ESMF). The ESMF layer is supplemented with the MAPL (Modeling, Analysis, and Prediction Layer) software toolkit developed at the GMAO, which facilitates the organization of the computational components into a hierarchical architecture. GEOS systems run in parallel using a horizontal decomposition of the Earth's sphere into processing elements (PEs). Communication between PEs is primarily through a message passing framework, using the message passing interface (MPI), and through explicit use of node-level shared memory access via the SHMEM (Symmetric Hierarchical Memory access) protocol. Production GEOS weather prediction systems currently run at 12.5-kilometer horizontal resolution with 72 vertical levels decomposed into PEs associated with 5,400 MPI processes. Research GEOS systems run at resolutions as fine as 1.5 kilometers globally using as many as 30,000 MPI processes. Looking forward, these systems can be expected to see a 2 times increase in horizontal resolution every two to three years, as well as less frequent increases in vertical resolution. Coupling these resolution changes with increases in complexity, the computational demands on the GEOS production and research systems should easily increase 100-fold over the next five years. Currently, our 12.5 kilometer weather prediction system narrowly meets the time-to-solution demands of a near-real-time production system. Work is now in progress to take advantage of a hybrid MPI-OpenMP parallelism strategy, in an attempt to achieve a modest two-fold speed-up to accommodate an immediate demand due to increased scientific complexity and an increase in vertical resolution. Pursuing demands that require a 10- to 100-fold increases or more, however, would require a detailed exploration of the computational profile of GEOS, as well as targeted solutions using more advanced high-performance computing technologies. Increased computing demands of 100-fold will be required within five years based on anticipated changes in the GEOS production systems, increases of 1000-fold can be anticipated over the next ten years.

ESMF

Methodology and Application of HPC I/O Characterization with MPIProf and IOT

Combining the strengths of MPIProf and IOT, an efficient and systematic method is devised for I/O characterization at the per-job, per-rank, per-file and per-call levels of HPC programs running on the NASA Advanced Supercomputing Center. This method is applied to answer four I/O questions in this paper. A total of 13 MPI programs and 15 cases, ranging from 24 to 5968 ranks, are analyzed to establish the I/O landscape from answers to the four questions. Four of the 13 programs use MPI I/O and the behavior of their collective writes depends on the specific implementation of the MPI library used. The SGI MPT library, the prevailing MPI library for our systems, was found to gather small writes from a large number of ranks to perform larger writes by a small subset of collective buffering ranks. The number of collective buffering ranks invoked by MPT depends on the Lustre stripe count and the number of nodes used for the run. A demonstration of varying the stripe count to achieve double-digit speedup of one program's I/O was presented. Another program, which concurrently opens private files by all ranks and could potentially create a heavy load on the Lustre servers, was identified. The ability to systematically characterize I/O for a large number of programs running on a supercomputer, seek I/O optimization opportunity and identify programs that could cause a high load and instability on the filesystems is important for pursuing exascale in a real production environment.

Characterization

Multiplicity dependent 𝐽/𝜓 and 𝜓⁡(2⁢𝑆) production at forward and backward rapidity in 𝑝 + 𝑝 collisions at $\sqrt{𝑠}$ = 200 GeV

Recent measurements of 𝐽/𝜓 production as a function of event charged-particle multiplicity at the collision energies of both the Large Hadron Collider (LHC) and the Relativistic Heavy Ion Collider (RHIC) show enhanced 𝐽/𝜓 production yields with increasing multiplicity. One potential explanation for this type of dependence is multiparton interactions (MPI). We present the first study of potential autocorrelations at RHIC energies and forward and backward rapidity of self-normalized 𝐽/𝜓 yields and 𝜓⁡(2⁢𝑆) to 𝐽/𝜓 ratio, as a function of self-normalized multiplicity in 𝑝 + 𝑝 collisions. In addition, detailed pythia studies tuned to RHIC energies were performed to investigate the MPI impacts. We find that the PHENIX data at RHIC are consistent with recent LHC measurements and can only be described by pythia calculations that include MPI effects. The forward and backward 𝜓⁡(2⁢𝑆) to 𝐽/𝜓 ratio is found to be less dependent on the charged-particle multiplicity.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS