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DOE OSTI2024

Enabling Low-Overhead HT-HPC Workflows at Extreme Scale using GNU Parallel

GNU Parallel is a versatile and powerful tool for process parallelization widely used in scientific computing. This paper demonstrates its effective application in high-performance computing (HPC) environments, particularly focusing on its scalability and efficiency in executing large-scale high-throughput high-performance computing (HT-HPC) workflows. Through real-world examples, we highlight GNU Parallel’s performance across various HPC workloads, including GPU computing, container-based workloads, and node-local NVMe storage. Our results on two leading supercomputers, OLCF’s Frontier and NERSC’s Perlmutter, showcase GNU Parallel’s rapid process dispatching ability and its capacity to maintain low overhead even at extreme scales. We explore GNU Parallel’s application in massive parallel file transfers using a scheduled Data Transfer Node (DTN) cluster, emphasizing its broad utility in diverse scientific workflows. Beyond its direct application as a viable workflow manager, GNU Parallel can be employed in conjunction with other workflow systems as a "last-mile" parallelizing driver and as a quick prototyping tool to design and extract parallel profiles from application executions. We then argue that the potential for GNU Parallel to transform workflow management at extreme scales is substantial, paving the way for more efficient and effective scientific discoveries.

Maheshwari, Ketan↗
DOE OSTI2015

Cluster-to-cluster data transfer with data compression over wide-area networks

The recent emergence of ultra high-speed networks up to 100 Gb/s has posed numerous challenges and has led to many investigations on efficient protocols to saturate 100 Gb/s links. However, end-to-end data transfers involve many components, not only protocols, affecting overall transfer performance. These components include disk I/O subsystem, additional computation associated with data streams, and network adapters. For example, achievable bandwidth by TCP may not be implementable if disk I/O or CPU becomes a bottleneck in end-to-end data transfer. In this paper, we first model all the system components involved in end-to-end data transfer as a graph. We then formulate the problem whose goal is to achieve maximum data transfer throughput using parallel data flows. We also propose a variable data flow GridFFP XIO stack to improve data transfer with data compression. Our contributions lie in how to optimize data transfers considering all the system components involved rather than in accurately modeling all the system components involved. Our proposed formulations and solutions are evaluated through experiments on the ESnet 100G testbed and a wide-area cluster-to-cluster testbed. The experimental results on the ESnet 100G testbed show that our approach is several times faster than Globus Online-8 x faster for datasets with many 10 MB files and 3-4 x faster for other datasets of larger size files. The experimental results on the cluster-to-cluster testbed show that our variable data flow approach is up to 4 x faster than a normal cluster data transfer.

Disk-to-Disk Transfer↗
DOE OSTI2011

Iso-Energy-Efficiency: An Approach to Power Constrained Parallel Computation

Future large scale high performance supercomputer systems require high energy efficiency to achieve exaflops computational power and beyond. Despite the need to understand energy efficiency in high-performance systems, there are few techniques to evaluate energy efficiency at scale. In this paper, we propose a system level iso-energy-efficiency model to analyze, evaluate and predict energy-performance of data intensive parallel applications with various execution patterns running on large scale power-aware clusters. Our analytical model can help users explore the effects of machine and application dependent characteristics on system energy efficiency and isolate efficient ways to scale system parameters (e.g. processor count, CPU power/frequency, workload size and network bandwidth) to balance energy use and performance. We derive our iso-energy-efficiency model and apply it to the NAS Parallel Benchmarks on two power-aware clusters. Our results indicate that the model accurately predicts total system energy consumption within 5% error on average for parallel applications with various execution and communication patterns. We demonstrate effective use of the model for various application contexts and in scalability decision-making.

Song, Shuaiwen↗
DOE OSTI2011

Quantum Monte Carlo Endstation for Petascale Computing

The major achievements enabled by QMC Endstation grant include * Performance improvement on clusters of x86 multi-core systems, especially on Cray XT systems * New and improved methods for the wavefunction optimizations * New forms of trial wavefunctions * Implementation of the full application on NVIDIA GPUs using CUDA The scaling studies of QMCPACK on large-scale systems show excellent parallel efficiency up to 216K cores on Jaguarpf (Cray XT5). The GPU implementation shows speedups of 10-15x over the CPU implementation on older generation of x86. We have implemented hybrid OpenMP/MPI scheme in QMC to take advantage of multi-core shared memory processors of petascale systems. Our hybrid scheme has several advantages over the standard MPI-only scheme. * Memory optimized: large read-only data to store one-body orbitals and other shared properties to represent the trial wave function and many-body Hamiltonian can be shared among threads, which reduces the memory footprint of a large-scale problem. * Cache optimized: the data associated with an active Walker are in cache during the compute-intensive drift-diffusion process and the operations on an Walker are optimized for cache reuse. Thread-local objects are used to ensure the data affinity to a thread. * Load balanced: Walkers in an ensemble are evenly distributed among threads and MPI tasks. The two-level parallelism reduces the population imbalance among MPI tasks and reduces the number of point-to-point communications of large messages (serialized objects) for the Walker exchange. * Communication optimized: the communication overhead, especially for the collective operations necessary to determine ET and measure the properties of an ensemble, is significantly lowered by using less MPI tasks. The multiple forms of parallelism afforded by QMC algorithms make them ideal candidates for acceleration in the many-core paradigm. We presented the results of our effort to port the QMCPACK simulation code to the NVIDIA CUDA GPU platform. We restructured the CPU algorithms to express additional parallelism, minimize GPU-CPU communication, and efficiently utilize the GPU memory hierarchy. Using mixed precision on GT200 GPUs and MPI for intercommunication and load balancing, we observe typical full-application speedups of approximately 10x to 15x relative to quad-core Xeon CPUs alone, while reproducing the double-precision CPU results within statistical error. We developed an all-electron quantum Monte Carlo (QMC) method for solids that does not rely on pseudopotentials, and used it to construct a primary ultra-high-pressure calibration based on the equation of state of cubic boron nitride. We computed the static contribution to the free energy with the QMC method and obtained the phonon contribution from density functional theory, yielding a high-accuracy calibration up to 900 GPa usable directly in experiment. We computed the anharmonic Raman frequency shift with QMC simulations as a function of pressure and temperature, allowing optical pressure calibration. In contrast to present experimental approaches, small systematic errors in the theoretical EOS do not increase with pressure, and no extrapolation is needed. This all-electron method is applicable to first-row solids, providing a new reference for ab initio calculations of solids and benchmarks for pseudopotential accuracy. We compared experimental and theoretical results on the momentum distribution and the quasiparticle renormalization factor in sodium. From an x-ray Compton-profile measurement of the valence-electron momentum density, we derived its discontinuity at the Fermi wavevector finding an accurate measure of the renormalization factor that we compared with quantum-Monte-Carlo and G0W0 calculations performed both on crystalline sodium and on the homogeneous electron gas. Our calculated results are in good agreement with the experiment. We have been studying the heat of formation for various Kubas complexes of molecular hydrogen on Ti(1,2)ethylene-nH2 using Diffusion Monte Carlo. This work has been started and is ongoing. We are studying systems involving 1 and 2 Ti bonding sites with up to 10 hydrogen molecules in numerous configurations. This work will establish a benchmark that will test the accuracy of density functional calculations and establish the feasibility of our methods for similar systems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Distributed-Memory Parallel Symmetric Nonnegative Matrix Factorization

We develop the first distributed-memory parallel implementation of Symmetric Nonnegative Matrix Factorization (SymNMF), a key data analytics kernel for clustering and dimensionality reduction. Our implementation includes two different algorithms for SymNMF, which give comparable results in terms of time and accuracy. The first algorithm is a parallelization of an existing sequential approach that uses solvers for non symmetric NMF. The second algorithm is a novel approach based on the Gauss-Newton method. It exploits second-order information without incurring large computational and memory costs. We evaluate the scalability of our algorithms on the Summit system at Oak Ridge National Laboratory, scaling up to 128 nodes (4,096 cores) with 70% efficiency. Additionally, we demonstrate our software on an image segmentation task.

Eswar, Srinivas↗
DOE OSTI2021

Parallelizing the Unpacking and Clustering of Detector Data for Reconstruction of Charged Particle Tracks on Multi-core CPUs and Many-core GPUs

We present results from parallelizing the unpacking and clustering steps of the raw data from the silicon strip modules for reconstruction of charged particle tracks. Throughput is further improved by concurrently processing multiple events using nested OpenMP parallelism on CPU or CUDA streams on GPU. The new implementation along with earlier work in developing a parallelized and vectorized implementation of the combinatoric Kalman filter algorithm has enabled efficient global reconstruction of the entire event on modern computer architectures. We demonstrate the performance of the new implementation on Intel Xeon and NVIDIA GPU architectures.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Probabilistic Cosmological Mass Mapping from Weak Lensing Shear

We infer gravitational lensing shear and convergence fields from galaxy ellipticity catalogs under a spatial process prior for the lensing potential. We demonstrate the performance of our algorithm with simulated Gaussian-distributed cosmological lensing shear maps and a reconstruction of the mass distribution of the merging galaxy cluster Abell 781 using galaxy ellipticities measured with the Deep Lens Survey. Given interim posterior samples of lensing shear or convergence fields on the sky, we describe an algorithm to infer cosmological parameters via lens field marginalization. In the most general formulation of our algorithm we make no assumptions about weak shear or Gaussian-distributed shape noise or shears. Because we require solutions and matrix determinants of a linear system of dimension that scales with the number of galaxies, we expect our algorithm to require parallel high-performance computing resources for application to ongoing wide field lensing surveys.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Water–Hydrocarbon Interactions in Anionic Pyrene Monohydrate

Interactions between water and polycyclic aromatic hydrocarbons are essential in many aspects of chemistry, from interstellar and atmospheric processes to interfacial hydrophobicity and wetting phenomena. Despite their growing importance, the intermolecular potentials of the water-hydrocarbon interactions are underdeveloped compared to water-water potentials, and there are similarly few experimental probes that are sensitive to the details of the water-hydrocarbon potential. We present a combined experimental and computational study of anionic pyrene monohydrate, one of the simplest water/hydrocarbon clusters. The action spectrum in the OH region of the mass-selected cluster ion provides a rigorous benchmark for intermolecular potentials and computational methodologies. We identify missing intermolecular interactions and shortcomings in conventional dynamics calculations by comparing experimental data to density functional theory and classical molecular dynamics calculations. Kinetic trapping is prevalent, even for one water molecule and one pyrene molecule, leading to slow equilibration in conventional molecular dynamics calculations, even on nanosecond timescales and at low temperatures (50 K). At constant energy, temperature fluctuations for the pair of molecules are substantial. Immersing the system in a bath of soft spheres and employing parallel tempering alleviates kinetic trapping and dampens temperature fluctuations, bringing the system closer to the thermodynamic limit. With such augmented sampling, a simple, flexible water model reproduces the linewidth and the asymmetric broadening of the symmetric OH stretching mode, which we assign to spectral diffusion. In the OH stretching region, dynamics calculations predict a more intense antisymmetric peak than experiments observe but do not predict the bimodal split symmetric peak that the experiments show. Furthermore, our work suggests that electronic polarization, missing in the empirical force field, is responsible for the first discrepancy and that quantum nuclear effects, captured neither in density functional theory nor in classical dynamics, may be responsible for the second.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

High-performance dynamic quantum clustering on graphics processors

Clustering methods in machine learning may benefit from borrowing metaphors from physics. Dynamic quantum clustering associates a Gaussian wave packet with the multidimensional data points and regards them as eigenfunctions of the Schroedinger equation. The clustering structure emerges by letting the system evolve and the visual nature of the algorithm has been shown to be useful in a range of applications. Furthermore, the method only uses matrix operations, which readily lend themselves to parallelization. In this paper, we develop an implementation on graphics hardware and investigate how this approach can accelerate the computations. We achieve a speedup of up to two magnitudes over a multicore CPU implementation, which proves that quantum-like methods and acceleration by graphics processing units have a great relevance to machine learning.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Reverse Computation for Rollback-based Fault Tolerance in Large Parallel Systems

Reverse computation is presented here as an important future direction in addressing the challenge of fault tolerant execution on very large cluster platforms for parallel computing. As the scale of parallel jobs increases, traditional checkpointing approaches suffer scalability problems ranging from computational slowdowns to high congestion at the persistent stores for checkpoints. Reverse computation can overcome such problems and is also better suited for parallel computing on newer architectures with smaller, cheaper or energy-efficient memories and file systems. Initial evidence for the feasibility of reverse computation in large systems is presented with detailed performance data from a particle simulation scaling to 65,536 processor cores and 950 accelerators (GPUs). Reverse computation is observed to deliver very large gains relative to checkpointing schemes when nodes rely on their host processors/memory to tolerate faults at their accelerators. A comparison between reverse computation and checkpointing with measurements such as cache miss ratios, TLB misses and memory usage indicates that reverse computation is hard to ignore as a future alternative to be pursued in emerging architectures.

Perumalla, Kalyan S↗
DOE OSTI2013

Taming parallel I/O complexity with auto-tuning

We present an auto-tuning system for optimizing I/O performance of HDF5 applications and demonstrate its value across platforms, applications, and at scale. The system uses a genetic algorithm to search a large space of tunable parameters and to identify effective settings at all layers of the parallel I/O stack. The parameter settings are applied transparently by the auto-tuning system via dynamically intercepted HDF5 calls. To validate our auto-tuning system, we applied it to three I/O benchmarks (VPIC, VORPAL, and GCRM) that replicate the I/O activity of their respective applications. We tested the system with different weak-scaling configurations (128, 2048, and 4096 CPU cores) that generate 30 GB to 1 TB of data, and executed these configurations on diverse HPC platforms (Cray XE6, IBM BG/P, and Dell Cluster). In all cases, the auto-tuning framework identified tunable parameters that substantially improved write performance over default system settings. In conclusion, we consistently demonstrate I/O write speedups between 2x and 100x for test configurations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Accelerating science: The usage of commercial clouds in ATLAS Distributed Computing

The ATLAS experiment at CERN is one of the largest scientific machines built to date and will have ever growing computing needs as the Large Hadron Collider collects an increasingly larger volume of data over the next 20 years. ATLAS is conducting R&D projects on Amazon Web Services and Google Cloud as complementary resources for distributed computing, focusing on some of the key features of commercial clouds: lightweight operation, elasticity and availability of multiple chip architectures. The proof of concept phases have concluded with the cloud-native, vendoragnostic integration with the experiment’s data and workload management frameworks. Google Cloud has been used to evaluate elastic batch computing, ramping up ephemeral clusters of up to O(100k) cores to process tasks requiring quick turnaround. Amazon Web Services has been exploited for the successful physics validation of the Athena simulation software on ARM processors. We have also set up an interactive facility for physics analysis allowing endusers to spin up private, on-demand clusters for parallel computing with up to 4 000 cores, or run GPU enabled notebooks and jobs for machine learning applications. The success of the proof of concept phases has led to the extension of the Google Cloud project, where ATLAS will study the total cost of ownership of a production cloud site during 15 months with 10k cores on average, fully integrated with distributed grid computing resources and continue the R&D projects.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

P SI4 1.4: Open-source software for high-throughput quantum chemistry

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree–Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4 's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. We announce a rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Real‐time XFEL data analysis at SLAC and NERSC: A trial run of nascent exascale experimental data analysis

X‐ray scattering experiments using free electron lasers (XFELs) are a powerful tool to determine the molecular structure and function of unknown samples (such as COVID‐19 viral proteins). XFEL experiments are a challenge to computing in two ways: (i) due to the high cost of running XFELs, a fast turnaround time from data acquisition to data analysis is essential to make informed decisions on experimental protocols; (ii) data‐collection rates are growing exponentially, requiring new scalable algorithms. Here we report our experiences analyzing data from two experiments at the Linac Coherent Light Source (LCLS) during September 2020. Raw data were analyzed on NERSC's Cori XC40 system, using the Superfacility paradigm: our workflow automatically moves raw data between LCLS and NERSC, where it is analyzed using the software package CCTBX. We achieved real time data analysis with a turnaround time from data acquisition to full molecular reconstruction in as little as 10 min—sufficient time for the experiment's operators to make informed decisions. By hosting the data analysis on Cori, and by automating LCLS‐NERSC interoperability, we achieved a data analysis rate which matches the data acquisition rate. Completing data analysis within 10 min is a first for XFEL experiments and an important milestone if we are to keep up with data‐collection trends.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Fast tree-based algorithms for DBSCAN for low-dimensional data on GPUs

DBSCAN is a well-known density-based clustering algorithm to discover arbitrary shape clusters. While conceptually simple in serial, the algorithm is challenging to efficiently parallelize on manycore GPU architectures. Common pitfalls, such as asynchronous range query calls, result in high thread execution divergence in many implementations. In this paper, we propose a new framework for GPU-accelerated DBSCAN, and describe two tree-based algorithms within that framework. Both algorithms fuse the search for neighbors with updating cluster information, but differ in their treatment of dense regions of the data. We show that the time taken to compute clusters is at most twice that of determination of the neighbors. We compare the proposed algorithms with existing CPU and GPU implementations, and demonstrate their competitiveness and performance using a fast traversal structure (bounding volume hierarchy) for low dimensional data. We also show that the memory usage can be reduced by processing object neighbors dynamically without storing them.

Prokopenko, Andrey↗
DOE OSTI2018

HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

Biological networks capture structural or functional properties of relevant entities such as molecules, proteins or genes. Characteristic examples are gene expression networks or protein–protein interaction networks, which hold information about functional affinities or structural similarities. Such networks have been expanding in size due to increasing scale and abundance of biological data. While various clustering algorithms have been proposed to find highly connected regions, Markov Clustering (MCL) has been one of the most successful approaches to cluster sequence similarity or expression networks. Despite its popularity, MCL’s scalability to cluster large datasets still remains a bottleneck due to high running times and memory demands. In this paper, we present High-performance MCL (HipMCL), a parallel implementation of the original MCL algorithm that can run on distributed-memory computers. We show that HipMCL can efficiently utilize 2000 compute nodes and cluster a network of ~70 million nodes with ~68 billion edges in ~2.4 h. By exploiting distributed-memory environments, HipMCL clusters large-scale networks several orders of magnitude faster than MCL and enables clustering of even bigger networks. Finally, HipMCL is based on MPI and OpenMP and is freely available under a modified BSD license.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Cross-scale efficient tensor contractions for coupled cluster computations through multiple programming model backends

Coupled-cluster methods provide highly accurate models of molecular structure through explicit numerical calculation of tensors representing the correlation between electrons. These calculations are dominated by a sequence of tensor contractions, motivating the development of numerical libraries for such operations. While based on matrix–matrix multiplication, these libraries are specialized to exploit symmetries in the molecular structure and in electronic interactions, and thus reduce the size of the tensor representation and the complexity of contractions. The resulting algorithms are irregular and their parallelization has been previously achieved via the use of dynamic scheduling or specialized data decompositions. We introduce our efforts to extend the Libtensor framework to work in the distributed memory environment in a scalable and energy-efficient manner. We achieve up to 240× speedup compared with the optimized shared memory implementation of Libtensor. We attain scalability to hundreds of thousands of compute cores on three distributed-memory architectures (Cray XC30 and XC40, and IBM Blue Gene/Q), and on a heterogeneous GPU-CPU system (Cray XK7). As the bottlenecks shift from being compute-bound DGEMM's to communication-bound collectives as the size of the molecular system scales, we adopt two radically different parallelization approaches for handling load-imbalance, tasking and bulk synchronous models. Nevertheless, we preserve a unified interface to both programming models to maintain the productivity of computational quantum chemists.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2016

Cross-scale Efficient Tensor Contractions for Coupled Cluster Computations Through Multiple Programming Model Backends

Coupled-cluster methods provide highly accurate models of molecular structure by explicit numerical calculation of tensors representing the correlation between electrons. These calculations are dominated by a sequence of tensor contractions, motivating the development of numerical libraries for such operations. While based on matrix-matrix multiplication, these libraries are specialized to exploit symmetries in the molecular structure and in electronic interactions, and thus reduce the size of the tensor representation and the complexity of contractions. The resulting algorithms are irregular and their parallelization has been previously achieved via the use of dynamic scheduling or specialized data decompositions. We introduce our efforts to extend the Libtensor framework to work in the distributed memory environment in a scalable and energy efficient manner. We achieve up to 240 speedup compared with the best optimized shared memory implementation. We attain scalability to hundreds of thousands of compute cores on three distributed-memory architectures, (Cray XC30&XC40, BlueGene/Q), and on a heterogeneous GPU-CPU system (Cray XK7). As the bottlenecks shift from being compute-bound DGEMM's to communication-bound collectives as the size of the molecular system scales, we adopt two radically different parallelization approaches for handling load-imbalance. Nevertheless, we preserve a uni ed interface to both programming models to maintain the productivity of computational quantum chemists.

74 ATOMIC AND MOLECULAR PHYSICS↗