# Publications - Paolo Bientinesi

### Submitted Papers

**HPTT: A High-Performance Tensor Transposition C++ Library**Submitted to the ARRAY 2017, April 2017.abstractwebPDFRecently we presented TTC, a domain-specific compiler for tensor transpositions. Despite the fact that the performance of the generated code is nearly optimal, due to its offline nature, TTC cannot be utilized in all the application codes in which the tensor sizes and the necessary tensor permutations are determined at runtime. To overcome this limitation, we introduce the open-source C++ library High-Performance Tensor Transposition (HPTT). Similar to TTC, HPTT incorporates optimizations such as blocking, multi-threading, and explicit vectorization; furthermore it decomposes any transposition into multiple loops around a so called micro-kernel. This modular design—inspired by BLIS—makes HPTT easy to port to different architectures, by only replacing the hand-vectorized micro-kernel (e.g., a 4x4 transpose). HPTT also offers an optional autotuning framework—guided by a performance model—that explores a vast search space of implementations at runtime (similar to FFTW). Across a wide range of different tensor transpositions and architectures (e.g., Intel Ivy Bridge, ARMv7, IBM Power7), HPTT attains a bandwidth comparable to that of SAXPY, and yields remarkable speedups over Eigen’s tensor transposition implementation. Most importantly, the integration of HPTT into the Cyclops Tensor Framework (CTF) improves the overall performance of tensor contractions by up to 3.1x.**Large Scale Parallel Computations in R through Elemental**Journal of Statistical Software, October 2016.abstractwebPDFEven though in recent years the scale of statistical analysis problems has increased tremendously, many statistical software tools are still limited to single-node computations. However, statistical analyses are largely based on dense linear algebra operations, which have been deeply studied, optimized and parallelized in the high-performance-computing community. To make high-performance distributed computations available for statistical analysis, and thus enable large scale statistical computations, we introduce RElem, an open source package that integrates the distributed dense linear algebra library Elemental into R. While on the one hand, RElem provides direct wrappers of Elemental's routines, on the other hand, it overloads various operators and functions to provide an entirely native R experience for distributed computations. We showcase how simple it is to port existing R programs to Relem and demonstrate that Relem indeed allows to scale beyond the single-node limitation of R with the full performance of Elemental without any overhead.**Accelerating scientific codes by performance and accuracy modeling**Journal of Scientific Computing, August 2016.abstractPDFScientific software is often driven by multiple parameters that affect both accuracy and performance. Since finding the optimal configuration of these parameters is a highly complex task, it extremely common that the software is used suboptimally. In a typical scenario, accuracy requirements are imposed, and attained through suboptimal performance. In this paper, we present a methodology for the automatic selection of parameters for simulation codes, and a corresponding prototype tool. To be amenable to our methodology, the target code must expose the parameters affecting accuracy and performance, and there must be formulas available for error bounds and computational complexity of the underlying methods. As a case study, we consider the particle-particle particle-mesh method (PPPM) from the LAMMPS suite for molecular dynamics, and use our tool to identify configurations of the input parameters that achieve a given accuracy in the shortest execution time. When compared with the configurations suggested by expert users, the parameters selected by our tool yield reductions in the time-to-solution ranging between 10% and 60%. In other words, for the typical scenario where a fixed number of core-hours are granted and simulations of a fixed number of timesteps are to be run, usage of our tool may allow up to twice as many simulations. While we develop our ideas using LAMMPS as computational framework and use the PPPM method for dispersion as case study, the methodology is general and valid for a range of software tools and methods.**Design of a high-performance GEMM-like Tensor-Tensor Multiplication**July 2016.

ACM Transactions on Mathematical Software (TOMS).abstractPDFWe present ''GEMM-like Tensor-Tensor multiplication'' (GETT), a novel approach to tensor contractions that mirrors the design of a high-performance general matrix-matrix multiplication (GEMM). The critical insight behind GETT is the identification of three index sets, involved in the tensor contraction, which enable us to systematically reduce an arbitrary tensor contraction to loops around a highly tuned ''macro-kernel''. This macro-kernel operates on suitably prepared (''packed'') sub-tensors that reside in a specified level of the cache hierarchy. In contrast to previous approaches to tensor contractions, GETT exhibits desirable features such as unit-stride memory accesses, cache-awareness, as well as full vectorization, without requiring auxiliary memory. To compare our technique with other modern tensor contractions, we integrate GETT alongside the so called Transpose-Transpose-GEMM-Transpose and Loops-over-GEMM approaches into an open source ''Tensor Contraction Code Generator'' (TCCG). The performance results for a wide range of tensor contractions suggest that GETT has the potential of becoming the method of choice: While GETT exhibits excellent performance across the board, its effectiveness for bandwidth-bound tensor contractions is especially impressive, outperforming existing approaches by up to 12.3x. More precisely, GETT achieves speedups of up to 1.42x over an equivalent-sized GEMM for bandwidth-bound tensor contractions while attaining up to 91.3% of peak floating-point performance for compute-bound tensor contractions.**TTC: A high-performance Compiler for Tensor Transpositions**ACM Transactions on Mathematical Software (TOMS), March 2016.abstractPDFWe present TTC, an open-source parallel compiler for multidimensional tensor transpositions. In order to generate high-performance C++ code, TTC explores a number of optimizations, including software prefetching, blocking, loop-reordering, and explicit vectorization. To evaluate the performance of multidimensional transpositions across a range of possible use-cases, we also release a benchmark covering arbitrary transpositions of up to six dimensions. Performance results show that the routines generated by TTC achieve close to peak memory bandwidth on both the Intel Haswell and the AMD Steamroller architectures, and yield significant performance gains over modern compilers. By implementing a set of pruning heuristics, TTC allows users to limit the number of potential solutions; this option is especially useful when dealing with high-dimensional tensors, as the search space might become prohibitively large. Experiments indicate that when only 100 potential solutions are considered, the resulting performance is about 99% of that achieved with exhaustive search.

### Journal Articles

**Recursive Algorithms for Dense Linear Algebra: The ReLAPACK Collection**ACM Transactions on Mathematical Software (TOMS), March 2017.

Accepted.@article{Peise2017:728, author = "Elmar Peise and Paolo Bientinesi", title = "Recursive Algorithms for Dense Linear Algebra: The ReLAPACK Collection", journal = "ACM Transactions on Mathematical Software (TOMS)", year = 2017, month = mar, note = "Accepted", institution = "AICES, RWTH Aachen University", url = "http://arxiv.org/pdf/1602.06763v1" }

abstractwebPDFbibtexTo exploit both memory locality and the full performance potential of highly tuned kernels, dense linear algebra libraries such as LAPACK commonly implement operations as blocked algorithms. However, to achieve next-to-optimal performance with such algorithms, significant tuning is required. On the other hand, recursive algorithms are virtually tuning free, and yet attain similar performance. In this paper, we first analyze and compare blocked and recursive algorithms in terms of performance, and then introduce ReLAPACK, an open-source library of recursive algorithms to seamlessly replace most of LAPACK's blocked algorithms. In many scenarios, ReLAPACK clearly outperforms reference LAPACK, and even improves upon the performance of optimizes libraries.**High-performance generation of the Hamiltonian and Overlap matrices in FLAPW methods**Computer Physics Communications, Volume 211, pp. 61 - 72, February 2017.

High Performance Computing for Advanced Modeling and Simulation of Materials.@article{Di_Napoli2017:318, author = "Edoardo {Di Napoli} and Elmar Peise and Markus Hrywniak and Paolo Bientinesi", title = "High-performance generation of the Hamiltonian and Overlap matrices in FLAPW methods", journal = "Computer Physics Communications", year = 2017, volume = 211, pages = "61 - 72", month = feb, note = "High Performance Computing for Advanced Modeling and Simulation of Materials", url = "http://arxiv.org/pdf/1602.06589v2" }

abstractwebPDFbibtexOne of the greatest effort of computational scientists is to translate the mathematical model describing a class of physical phenomena into large and complex codes. Many of these codes face the difficulty of implementing the mathematical operations in the model in terms of low level optimized kernels offering both performance and portability. Legacy codes suffers from the additional curse of rigid design choices based on outdated performance metrics (e.g. minimization of memory footprint). Using a representative code from the Materials Science community, we propose a methodology to restructure the most expensive operations in terms of an optimized combination of dense linear algebra kernels. The resulting algorithm guarantees an increased performance and an extended life span of this code enabling larger scale simulations.**Large-Scale Linear Regression: Development of High-Performance Routines**Applied Mathematics and Computation, Volume 275, pp. 411-421, 15 February 2016.@article{Frank2016:90, author = "Alvaro Frank and Diego Fabregat-Traver and Paolo Bientinesi", title = "Large-Scale Linear Regression: Development of High-Performance Routines", journal = "Applied Mathematics and Computation", year = 2016, volume = 275, pages = "411-421", month = feb, url = "http://arxiv.org/abs/1504.07890" }

abstractwebPDFbibtexIn statistics, series of ordinary least squares problems (OLS) are used to study the linear correlation among sets of variables of interest; in many studies, the number of such variables is at least in the millions, and the corresponding datasets occupy terabytes of disk space. As the availability of large-scale datasets increases regularly, so does the challenge in dealing with them. Indeed, traditional solvers---which rely on the use of ``black-box'' routines optimized for one single OLS---are highly inefficient and fail to provide a viable solution for big-data analyses. As a case study, in this paper we consider a linear regression consisting of two-dimensional grids of related OLS problems that arise in the context of genome-wide association analyses, and give a careful walkthrough for the development of {\sc ols-grid}, a high-performance routine for shared-memory architectures; analogous steps are relevant for tailoring OLS solvers to other applications. In particular, we first illustrate the design of efficient algorithms that exploit the structure of the OLS problems and eliminate redundant computations; then, we show how to effectively deal with datasets that do not fit in main memory; finally, we discuss how to cast the computation in terms of efficient kernels and how to achieve scalability. Importantly, each design decision along the way is justified by simple performance models. {\sc ols-grid} enables the solution of $10^{11}$ correlated OLS problems operating on terabytes of data in a matter of hours.**High Performance Solutions for Big-data GWAS**Parallel Computing, Volume 42, pp. 75 - 87, February 2015.

Special issue on Parallelism in Bioinformatics.@article{Peise2015:754, author = "Elmar Peise and Diego Fabregat-Traver and Paolo Bientinesi", title = "High Performance Solutions for Big-data GWAS", journal = "Parallel Computing", year = 2015, volume = 42, pages = "75 - 87", month = feb, note = "Special issue on Parallelism in Bioinformatics", url = "http://arxiv.org/pdf/1403.6426v1" }

abstractwebPDFbibtexIn order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which exceed the main memory of contemporary computers, one faces two distinct challenges: 1) Millions of polymorphisms and thousands of phenotypes come at the cost of hundreds of gigabytes of data, which can only be kept in secondary storage; 2) the relatedness of the test population is represented by a relationship matrix, which, for large populations, can only fit in the combined main memory of a distributed architecture. In this paper, by using distributed resources such as Cloud or clusters, we address both challenges: The genotype and phenotype data is streamed from secondary storage using a double buffering technique, while the relationship matrix is kept across the main memory of a distributed memory system. With the help of these solutions, we develop separate algorithms for studies involving only one or a multitude of traits. We show that these algorithms sustain high-performance and allow the analysis of enormous datasets.**Big-Data, High-Performance, Mixed Models Based Genome-Wide Association Analysis**F1000Research, Volume 3(200), August 2014.

Open peer reviews.@article{Fabregat-Traver2014:430, author = "Diego Fabregat-Traver and Sodbo Sharapov and {Caroline } Hayward and {Igor } Rudan and {Harry } Campbell and {Yurii S.} Aulchenko and Paolo Bientinesi", title = "Big-Data, High-Performance, Mixed Models Based Genome-Wide Association Analysis", journal = "F1000Research", year = 2014, volume = 3, number = 200, month = aug, note = "Open peer reviews", howpublished = "F1000Research" }

abstractwebbibtexTo raise the power of genome-wide association studies (GWAS) and avoid false-positive results, one can rely on mixed model based tests. When large samples are used, and especially when multiple traits are to be studied in the omics context, this approach becomes computationally unmanageable. Here, we develop new methods for analysis of arbitrary number of traits, and demonstrate that for the analysis of single-trait and multiple-trait GWAS, different methods are optimal. We implement these methods in a high-performance computing framework that uses state-of-the-art linear algebra kernels, incorporates optimizations, and avoids redundant computations, thus increasing throughput while reducing memory usage and energy consumption. We show that compared to existing libraries, the OmicABEL software---which implements these methods---achieves speed-ups of up to three orders of magnitude. As a consequence, samples of tens of thousands of individuals as well as samples phenotyped for many thousands of ''omics'' measurements can be analyzed for association with millions of omics features without the need for super-computers.**Computing Petaflops over Terabytes of Data: The Case of Genome-Wide Association Studies**ACM Transactions on Mathematical Software (TOMS), Volume 40(4), pp. 27:1-27:22, June 2014.@article{Fabregat-Traver2014:798, author = "Diego Fabregat-Traver and Paolo Bientinesi", title = "Computing Petaflops over Terabytes of Data: The Case of Genome-Wide Association Studies", journal = "ACM Transactions on Mathematical Software (TOMS)", year = 2014, volume = 40, number = 4, pages = "27:1--27:22", month = jun, url = "http://arxiv.org/pdf/1210.7683v1" }

abstractwebPDFbibtexIn many scientific and engineering applications one has to solve not one but a sequence of instances of the same problem. Often times, the problems in the sequence are linked in a way that allows intermediate results to be reused. A characteristic example for this class of applications is given by the Genome-Wide Association Studies (GWAS), a widely spread tool in computational biology. GWAS entails the solution of up to trillions ($10^{12}$) of correlated generalized least-squares problems, posing a daunting challenge: the performance of petaflops ($10^{15}$ floating-point operations) over terabytes of data residing on disk. In this paper, we design an efficient algorithm for performing GWAS on multi-core architectures. This is accomplished in three steps. First, we show how to exploit the relation among successive problems, thus reducing the overall computational complexity. Then, through an analysis of the required data transfers, we identify how to eliminate any overhead due to input/output operations. Finally, we study how to decompose computation into tasks to be distributed among the available cores, to attain high performance and scalability. We believe the paper contributes valuable guidelines of general applicability for computational scientists on how to develop and optimize numerical algorithms.**Towards an Efficient Use of the BLAS Library for Multilinear Tensor Contractions**Applied Mathematics and Computation, Volume 235, pp. 454-468, May 2014.@article{Di_Napoli2014:210, author = "Edoardo {Di Napoli} and Diego Fabregat-Traver and Gregorio Quintana-Orti and Paolo Bientinesi", title = "Towards an Efficient Use of the BLAS Library for Multilinear Tensor Contractions", journal = "Applied Mathematics and Computation", year = 2014, volume = 235, pages = "454--468", month = may, url = "http://arxiv.org/pdf/1307.2100" }

abstractwebPDFbibtexMathematical operators whose transformation rules constitute the building blocks of a multi-linear algebra are widely used in physics and engineering applications where they are very often represented as tensors. In the last century, thanks to the advances in tensor calculus, it was possible to uncover new research fields and make remarkable progress in the existing ones, from electromagnetism to the dynamics of fluids and from the mechanics of rigid bodies to quantum mechanics of many atoms. By now, the formal mathematical and geometrical properties of tensors are well defined and understood; conversely, in the context of scientific and high-performance computing, many tensor-related problems are still open. In this paper, we address the problem of efficiently computing contractions among two tensors of arbitrary dimension by using kernels from the highly optimized BLAS library. In particular, we establish precise conditions to determine if and when GEMM, the kernel for matrix products, can be used. Such conditions take into consideration both the nature of the operation and the storage scheme of the tensors, and induce a classification of the contractions into three groups. For each group, we provide a recipe to guide the users towards the most effective use of BLAS.**Solving Sequences of Generalized Least-Squares Problems on Multi-threaded Architectures**Applied Mathematics and Computation, Volume 234, pp. 606-617, May 2014.@article{Fabregat-Traver2014:430, author = "Diego Fabregat-Traver and {Yurii S.} Aulchenko and Paolo Bientinesi", title = "Solving Sequences of Generalized Least-Squares Problems on Multi-threaded Architectures", journal = "Applied Mathematics and Computation", year = 2014, volume = 234, pages = "606--617", month = may, url = "http://arxiv.org/pdf/1210.7325v1" }

abstractwebPDFbibtexGeneralized linear mixed-effects models in the context of genome-wide association studies (GWAS) represent a formidable computational challenge: the solution of millions of correlated generalized least-squares problems, and the processing of terabytes of data. We present high performance in-core and out-of-core shared-memory algorithms for GWAS: By taking advantage of domain-specific knowledge, exploiting multi-core parallelism, and handling data efficiently, our algorithms attain unequalled performance. When compared to GenABEL, one of the most widely used libraries for GWAS, on a 12-core processor we obtain 50-fold speedups. As a consequence, our routines enable genome studies of unprecedented size.**Improved Accuracy and Parallelism for MRRR-based Eigensolvers**SIAM Journal of Scientific Computing, Volume 36(2), pp. 240-263, April 2014.@article{Petschow2014:60, author = "Matthias Petschow and {Enrique S.} Quintana-Orti and Paolo Bientinesi", title = "Improved Accuracy and Parallelism for MRRR-based Eigensolvers", journal = "SIAM Journal of Scientific Computing", year = 2014, volume = 36, number = 2, pages = "240--263", month = apr, url = "http://arxiv.org/pdf/1304.1864v3" }

abstractwebPDFbibtexThe real symmetric tridiagonal eigenproblem is of outstanding importance in numerical computations; it arises frequently as part of eigensolvers for standard and generalized dense Hermitian eigenproblems that are based on a reduction to real tridiagonal form. For its solution, the algorithm of Multiple Relatively Robust Representations (MRRR) is among the fastest methods. Although fast, the solvers based on MRRR do not deliver the same accuracy as competing methods like Divide & Conquer or the QR algorithm. In this paper, we demonstrate that the use of mixed precisions leads to improved accuracy of MRRR-based eigensolvers with limited or no performance penalty. As a result, we obtain eigensolvers that are not only equally or more accurate than the best available methods, but also - under most circumstances - faster and more scalable than the competition.**Multilevel Summation for Dispersion: A Linear-Time Algorithm for 1/r^6 Potentials**Journal of Chemical Physics, Volume 140, pp. 024105, January 2014.@article{Tameling2014:590, author = "Daniel Tameling and Paul Springer and Paolo Bientinesi and {Ahmed E.} Ismail", title = "Multilevel Summation for Dispersion: A Linear-Time Algorithm for 1/r^6 Potentials", journal = "Journal of Chemical Physics", year = 2014, volume = 140, pages = 24105, month = jan, url = "http://arxiv.org/abs/1308.4005" }

abstractwebPDFbibtexThe multilevel summation (MLS) method was developed to evaluate long-range interactions in molecular dynamics (MD) simulations. MLS was initially introduced for Coulombic potentials; we have extended this method to dispersion interactions. While formally short-ranged, for an accurate calculation of forces and energies in cases such as in interfacial systems, dispersion potentials require long-range methods. Since long-range solvers tend to dominate the time needed to perform MD calculations, increasing their performance is of vital importance. The MLS method offers some significant advantages when compared to mesh-based Ewald methods like the particle-particle particle-mesh and particle mesh Ewald methods. Unlike mesh-based Ewald methods, MLS does not use fast Fourier transforms and is thus not limited by communication and bandwidth concerns. In addition, it scales linearly in the number of particles, as compared to the O(N log N) complexity of the mesh-based Ewald methods. While the structure of the MLS method is invariant for different potentials, every algorithmic step had to be adapted to accommodate the 1/r^6 form of the dispersion interactions. In addition, we have derived error bounds, similar to those obtained by Hardy for the electrostatic MLS. Using a prototype implementation, we can already demonstrate the linear scaling of the MLS method for dispersion, and present results establishing the accuracy and efficiency of the method.**Application-tailored Linear Algebra Algorithms: A Search-Based Approach**International Journal of High Performance Computing Applications (IJHPCA), Volume 27(4), pp. 425 - 438, November 2013.@article{Fabregat-Traver2013:4, author = "Diego Fabregat-Traver and Paolo Bientinesi", title = "Application-tailored Linear Algebra Algorithms: A Search-Based Approach", journal = "International Journal of High Performance Computing Applications (IJHPCA)", year = 2013, volume = 27, number = 4, pages = "425 - 438", month = nov, url = "http://arxiv.org/abs/1211.5904" }

abstractwebPDFbibtexIn this paper, we tackle the problem of automatically generating algorithms for linear algebra operations by taking advantage of problem-specific knowledge. In most situations, users possess much more information about the problem at hand than what current libraries and computing environments accept; evidence shows that if properly exploited, such information leads to uncommon/unexpected speedups. We introduce a knowledge-aware linear algebra compiler that allows users to input matrix equations together with properties about the operands and the problem itself; for instance, they can specify that the equation is part of a sequence, and how successive instances are related to one another. The compiler exploits all this information to guide the generation of algorithms, to limit the size of the search space, and to avoid redundant computations. We applied the compiler to equations arising as part of sensitivity and genome studies; the algorithms produced exhibit, respectively, 100- and 1000-fold speedups.**Dissecting the FEAST Algorithm for Generalized Eigenproblems**Journal of Computational and Applied Mathematics, Volume 244, pp. 1-9, May 2013.@article{Kraemer2013:188, author = "Lukas Kraemer and Edoardo {Di Napoli} and {Martin } Galgon and Bruno Lang and Paolo Bientinesi", title = "Dissecting the FEAST Algorithm for Generalized Eigenproblems", journal = "Journal of Computational and Applied Mathematics", year = 2013, volume = 244, pages = "1--9", month = may, url = "http://arxiv.org/abs/1204.1726" }

abstractwebPDFbibtexWe analyze the FEAST method for computing selected eigenvalues and eigenvectors of large sparse matrix pencils. After establishing the close connection between FEAST and the well-known Rayleigh-Ritz method, we identify several critical issues that influence convergence and accuracy of the solver: the choice of the starting vector space, the stopping criterion, how the inner linear systems impact the quality of the solution, and the use of FEAST for computing eigenpairs from multiple intervals. We complement the study with numerical examples, and hint at possible improvements to overcome the existing problems.**High-Performance Solvers for Dense Hermitian Eigenproblems**SIAM Journal on Scientific Computing, Volume 35(1), pp. C1-C22, January 2013.@article{Petschow2013:208, author = "Matthias Petschow and Elmar Peise and Paolo Bientinesi", title = "High-Performance Solvers for Dense Hermitian Eigenproblems", journal = "SIAM Journal on Scientific Computing", year = 2013, volume = 35, number = 1, pages = "C1-C22", month = jan, url = "http://arxiv.org/pdf/1205.2107.pdf" }

abstractwebPDFbibtexWe introduce a new collection of solvers - subsequently called EleMRRR - for large-scale dense Hermitian eigenproblems. EleMRRR solves various types of problems: generalized, standard, and tridiagonal eigenproblems. Among these, the last is of particular importance as it is a solver on its own right, as well as the computational kernel for the first two; we present a fast and scalable tridiagonal solver based on the Algorithm of Multiple Relatively Robust Representations - referred to as PMRRR. Like the other EleMRRR solvers, PMRRR is part of the freely available Elemental library, and is designed to fully support both message-passing (MPI) and multithreading parallelism (SMP). As a result, the solvers can equally be used in pure MPI or in hybrid MPI-SMP fashion. We conducted a thorough performance study of EleMRRR and ScaLAPACK's solvers on two supercomputers. Such a study, performed with up to 8,192 cores, provides precise guidelines to assemble the fastest solver within the ScaLAPACK framework; it also indicates that EleMRRR outperforms even the fastest solvers built from ScaLAPACK's components.**Modeling Performance through Memory-Stalls**ACM SIGMETRICS Performance Evaluation Review, Volume 40(2), pp. 86-91, October 2012.@article{Iakymchuk2012:120, author = "Roman Iakymchuk and Paolo Bientinesi", title = "Modeling Performance through Memory-Stalls", journal = "ACM SIGMETRICS Performance Evaluation Review", year = 2012, volume = 40, number = 2, pages = "86--91", month = oct, publisher = "ACM", address = "New York, NY, USA", url = "http://hpac.rwth-aachen.de/~pauldj/pubs/pmbs.pdf" }

abstractwebPDFbibtexWe aim at modeling the performance of linear algebra algorithms without executing either the algorithms or any parts of them. The performance of an algorithm can be expressed in terms of the time spent on CPU execution and memory-stalls. The main concern of this paper is to build analytical models to accurately predict memory-stalls. The scenario in which data resides in the L2 cache is considered; with this assumption, only L1 cache misses occur. We construct an analytical formula for modeling the L1 cache misses of fundamental linear algebra operations such as those included in the Basic Linear Algebra Subprograms (BLAS) library. The number of cache misses occurring in higher-level algorithms--like a matrix factorization--is then predicted by combining the models for the appropriate BLAS subroutines. As case studies, we consider the LU factorization and GER--a BLAS operation and a building block for the LU factorization. We validate the models on both Intel and AMD processors, attaining remarkably accurate performance predictions.**Correlations in Sequences of Generalized Eigenproblems Arising in Density Functional Theory**Computer Physics Communications (CPC), Volume 183(8), pp. 1674-1682, August 2012.@article{Di_Napoli2012:160, author = "Edoardo {Di Napoli} and Stefan Bluegel and Paolo Bientinesi", title = "Correlations in Sequences of Generalized Eigenproblems Arising in Density Functional Theory", journal = "Computer Physics Communications (CPC)", year = 2012, volume = 183, number = 8, pages = "1674-1682", month = aug, url = "http://arxiv.org/pdf/1108.2594v1" }

abstractwebPDFbibtexDensity Functional Theory (DFT) is one of the most used {\em ab initio} theoretical frameworks in materials science. It derives the ground state properties of multi-atomic ensembles directly from the computation of their one-particle density \nr . In DFT-based simulations the solution is calculated through a chain of successive self-consistent cycles; in each cycle a series of coupled equations (Kohn-Sham) translates to a large number of generalized eigenvalue problems whose eigenpairs are the principal means for expressing \nr. A simulation ends when \nr\ has converged to the solution within the required numerical accuracy. This usually happens after several cycles, resulting in a process calling for the solution of many sequences of eigenproblems. In this paper, the authors report evidence showing unexpected correlations between adjacent eigenproblems within each sequence and suggest the investigation of an alternative computational approach: information extracted from the simulation at one step of the sequence is used to compute the solution at the next step. The implications are multiple: from increasing the performance of material simulations, to the development of a mixed direct-iterative solver, to modifying the mathematical foundations of the DFT computational paradigm in use, thus opening the way to the investigation of new materials.**Solving Dense Generalized Eigenproblems on Multi-Threaded Architectures**Applied Mathematics and Computation, Volume 218(22), pp. 11279-11289, July 2012.@article{Aliaga2012:420, author = "Jose' Aliaga and Paolo Bientinesi and Davor Davidovic and Edoardo {Di Napoli} and Francisco Igual and {Enrique S.} Quintana-Orti", title = "Solving Dense Generalized Eigenproblems on Multi-Threaded Architectures", journal = "Applied Mathematics and Computation", year = 2012, volume = 218, number = 22, pages = "11279-11289", month = jul, url = "http://arxiv.org/pdf/1111.6374v1" }

abstractwebPDFbibtexWe compare two approaches to compute a portion of the spectrum of dense symmetric definite generalized eigenproblems: one is based on the reduction to tridiagonal form, and the other on the Krylov-subspace iteration. Two large-scale applications, arising in molecular dynamics and materials science, are employed to investigate the contributions of the application, architecture, and parallelism of the method to the performance of the solvers. The experimental results on a state-of-the-art 8-core platform, equipped with a graphics processing unit (GPU), reveal that in real applications, iterative Krylov-subspace methods can be a competitive approach also for the solution of dense problems.**Deriving Dense Linear Algebra Libraries**Formal Aspects of Computing, pp. 1-13, January 2012.@article{Bientinesi2012:978, author = "Paolo Bientinesi and {John A.} Gunnels and {Margaret E.} Myers and {Enrique S.} Quintana-Orti and Tyler Rhodes and Robert {van de Geijn} and Field {Van Zee}", title = "Deriving Dense Linear Algebra Libraries", journal = "Formal Aspects of Computing", year = 2012, pages = "1--13", month = jan, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/FormAspComp.pdf" }

abstractwebPDFbibtexStarting in the late 1960s computer scientists including Dijkstra and Hoare advocated goal-oriented program- ming and the formal derivation of algorithms. The chief impediment to realizing this for loop-based programs was that a priori determination of loop-invariants, a prerequisite for developing loops, was a task too complex for any but the simplest of operations. Around 2000, these techniques were for the first time successfully applied to the domain of high-performance dense linear algebra libraries. This has led to a multitude of papers, mostly published in the ACM Transactions for Mathematical Software, as well as a system for the mechanical derivation of algorithms and a high-performance linear algebra library, libflame, that includes more than a thousand vari- ants of algorithms for more than a hundred linear algebra operations. To our knowledge, this success story has unfolded with limited awareness on the part the formal methods community. This paper reports on ten years of experience and is meant to raise that awareness.**MR3-SMP: A Symmetric Tridiagonal Eigensolver for Multi-Core Architectures**Parallel Computing, Volume 37(12), December 2011.@article{Petschow2011:254, author = "Matthias Petschow and Paolo Bientinesi", title = "MR3-SMP: A Symmetric Tridiagonal Eigensolver for Multi-Core Architectures", journal = "Parallel Computing", year = 2011, volume = 37, number = 12, month = dec, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/MR3-SMP-TR.pdf" }

abstractwebPDFbibtexThe computation of eigenvalues and eigenvectors of symmetric tridiagonal matrices arises frequently in applications; often as one of the steps in the solution of Hermitian and symmetric eigenproblems. While several accurate and efficient methods for the tridiagonal eigenproblem exist, their corresponding implementations usually target uni-processors or large distributed memory systems. Our new eigensolver MR3-SMP is instead specifically designed for multi-core and many-core general purpose processors, which today have effectively replaced uni-processors. We show that in most cases MR3-SMP is faster and achieves better speedups than state-of-the-art eigensolvers for uni-processors and distributed-memory systems.**Condensed Forms for the Symmetric Eigenvalue Problem on Multi-threaded Architectures**Concurrency and Computation: Practice and Experience, Volume 23(7), May 2011.@article{Bientinesi2011:754, author = "Paolo Bientinesi and Francisco Igual and Daniel Kressner and Matthias Petschow and {Enrique S.} Quintana-Orti", title = "Condensed Forms for the Symmetric Eigenvalue Problem on Multi-threaded Architectures", journal = "Concurrency and Computation: Practice and Experience", year = 2011, volume = 23, number = 7, month = may, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/red-multi-TR.pdf" }

abstractwebPDFbibtexWe investigate the performance of the routines in LAPACK and the Successive Band Reduction (SBR) toolbox for the reduction of a dense matrix to tridiagonal form, a crucial preprocessing stage in the solution of the symmetric eigenvalue problem, on general-purpose multi-core processors. In response to the advances of hardware accelerators, we also modify the code in the SBR toolbox to accelerate the computation by off-loading a significant part of the operations to a graphics processor (GPU). The performance results illustrate the parallelism and scalability of these algorithms on current high-performance multi-core and many-core architectures.**Goal-Oriented and Modular Stability Analysis**SIAM Journal on Matrix Analysis and Applications, Volume 32(1), pp. 286 - 308, March 2011.@article{Bientinesi2011:810, author = "Paolo Bientinesi and Robert {van de Geijn}", title = "Goal-Oriented and Modular Stability Analysis", journal = "SIAM Journal on Matrix Analysis and Applications", year = 2011, volume = 32, number = 1, pages = "286 -- 308", month = mar, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/Stability-74105.pdf" }

abstractwebPDFbibtexWe introduce a methodology for obtaining inventories of error results for families of numerical dense linear algebra algorithms. The approach for deriving the analyses is goal-oriented, systematic, and layered. The presentation places the analysis side-by-side with the algorithm so that it is obvious where roundoff error is introduced. The approach supports the analysis of more complex algorithms, such as the blocked LU factorization. For this operation we derive a tighter error bound than has been previously reported in the literature.**Sparse Direct Factorizations through Unassembled Hyper-Matrices**Computer Methods in Applied Mechanics and Engineering, Volume 199(9), pp. 430-438, January 2010.@article{Bientinesi2010:700, author = "Paolo Bientinesi and Victor Eijkhout and Kyungjoo Kim and Jason Kurtz and Robert {van de Geijn}", title = "Sparse Direct Factorizations through Unassembled Hyper-Matrices", journal = "Computer Methods in Applied Mechanics and Engineering", year = 2010, volume = 199, number = 9, pages = "430--438", month = jan, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/UHM-TR-09.pdf" }

abstractwebPDFbibtexWe set out to efficiently compute the solution of a sequence of linear systems Aixi = bi, where the matrix Ai is tightly related to matrix Ai-1. In the setting of an hp-adaptive Finite Element Method, the sequence of matrices Ai results from successive local refinements of the problem domain. At any step i > 1, a factorization already exists and it is the updated linear system relative to the refined mesh for which a factorization must be computed in the least amount of time. This observation holds the promise of a tremendous reduction in the cost of an individual refinement step. We argue that traditional matrix storage schemes, whether dense or sparse, are a bottleneck, limiting the potential efficiency of the solvers. We propose a new hierarchical data structure, the Unassembled Hyper-Matrix (UHM), which allows the matrix to be stored as a tree of unassembled element matrices, hierarchically ordered to mirror the refinement history of the physical domain. The factorization of such an UHM proceeds in terms of element matrices, only assembling nodes when they need to be eliminated. Efficiency comes in terms of both performance and space requirements.**Families of Algorithms Related to the Inversion of a Symmetric Positive Definite Matrix**ACM Transactions on Mathematical Software, Volume 35(1), July 2008.@article{Bientinesi2008:648, author = "Paolo Bientinesi and Brian Gunter and Robert {van de Geijn}", title = "Families of Algorithms Related to the Inversion of a Symmetric Positive Definite Matrix", journal = "ACM Transactions on Mathematical Software", year = 2008, volume = 35, number = 1, month = jul, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/SPDInv.pdf" }

abstractwebPDFbibtexWe study the high-performance implementation of the inversion of a Symmetric Positive Definite (SPD) matrix on architectures ranging from sequential processors to Symmetric MultiProcessors to distributed memory parallel computers. This inversion is traditionally accomplished in three Ã¢??sweepsÃ¢??: a Cholesky factorization of the SPD matrix, the inversion of the resulting triangular matrix, and finally the multiplication of the inverted triangular matrix by its own transpose. We state different algorithms for each of these sweeps as well as algorithms that compute the result in a single sweep. One algorithm outperforms the current ScaLAPACK implementation by 20-30 percent due to improved load-balance on a distributed memory architecture.**Scalable Parallelization of FLAME Code via the Workqueuing Model**ACM Transactions on Mathematical Software, Volume 34(2), March 2008.@article{Van_Zee2008:598, author = "Field {Van Zee} and Paolo Bientinesi and Tze {Meng Low} and Robert {van de Geijn}", title = "Scalable Parallelization of FLAME Code via the Workqueuing Model", journal = "ACM Transactions on Mathematical Software", year = 2008, volume = 34, number = 2, month = mar }

abstractwebbibtexWe discuss the OpenMP parallelization of linear algebra algorithms that are coded using the Formal Linear Algebra Methods Environment (FLAME) API. This API expresses algorithms at a higher level of abstraction, avoids the use loop and array indices, and represents these algorithms as they are formally derived and presented. We report on two implementations of the workqueuing model, neither of which requires the use of explicit indices to specify parallelism. The first implementation uses the experimental taskq pragma, which may influence the adoption of a similar construct into OpenMP 3.0. The second workqueuing implementation is domain-specific to FLAME but allows us to illustrate the benefits of sorting tasks according to their computational cost prior to parallel execution. In addition, we discuss how scalable parallelization of dense linear algebra algorithms via OpenMP will require a two-dimensional partitioning of operands much like a 2D data distribution is needed on distributed memory architectures. We illustrate the issues and solutions by discussing the parallelization of the symmetric rank-k update and report impressive performance on an SGI system with 14 Itanium2 processors.**Representing Linear Algebra Algorithms in Code: The FLAME APIs**ACM Transactions on Mathematical Software, Volume 31(1), March 2005.@article{Bientinesi2005:504, author = "Paolo Bientinesi and {Enrique S.} Quintana-Orti and Robert {van de Geijn}", title = "Representing Linear Algebra Algorithms in Code: The FLAME APIs", journal = "ACM Transactions on Mathematical Software", year = 2005, volume = 31, number = 1, month = mar, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/FLAME-API.pdf" }

abstractwebPDFbibtexIn this article, we present a number of Application Program Interfaces (APIs) for coding linear algebra algorithms. On the surface, these APIs for the MATLAB M-script and C programming languages appear to be simple, almost trivial, extensions of those languages. Yet with them, the task of programming and maintaining families of algorithms for a broad spectrum of linear algebra operations is greatly simplified. In combination with our Formal Linear Algebra Methods Environment (FLAME) approach to deriving such families of algorithms, dozens of algorithms for a single linear algebra operation can be derived, verified to be correct, implemented, and tested, often in a matter of minutes per algorithm. Since the algorithms are expressed in code much like they are explained in a classroom setting, these APIs become not just a tool for implementing libraries, but also a valuable tool for teaching the algorithms that are incorporated in the libraries. In combination with an extension of the Parallel Linear Algebra Package (PLAPACK) API, the approach presents a migratory path from algorithm to MATLAB implementation to high-performance sequential implementation to parallel implementation. Finally, the APIs are being used to create a repository of algorithms and implementations for linear algebra operations, the FLAME Interface REpository (FIRE), which already features hundreds of algorithms for dozens of commonly encountered linear algebra operations.**The Science of Deriving Dense Linear Algebra Algorithms**ACM Transactions on Mathematical Software, Volume 31(1), March 2005.@article{Bientinesi2005:460, author = "Paolo Bientinesi and {John A.} Gunnels and {Margaret E.} Myers and {Enrique S.} Quintana-Orti and Robert {van de Geijn}", title = "The Science of Deriving Dense Linear Algebra Algorithms", journal = "ACM Transactions on Mathematical Software", year = 2005, volume = 31, number = 1, month = mar, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/Recipe.ps" }

abstractwebPDFbibtexIn this article we present a systematic approach to the derivation of families of high-performance algorithms for a large set of frequently encountered dense linear algebra operations. As part of the derivation a constructive proof of the correctness of the algorithm is generated. The article is structured so that it can be used as a tutorial for novices. However, the method has been shown to yield new high-performance algorithms for well-studied linear algebra operations and should also be of interest to those who wish to produce best-in-class high-performance codes.**A Parallel Eigensolver for Dense Symmetric Matrices Based on Multiple Relatively Robust Representations**SIAM Journal on Scientific Computing, Volume 27(1), 2005.@article{Bientinesi2005:550, author = "Paolo Bientinesi and Inderjit Dhillon and Robert {van de Geijn}", title = "A Parallel Eigensolver for Dense Symmetric Matrices Based on Multiple Relatively Robust Representations", journal = "SIAM Journal on Scientific Computing", year = 2005, volume = 27, number = 1, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/PMR3.pdf" }

abstractwebPDFbibtexWe present a new parallel algorithm for the dense symmetric eigenvalue/eigenvector problem that is based upon the tridiagonal eigensolver, Algorithm MR3, recently developed by Dhillon and Parlett. Algorithm MR3 has a complexity of O(n2) operations for computing all eigenvalues and eigenvectors of a symmetric tridiagonal problem. Moreover the algorithm requires only O(n) extra workspace and can be adapted to compute any subset of k eigenpairs in O(nk) time. In contrast, all earlier stable parallel algorithms for the tridiagonal eigenproblem require O(n3) operations in the worst case, while some implementations, such as divide and conquer, have an extra O(n2) memory requirement. The proposed parallel algorithm balances the workload equally among the processors by traversing a matrix-dependent representation tree which captures the sequence of computations performed by Algorithm MR3. The resulting implementation allows problems of very large size to be solved efficiently---the largest dense eigenproblem solved in-core on a 256 processor machine with 2 GBytes of memory per processor is for a matrix of size 128,000 x 128,000, which required about 8 hours of CPU time. We present comparisons with other eigensolvers and results on matrices that arise in the applications of computational quantum chemistry and finite element modeling of automobile bodies.**On Numerical Approximation of Electrostatic Energy in 3D**Journal of Computational Physics, Volume 146(2), pp. 707-725, November 1998.@article{Finocchiaro1998:418, author = "Daniele Finocchiaro and Marco Pellegrini and Paolo Bientinesi", title = "On Numerical Approximation of Electrostatic Energy in 3D", journal = "Journal of Computational Physics", year = 1998, volume = 146, number = 2, pages = "707-725", month = nov, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/jcp-final.pdf" }

abstractwebPDFbibtexApproximating the Coulomb self-energy of a charge distribution within a three-dimensional domain and the mutual Coulomb energy of two charge distributions often constitutes a computational bottleneck in the simulation of physical systems. The present article reports on a recently developed computational technique aimed at the numerical evaluation of the six-dimensional integrals arising from Coulomb interactions. Techniques from integral geometry are used to show a reduction of the domain from six-dimensional to two-dimensional. In the process analytic singularities due to Coulomb's law are eliminated. Experimental results on the self-energy of a charged cube show that the proposed method converges rapidly and is competitive with methods proposed in the literature for similar integration problems.

### Book Chapter

**HPC on Competitive Cloud Resources**In Handbook of Cloud Computing, pp. 493-516, Springer, 2010.PDFbibtex@inbook{Bientinesi2010:54, author = "Paolo Bientinesi and Roman Iakymchuk and Jeff Napper", title = "HPC on Competitive Cloud Resources", pages = "493--516", publisher = "Springer", year = 2010, editor = "Borko Furht and Armando Escalante", booktitle = "In Handbook of Cloud Computing", institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen University", url = "http://hpac.rwth-aachen.de/~iakymchuk/pub/AICES-2010-06-01.pdf" }

### Peer Reviewed Conference Publications

**LAMMPS' PPPM Long-Range Solver for the Second Generation Xeon Phi**Proceedings of the ISC HPC 2017, June 2017.@inproceedings{McDoniel2017:890, author = "William McDoniel and Markus Höhnerbach and Rodrigo Canales and {Ahmed E.} Ismail and Paolo Bientinesi", title = "LAMMPS' PPPM Long-Range Solver for the Second Generation Xeon Phi", year = 2017, month = jun, url = "https://arxiv.org/pdf/1702.04250.pdf" }

abstractPDFbibtexMolecular Dynamics is an important tool for computational biologists, chemists, and materials scientists, consuming a sizable amount of supercomputing resources. Many of the investigated systems contain charged particles, which can only be simulated accurately using a long-range solver, such as PPPM. We extend the popular LAMMPS molecular dynamics code with an implementation of PPPM particularly suitable for the second generation Intel Xeon Phi. Our main target is the optimization of computational kernels by means of vectorization, and we observe speedups in these kernels of up to 12x. These improvements carry over to LAMMPS users, with overall speedups ranging between 2-3x, without requiring users to retune input parameters. Furthermore, our optimizations make it easier for users to determine optimal input parameters for attaining top performance.**TTC: A Tensor Transposition Compiler for Multiple Architectures**Proceedings of the 3rd International Workshop on Libraries, Languages and Compilers for Programming (ARRAY 2016), June 2016.@inproceedings{Springer2016:940, author = "Paul Springer and Aravind Sankaran and Paolo Bientinesi", title = "TTC: A Tensor Transposition Compiler for Multiple Architectures", year = 2016, month = jun, url = "https://arxiv.org/pdf/1607.01249.pdf" }

abstractPDFbibtexWe consider the problem of transposing tensors of arbitrary dimension and describe TTC, an open source domain-specific parallel compiler. TTC generates optimized parallel C++/CUDA C code that achieves a significant fraction of the system's peak memory bandwidth. TTC exhibits high performance across multiple architectures, including modern AVX-based systems (e.g.,~Intel Haswell, AMD Steamroller), Intel's Knights Corner as well as different CUDA-based GPUs such as NVIDIA's Kepler and Maxwell architectures. We report speedups of TTC over a meaningful baseline implementation generated by external C++ compilers; the results suggest that a domain-specific compiler can outperform its general purpose counterpart significantly: For instance, comparing with Intel's latest C++ compiler on the Haswell and Knights Corner architecture, TTC yields speedups of up to 8x and 32x, respectively. We also showcase TTC's support for multiple leading dimensions, making it a suitable candidate for the generation of performance-critical packing functions that are at the core of the ubiquitous BLAS 3 routines.**The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability**Proceedings of the SC 2016, 2016.

Selected for Reproducibility Initiative at SC17.@inproceedings{HÃ¶hnerbach2016:78, author = "Markus Höhnerbach and {Ahmed E.} Ismail and Paolo Bientinesi", title = "The Vectorization of the Tersoff Multi-Body Potential: An Exercise in Performance Portability", year = 2016, note = "Selected for Reproducibility Initiative at SC17", url = "https://arxiv.org/pdf/1607.02904v1" }

abstractwebPDFbibtexMolecular dynamics simulations, an indispensable research tool in computational chemistry and materials science, consume a significant portion of the supercomputing cycles around the world. We focus on multi-body potentials and aim at achieving performance portability. Compared with well-studied pair potentials, multibody potentials deliver increased simulation accuracy but are too complex for effective compiler optimization. Because of this, achieving cross-platform performance remains an open question. By abstracting from target architecture and computing precision, we develop a vectorization scheme applicable to both CPUs and accelerators. We present results for the Tersoff potential within the molecular dynamics code LAMMPS on several architectures, demonstrating efficiency gains not only for computational kernels, but also for large-scale simulations. On a cluster of Intel Xeon Phi's, our optimized solver is between 3 and 5 times faster than the pure MPI reference.**The Tersoff many-body potential: Sustainable performance through vectorization**Proceedings of the SC15 Workshop: Producing High Performance and Sustainable Software for Molecular Simulation, November 2015.@inproceedings{HÃ¶hnerbach2015:718, author = "Markus Höhnerbach and {Ahmed E.} Ismail and Paolo Bientinesi", title = "The Tersoff many-body potential: Sustainable performance through vectorization", year = 2015, month = nov, url = "http://hpac.rwth-aachen.de/ipcc/sc15_paper.pdf" }

abstractPDFbibtexThis contribution discusses the effectiveness and the sustainability of vectorization in molecular dynamics. As a case study, we present results for multi-body potentials on a range of vector instruction sets, targeting both CPUs and accelerators such as GPUs and the Intel Xeon Phi. The shared-memory and distributed-memory parallelization of MD simulations are problems that have been extensively treated; by contrast, vectorization is a relatively unexplored dimension. However, given both the increasing number of vector units available in the computing architectures, and the increasing width of such units, it is imperative to write algorithms and code for taking advantage of vector instructions. We chose to investigate multi-body potentials, as they are not as easily vectorizable as the pair potentials. As a matter of fact, their optimization pushes the boundaries of current compiler technology: our experience suggests that for such problems, compilers alone are not able to deliver appreciable speedups. By constrast, by resorting to the explicit use of instrinsics, we demonstrate significant improvements both on CPUs and the Intel Xeon Phi. Nonetheless, it is clear that the direct use of intrinsics is not a sustainable solution, not only for the effort and expertise it requires, but also because it hinders readability, extensibility and maintainability of code. In our case study, we wrote a C++ implementation of the Tersoff potential for the LAMMPS molecular dynamics simulation package. To alleviate the difficulty of using intrinsics, we used a template-based approach and abstracted from the instruction set, the vector length and the floating point precision. Instead of having to write 18 different kernels, this approach allowed us to only have one source code, from which all implementations (scalar, SSE, AVX, AVX2, AVX512, and IMCI, in single, double, and mixed precision) are automatically derived. Such an infrastructure makes it possible to compare kernels and identify which algorithms are suitable for which architecture. Without optimizations, we observed that a Intel Xeon E5-2650 CPU (Sandy Bridge) is considerably faster than a Xeon Phi. With our optimizations, the performance of both CPU and accelerator improved, and thanks to its wide vector units, the Xeon Phi takes the lead. For the future, besides monitoring the compilers' improvements, one should evaluate OpenMP 4.1 and its successors, which will include support for directive-based vectorization.**A Scalable, Linear-Time Dynamic Cutoff Algorithm for Molecular Dynamics**High Performance Computing, Lecture Notes in Computer Science, Volume 9137, pp. 155-170, Springer International Publishing, July 2015.@inproceedings{Springer2015:450, author = "Paul Springer and {Ahmed E.} Ismail and Paolo Bientinesi", title = "A Scalable, Linear-Time Dynamic Cutoff Algorithm for Molecular Dynamics", booktitle = "High Performance Computing ", year = 2015, volume = 9137, series = "Lecture Notes in Computer Science", pages = "155-170", month = jul, publisher = "Springer International Publishing", url = "http://hpac.rwth-aachen.de/~springer/dcm_isc15.pdf" }

abstractwebPDFbibtexRecent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial sys- tems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems of arbitrarily large size. The idea consists in adopting a cutoff-based method in which the cutoff is cho- sen on a particle-by-particle basis, according to the distance from the interface. Computationally, the challenge is shifted from the long-range solvers to the detection of the interfaces and to the computation of the particle-interface distances. For these tasks, we present linear-time algo- rithms that do not rely on global communication patterns. As a result, the DCM algorithm is suited for large systems of particles and mas- sively parallel computers. To demonstrate its potential, we integrated DCM into the LAMMPS open-source molecular dynamics package, and simulated large liquid/vapor systems on two supercomputers: SuperMuc and JUQUEEN. In all cases, the accuracy of DCM is comparable to the traditional particle-particle particle-mesh (PPPM) algorithm, while the performance is considerably superior for large numbers of particles. For JUQUEEN, we provide timings for simulations running on the full system (458, 752 cores), and show nearly perfect strong and weak scaling.**On the Performance Prediction of BLAS-based Tensor Contractions**High Performance Computing Systems. Performance Modeling, Benchmarking, and Simulation, Lecture Notes in Computer Science, Volume 8966, pp. 193-212, Springer International Publishing, April 2015.@inproceedings{Peise2015:380, author = "Elmar Peise and Diego Fabregat-Traver and Paolo Bientinesi", title = "On the Performance Prediction of BLAS-based Tensor Contractions", booktitle = "High Performance Computing Systems. Performance Modeling, Benchmarking, and Simulation", year = 2015, editor = "Jarvis, Stephen A. and Wright, Steven A. and Hammond, Simon D.", volume = 8966, series = "Lecture Notes in Computer Science", pages = "193-212", month = apr, publisher = "Springer International Publishing", url = "http://arxiv.org/pdf/1409.8608v1" }

abstractwebPDFbibtexTensor operations are surging as the computational building blocks for a variety of scientific simulations and the development of high-performance kernels for such operations is known to be a challenging task. While for operations on one- and two-dimensional tensors there exist standardized interfaces and highly-optimized libraries (BLAS), for higher dimensional tensors neither standards nor highly-tuned implementations exist yet. In this paper, we consider contractions between two tensors of arbitrary dimensionality and take on the challenge of generating high-performance implementations by resorting to sequences of BLAS kernels. The approach consists in breaking the contraction down into operations that only involve matrices or vectors. Since in general there are many alternative ways of decomposing a contraction, we are able to methodically derive a large family of algorithms. The main contribution of this paper is a systematic methodology to accurately identify the fastest algorithms in the bunch, without executing them. The goal is instead accomplished with the help of a set of cache-aware micro-benchmarks for the underlying BLAS kernels. The predictions we construct from such benchmarks allow us to reliably single out the best-performing algorithms in a tiny fraction of the time taken by the direct execution of the algorithms.**A Study on the Influence of Caching: Sequences of Dense Linear Algebra Kernels**High Performance Computing for Computational Science -- VECPAR 2014, Lecture Notes in Computer Science, Volume 8969, pp. 245-258, Springer International Publishing, April 2015.@inproceedings{Peise2015:250, author = "Elmar Peise and Paolo Bientinesi", title = "A Study on the Influence of Caching: Sequences of Dense Linear Algebra Kernels", booktitle = "High Performance Computing for Computational Science -- VECPAR 2014", year = 2015, editor = "Daydé, Michel and Marques, Osni and Nakajima, Kengo", volume = 8969, series = "Lecture Notes in Computer Science", pages = "245-258", month = apr, publisher = "Springer International Publishing", url = "https://arxiv.org/pdf/1402.5897v1" }

abstractwebPDFbibtexIt is universally known that caching is critical to attain high- performance implementations: In many situations, data locality (in space and time) plays a bigger role than optimizing the (number of) arithmetic floating point operations. In this paper, we show evidence that at least for linear algebra algorithms, caching is also a crucial factor for accurate performance modeling and performance prediction.**Scalable and Efficient Linear Algebra Kernel Mapping for Low Energy Consumption on the Layers CGRA**Applied Reconfigurable Computing, Lecture Notes in Computer Science, Volume 9040, pp. 301-310, January 2015.@inproceedings{Rakossy2015:898, author = "{Zoltan Endre } Rakossy and Dominik Stengele and {Axel } Acosta-Aponte and Saumitra Chafekar and Paolo Bientinesi and {Anupam } Chattopadhyay", title = "Scalable and Efficient Linear Algebra Kernel Mapping for Low Energy Consumption on the Layers CGRA", booktitle = "Applied Reconfigurable Computing", year = 2015, volume = 9040, series = "Lecture Notes in Computer Science", pages = "301-310", month = jan, organization = "Ruhr-Universität Bochum", url = "http://arc2015.esit.rub.de" }

abstractwebPDFbibtexA scalable mapping is proposed for 3 important kernels from the Numerical Linear Algebra domain, to exploit architectural features to reach asymptotically optimal efficiency and a low energy consumption. Performance and power evaluations were done with input data set matrix sizes ranging from 64×64 to 16384×16384. 12 architectural variants with up to 10×10 processing elements were used to explore scalability of the mapping and the architecture, achieving < 10% energy increase for architectures up to 8×8 PEs coupled with performance speed-ups of more than an order of magnitude. This enables a clean area-performance trade-off on the Layers architecture while keeping energy constant over the variants.**Streaming Data from HDD to GPUs for Sustained Peak Performance**Proceedings of the Euro-Par 2013, 19th International European Conference on Parallel and Distributed Computing, Lecture Notes in Computer Science, Volume 8097, pp. 788-799, Springer Berlin Heidelberg, May 2013.@inproceedings{Beyer2013:618, author = "Lucas Beyer and Paolo Bientinesi", title = "Streaming Data from HDD to GPUs for Sustained Peak Performance", year = 2013, volume = 8097, series = "Lecture Notes in Computer Science", pages = "788-799", month = may, publisher = "Springer Berlin Heidelberg", url = "http://arxiv.org/pdf/1302.4332v1.pdf" }

abstractwebPDFbibtexIn the context of the genome-wide association studies (GWAS), one has to solve long sequences of generalized least-squares problems; such a task has two limiting factors: execution time --often in the range of days or weeks-- and data management --data sets in the order of Terabytes. We present an algorithm that obviates both issues. By pipelining the computation, and thanks to a sophisticated transfer strategy, we stream data from hard disk to main memory to GPUs and achieve sustained peak performance; with respect to a highly-optimized CPU implementation, our algorithm shows a speedup of 2.6x. Moreover, the approach lends itself to multiple GPUs and attains almost perfect scalability. When using 4 GPUs, we observe speedups of 9x over the aforementioned implementation, and 488x over a widespread biology library.**Algorithms for Large-scale Whole Genome Association Analysis**Proceedings of the 20th European MPI Users' Group Meeting, EuroMPI '13, pp. 229-234, ACM, 2013.@inproceedings{Peise2013:504, author = "Elmar Peise and Diego Fabregat-Traver and {Yurii S.} Aulchenko and Paolo Bientinesi", title = "Algorithms for Large-scale Whole Genome Association Analysis ", booktitle = "Proceedings of the 20th European MPI Users' Group Meeting", year = 2013, series = "EuroMPI '13", pages = "229--234 ", address = "New York, NY, USA", publisher = "ACM", url = "http://arxiv.org/pdf/1304.2272v1" }

abstractwebPDFbibtexIn order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which exceed the main memory of contemporary computers, one faces two distinct challenges: 1) Millions of polymorphisms come at the cost of hundreds of Gigabytes of genotype data, which can only be kept in secondary storage; 2) the relatedness of the test population is represented by a covariance matrix, which, for large populations, can only fit in the combined main memory of a distributed architecture. In this paper, we present solutions for both challenges: The genotype data is streamed from and to secondary storage using a double buffering technique, while the covariance matrix is kept across the main memory of a distributed memory system. We show that these methods sustain high-performance and allow the analysis of enormous datasets.**A Domain-Specific Compiler for Linear Algebra Operations**High Performance Computing for Computational Science -- VECPAR 2010, Lecture Notes in Computer Science, Volume 7851, pp. 346-361, Springer, 2013.@inproceedings{Fabregat-Traver2013:340, author = "Diego Fabregat-Traver and Paolo Bientinesi", title = "A Domain-Specific Compiler for Linear Algebra Operations", booktitle = "High Performance Computing for Computational Science -- VECPAR 2010", year = 2013, editor = "M. Dayde, O. Marques, and K. Nakajima", volume = 7851, series = "Lecture Notes in Computer Science", pages = "346--361", address = "Heidelberg", publisher = "Springer", url = "http://arxiv.org/pdf/1205.5975v1" }

abstractwebPDFbibtexWe present a prototypical linear algebra compiler that automatically exploits domain-specific knowledge to generate high-performance algorithms. The input to the compiler is a target equation together with knowledge of both the structure of the problem and the properties of the operands. The output is a variety of high-performance algorithms to solve the target equation. Our approach consists in the decomposition of the input equation into a sequence of library-supported kernels. Since in general such a decomposition is not unique, our compiler returns not one but a number of algorithms. The potential of the compiler is shown by means of its application to a challenging equation arising within the*genome-wide association study*. As a result, the compiler produces multiple "best" algorithms that outperform the best existing libraries.**Performance Modeling for Dense Linear Algebra**Proceedings of the 2012 SC Companion: High Performance Computing, Networking Storage and Analysis (PMBS12), SCC '12, pp. 406-416, IEEE Computer Society, November 2012.@inproceedings{Peise2012:50, author = "Elmar Peise and Paolo Bientinesi", title = "Performance Modeling for Dense Linear Algebra", booktitle = "Proceedings of the 2012 SC Companion: High Performance Computing, Networking Storage and Analysis (PMBS12)", year = 2012, series = "SCC '12", pages = "406--416", address = "Washington, DC, USA", month = nov, publisher = "IEEE Computer Society", url = "http://arxiv.org/pdf/1209.2364" }

abstractwebPDFbibtexIt is well known that the behavior of dense linear algebra algorithms is greatly influenced by factors like target architecture, underlying libraries and even problem size; because of this, the accurate prediction of their performance is a real challenge. In this article, we are not interested in creating accurate models for a given algorithm, but in correctly ranking a set of equivalent algorithms according to their performance. Aware of the hierarchical structure of dense linear algebra routines, we approach the problem by developing a framework for the automatic generation of statistical performance models for BLAS and LAPACK libraries. This allows us to obtain predictions through evaluating and combining such models. We demonstrate that our approach is successful in both single- and multi-core environments, not only in the ranking of algorithms but also in tuning their parameters.**An Example of Symmetry Exploitation for Energy-related Eigencomputations**INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009: (ICCMSE 2009), AIP Conference Proceedings, Volume 1504, pp. 1134-1137, 2012.@inproceedings{Petschow2012:860, author = "Matthias Petschow and Edoardo {Di Napoli} and Paolo Bientinesi", title = "An Example of Symmetry Exploitation for Energy-related Eigencomputations", booktitle = "INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009: (ICCMSE 2009)", year = 2012, volume = 1504, series = "AIP Conference Proceedings", pages = "1134--1137", url = "http://link.aip.org/link/doi/10.1063/1.4772126" }

abstractwebPDFbibtexOne of the most used approaches in simulating materials is the tight-binding approximation. When using this method in a material simulation, it is necessary to compute the eigenvalues and eigenvectors of the Hamiltonian describing the system. In general, the system possesses few explicit symmetries. Due to them, the problem has many degenerate eigenvalues. The ambiguity in choosing a orthonormal basis of the invariant subspaces, associated with degenerate eigenvalues, will result in eigenvectors which are not invariant under the action of the symmetry operators in matrix form. A meaningful computation of the eigenvectors needs to take those symmetries into account. A natural choice is a set of eigenvectors, which simultaneously diagonalizes the Hamiltonian and the symmetry matrices. This is possible because all the matrices commute with each other. The simultaneous eigenvectors and the corresponding eigenvalues will be in a parametrized form in terms of the lattice momentum components. This functional dependence of the eigenvalues is the dispersion relation and describes the band structure of a material. Therefore it is important to find this functional dependence in any numerical computation related to material properties.**Execution-Less Performance Modeling**Proceedings of the Second International Workshop on Performance Modeling, Benchmarking and Simulation of High-Performance Computing Systems (PMBS11) held as part of the Supercomputing Conference (SC11), November 2011.webbibtex@inproceedings{Iakymchuk2011:258, author = "Roman Iakymchuk and Paolo Bientinesi", title = "Execution-Less Performance Modeling", booktitle = "Proceedings of the Second International Workshop on Performance Modeling, Benchmarking and Simulation of High-Performance Computing Systems (PMBS11) held as part of the Supercomputing Conference (SC11)", year = 2011, address = "Seattle, USA", month = nov, institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen University" }

**High-Performance Parallel Computations using Python as High-Level Language**Euro-Par 2010, Parallel Processing Workshops, Lecture Notes in Computer Science, Volume 6586, pp. 541-548, Springer, 2011.@inproceedings{Masini2011:8, author = "Stefano Masini and Paolo Bientinesi", title = "High-Performance Parallel Computations using Python as High-Level Language", booktitle = "Euro-Par 2010, Parallel Processing Workshops", year = 2011, editor = "Guarracino, M.R.; Vivien, F.; Traff, J.L.; Cannataro, M.; Danelutto, M.; Hast, A.; Perla, F.; KnÃï¿½ï¿½Ã¯Â¿Â½Ãï¿½ï¿½Ãï¿½Â¼pfer, A.; Di Martino, B.; Alexander, M. ", volume = 6586, series = "Lecture Notes in Computer Science", pages = "541--548", publisher = "Springer", url = "http://hpac.rwth-aachen.de/~pauldj/pubs/Python-TR.pdf" }

abstractwebPDFbibtexHigh-performance and parallel computations have always represented a challenge in terms of code optimization and memory usage, and have typically been tackled with languages that allow a low-level management of resources, like Fortran, C and C++. Nowadays, most of the implementation effort goes into constructing the bookkeeping logic that binds together functionalities taken from standard libraries. Because of the increasing complexity of this kind of codes, it becomes more and more necessary to keep it well organized through proper software engineering practices. Indeed, in the presence of chaotic implementations, reasoning about correctness is difficult, even when limited to specific aspects like concurrency; moreover, due to the lack in flexibility of the code, making substantial changes for experimentation becomes a grand challenge. Since the bookkeeping logic only accounts for a tiny fraction of the total execution time, we believe that for such a task it can be afforded to introduce an overhead due to a high-level language. We consider Python as a preliminary candidate with the intent of improving code readability, flexibility and, in turn, the level of confidence with respect to correctness. In this study, the bookkeeping logic of SMP-MRRR, a C & Fortran highly optimized multi-core eigensolver, is ported to Python. We report here on the porting process and on the pros and cons of using a high-level language in a high-performance parallel library.**Improving High-Performance Computations on Clouds Through Resource Underutilization**Proceedings of ACM 26th Symposium on Applied Computing, pp. 119-126, ACM, 2011.@inproceedings{Iakymchuk2011:404, author = "Roman Iakymchuk and Jeff Napper and Paolo Bientinesi", title = "Improving High-Performance Computations on Clouds Through Resource Underutilization", booktitle = "Proceedings of ACM 26th Symposium on Applied Computing", year = 2011, pages = "119--126 ", address = "Taichung, Taiwan", publisher = "ACM" }

abstractwebbibtexWe investigate the effects of shared resources for high-performance computing in a commercial cloud environment where multiple virtual machines share a single hardware node. Although good performance is occasionally obtained, contention degrades the expected performance and introduces significant variance. Using the DGEMM kernel and the HPL benchmark, we show that the underutilization of resources considerably improves expected performance by reducing contention for the CPU and cache space. For instance, for some cluster configurations, the solution is reached almost an order of magnitude earlier on average when the available resources are underutilized. The performance benefits for single node computations are even more impressive: Underutilization improves the expected execution time by two orders of magnitude. Finally, in contrast to unshared clusters, extending underutilized clusters by adding more nodes often improves the execution time due to an increased parallelism even with a slow interconnect. In the best case, by underutilizing the nodes performance was improved enough to entirely offset the cost of an extra node in the cluster.**Automatic Generation of Loop-Invariants for Matrix Operations**Computational Science and its Applications, International Conference, pp. 82-92, IEEE Computer Society, 2011.@inproceedings{Fabregat-Traver2011:238, author = "Diego Fabregat-Traver and Paolo Bientinesi", title = "Automatic Generation of Loop-Invariants for Matrix Operations", booktitle = "Computational Science and its Applications, International Conference", year = 2011, pages = "82-92", address = "Los Alamitos, CA, USA", publisher = "IEEE Computer Society", url = "http://hpac.rwth-aachen.de/aices/preprint/documents/AICES-2011-02-01.pdf" }

abstractwebPDFbibtexIn recent years it has been shown that for many linear algebra operations it is possible to create families of algorithms following a very systematic procedure. We do not refer to the fine tuning of a known algorithm, but to a methodology for the actual generation of both algorithms and routines to solve a given target matrix equation. Although systematic, the methodology relies on complex algebraic manipulations and non-obvious pattern matching, making the procedure challenging to be performed by hand, our goal is the development of a fully automated system that from the sole description of a target equation creates multiple algorithms and routines. We present CL1ck, a symbolic system written in Mathematica, that starts with an equation, decomposes it into multiple equations, and returns a set of loop-invariants for the algorithms -- yet to be generated -- that will solve the equation. In a successive step each loop-invariant is then mapped to its corresponding algorithm and routine. For a large class of equations, the methodology generates known algorithms as well as many previously unknown ones. Most interestingly, the methodology unifies algorithms traditionally developed in isolation. As an example, the five well known algorithms for the LU factorization are for the first time unified under a common root.**Knowledge-Based Automatic Generation of Partitioned Matrix Expressions**Computer Algebra in Scientific Computing, Lecture Notes in Computer Science, Volume 6885, pp. 144-157, Springer, 2011.@inproceedings{Fabregat-Traver2011:54, author = "Diego Fabregat-Traver and Paolo Bientinesi", title = "Knowledge-Based Automatic Generation of Partitioned Matrix Expressions", booktitle = "Computer Algebra in Scientific Computing", year = 2011, editor = "Gerdt, Vladimir and Koepf, Wolfram and Mayr, Ernst and Vorozhtsov, Evgenii", volume = 6885, series = "Lecture Notes in Computer Science", pages = "144-157", address = "Heidelberg", publisher = "Springer", url = "http://hpac.rwth-aachen.de/aices/preprint/documents/AICES-2011-01-03.pdf" }

abstractwebPDFbibtexIn a series of papers it has been shown that for many linear algebra operations it is possible to generate families of algorithms by following a systematic procedure. Although powerful, such a methodology involves complex algebraic manipulation, symbolic computations and pattern matching, making the generation a process challenging to be performed by hand. We aim for a fully automated system that from the sole description of a target operation creates multiple algorithms without any human intervention. Our approach consists of three main stages. The first stage yields the core object for the entire process, the Partitioned Matrix Expression (PME), which establishes how the target problem may be decomposed in terms of simpler sub-problems. In the second stage the PME is inspected to identify predicates, the Loop-Invariants, to be used to set up the skeleton of a family of proofs of correctness. In the third and last stage the actual algorithms are constructed so that each of them satisfies its corresponding proof of correctness. In this paper we focus on the first stage of the process, the automatic generation of Partitioned Matrix Expressions. In particular, we discuss the steps leading to a PME and the knowledge necessary for a symbolic system to perform such steps. We also introduce Cl1ck, a prototype system written in Mathematica that generates PMEs automatically.**Matrix Structure Exploitation in Generalized Eigenproblems Arising in Density Functional Theory**ICNAAM 2010: International Conference of Numerical Analysis and Applied Mathematics 2010, AIP Conference Proceedings, Volume 1281, pp. 937-940, American Institute of Physics, 2010.@inproceedings{Di_Napoli2010:830, author = "Edoardo {Di Napoli} and Paolo Bientinesi", title = "Matrix Structure Exploitation in Generalized Eigenproblems Arising in Density Functional Theory", booktitle = "ICNAAM 2010: International Conference of Numerical Analysis and Applied Mathematics 2010", year = 2010, volume = 1281, series = "AIP Conference Proceedings", pages = "937--940", publisher = "American Institute of Physics", url = "http://hpac.rwth-aachen.de/~pauldj/pubs/ICNAAM-Edo-TR.pdf" }

abstractwebPDFbibtexIn this short paper, the authors report a new computational approach in the context of Density Functional Theory (DFT). It is shown how it is possible to speed up the self-consistent cycle (iteration) characterizing one of the most well-known DFT implementations: FLAPW. Generating the Hamiltonian and overlap matrices and solving the associated generalized eigenproblems A x = l B x constitute the two most time-consuming fractions of each iteration. Two promising directions, implementing the new methodology, are presented that will ultimately improve the performance of the generalized eigensolver and save computational time.**Benchmarking Different Direct Solution Methods For Large Power System Simulation**Grand Challenges in Modeling & Simulation, SummerSIM'10, pp. 280-284, 2010.bibtex@inproceedings{Benigni2010:654, author = "Andrea Benigni and Paolo Bientinesi and Antonello Monti", title = "Benchmarking Different Direct Solution Methods For Large Power System Simulation", booktitle = "Grand Challenges in Modeling & Simulation, SummerSIM'10", year = 2010, pages = "280--284 " }

**Towards Mechanical Derivation of Krylov Solver Libraries**Proceedings of the ICCS2010, Procedia Computer Science, Volume 1(1), pp. 1805-1813, 2010.@inproceedings{Eijkhout2010:480, author = "Victor Eijkhout and Paolo Bientinesi and Robert {van de Geijn}", title = "Towards Mechanical Derivation of Krylov Solver Libraries", year = 2010, volume = 1, number = 1, series = "Procedia Computer Science", pages = "1805--1813", url = "http://hpac.rwth-aachen.de/~pauldj/pubs/Krylov-TR.pdf" }

abstractwebPDFbibtexIn a series of papers, it has been shown that algorithms for dense linear algebra operations can be systematically and even mechanically derived from the mathematical specification of the operation. A frequent question has been whether the methodology can be broadened to iterative methods. In this paper, we show preliminary evidence that this is indeed the case for so-called Krylov subspace methods. Our aims with this are two-fold: first of all, we show how the FLAME paradigm can simplify the derivation of subspace iteration methods. In view of this, the fact that we only derive the classical conjugate gradient method should be viewed as a promise for the future, rather than as a limitation of this approach. Secondly, and more importantly, our use of FLAME shows how mechanical reasoning can derive full algorithm specifications from the constraints (for instance, orthogonality conditions) on the generated results. If we tie this to ongoing research in automatic optimized code generated in FLAME, we see that this research is a necessary building block towards automatic generation of optimized library software.**On Parallelizing the MRRR Algorithm for Data-Parallel Coprocessors**Proceedings of the PPAM 2009, Eighth International Conference on Parallel Processing and Applied Mathematics, Lecture Notes in Computer Science, Volume 6067, Springer, 2010.@inproceedings{Lessig2010:138, author = "Christian Lessig and Paolo Bientinesi", title = "On Parallelizing the MRRR Algorithm for Data-Parallel Coprocessors", year = 2010, volume = 6067, series = "Lecture Notes in Computer Science", publisher = "Springer", url = "http://hpac.rwth-aachen.de/~pauldj/pubs/MRRR-GPU.pdf" }

abstractwebPDFbibtexThe eigenvalues and eigenvectors of a symmetric matrix are needed in a myriad of applications in computational engineering and computational science. One of the fastest and most accurate eigensolvers is the Algorithm of Multiple Relatively Robust Representations (MRRR). This is the first stable algorithm that computes k eigenvalues and eigenvectors of a tridiagonal symmetric matrix in O(nk) time. We present a parallelization of the MRRR algorithm for data parallel coprocessors using the CUDA programming environment. The results clearly demonstrate the potential of data-parallel coprocessors for scientific computations: when comparing against routine sstemr, LAPACKâï¿½ï¿½s implementation of MRRR, our parallel algorithm provides 10-fold speedups.**Reduction to Condensed Forms for Symmetric Eigenvalue Problems on Multi-core Architectures**Proceedings of the PPAM 2009, Eighth International Conference on Parallel Processing and Applied Mathematics, Lecture Notes in Computer Science, Volume 6067, Springer, 2010.@inproceedings{Bientinesi2010:970, author = "Paolo Bientinesi and Francisco Igual and Daniel Kressner and {Enrique S.} Quintana-Orti", title = "Reduction to Condensed Forms for Symmetric Eigenvalue Problems on Multi-core Architectures", year = 2010, volume = 6067, series = "Lecture Notes in Computer Science", publisher = "Springer" }

abstractwebbibtexWe investigate the performance of the routines in LAPACK and the Successive Band Reduction (SBR) toolbox for the reduction of a dense matrix to tridiagonal form, a crucial preprocessing stage in the solution of the symmetric eigenvalue problem, on general-purpose multi-core processors. In response to the advances of hardware accelerators, we also modify the code in SBR to accelerate the computation by off-loading a significant part of the operations to a graphics processor (GPU). Performance results illustrate the parallelism and scalability of these algorithms on current high-performance multi-core architectures.**The Algorithm of Multiple Relatively Robust Representations for Multi-Core Processors**Proceedings of the PARA 2010, Reykjavik, Iceland, June 6-9, 2010, Lecture Notes in Computer Science, Volume 7133, pp. 152-161, Springer, 2010.@inproceedings{Petschow2010:754, author = "Matthias Petschow and Paolo Bientinesi", title = "The Algorithm of Multiple Relatively Robust Representations for Multi-Core Processors", year = 2010, editor = "Jonasson, Kristjan", volume = 7133, series = "Lecture Notes in Computer Science", pages = "152--161", publisher = "Springer", url = "http://hpac.rwth-aachen.de/aices/preprint/documents/AICES-2010-09-04.pdf" }

abstractwebPDFbibtexThe algorithm of Multiple Relatively Robust Representations (MRRR or MR3) computes k eigenvalues and eigenvectors of a symmetric tridiagonal matrix in O(nk) arithmetic operations. Large problems can be effectively tackled with existing distributed-memory parallel implementations of MRRR; small and medium size problems can instead make use of LAPACK's routine xSTEMR. However, xSTEMR is optimized for single-core CPUs, and does not take advantage of today's multi-core and future many-core architectures. In this paper we discuss some of the issues and trade-offs arising in the design of MR3-SMP, an algorithm for multi-core CPUs and SMP systems. Experiments on application matrices indicate that MR3-SMP is both faster and obtains better speedups than all the tridiagonal eigensolvers included in LAPACK and Intel's Math Kernel Library (MKL).**Automatic Generation of Partitioned Matrix Expressions for Matrix Operations.**Proceedings of the 8th International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2010), AIP Conference Proceedings, Volume 1281, pp. 774-777, 2010.@inproceedings{Fabregat-Traver2010:304, author = "Diego Fabregat-Traver and Paolo Bientinesi", title = "Automatic Generation of Partitioned Matrix Expressions for Matrix Operations.", year = 2010, volume = 1281, series = "AIP Conference Proceedings", pages = "774-777", url = "http://hpac.rwth-aachen.de/aices/preprint/documents/AICES-2010-10-01.pdf" }

abstractwebPDFbibtexWe target the automatic generation of formally correct algorithms and routines for linear algebra operations. Given the broad variety of architectures and configurations with which scientists deal, there does not exist one algorithmic variant that is suitable for all scenarios. Therefore, we aim to generate a family of algorithmic variants to attain high-performance for a broad set of scenarios. One of the authors has previously demonstrated that automatic derivation of a family of algorithms is possible when the Partitioned Matrix Expression (PME) of the target operation is available. The PME is a recursive definition that states the relations between submatrices in the input and the output operands. In this paper we describe all the steps involved in the automatic derivation of PMEs, thus making progress towards a fully automated system.**Can Cloud Computing Reach the TOP500?**UCHPC-MAW '09 Proceedings of the combined workshops on UnConventional high performance computing workshop plus memory access workshop, pp. 17-20, 2009.

In conjunction with the 2009 ACM International Conference on Computing Frontiers.@inproceedings{Napper2009:804, author = "Jeff Napper and Paolo Bientinesi", title = "Can Cloud Computing Reach the TOP500?", booktitle = "UCHPC-MAW '09 Proceedings of the combined workshops on UnConventional high performance computing workshop plus memory access workshop ", year = 2009, pages = "17--20", note = "In conjunction with the 2009 ACM International Conference on Computing Frontiers", url = "http://hpac.rwth-aachen.de/~pauldj/pubs/EC2-Cloud.pdf" }

abstractwebPDFbibtexComputing as a utility has reached the mainstream. Scientists can now rent time on large commercial clusters through several vendors. The cloud computing model provides flexible support for "pay as you go" systems. In addition to no upfront investment in large clusters or supercomputers, such systems incur no maintenance costs. Furthermore, they can be expanded and reduced on-demand in real-time. Current cloud computing performance falls short of systems specifically designed for scientific applications. Scientific computing needs are quite different from those of web applications--composed primarily of database queries--that have been the focus of cloud computing vendors. In this paper we investigate the use of cloud computing for high-performance numerical applications. In particular, we assume unlimited monetary resources to answer the question, "How high can a cloud computing service get in the TOP500 list?" We show results for the Linpack benchmark on different allocations on Amazon EC2.**Multi-dimensional Array Operations for Signal Processing Algorithms**PARA 2008: 9th International Workshop on State-of-the-Art in Scientific and Parallel Computing, 2008.

To be published.@inproceedings{Bientinesi2008:640, author = "Paolo Bientinesi and Nikos Pitsianis and Xiaobai Sun", title = "Multi-dimensional Array Operations for Signal Processing Algorithms", booktitle = "PARA 2008: 9th International Workshop on State-of-the-Art in Scientific and Parallel Computing", year = 2008, note = "To be published", url = "http://hpac.rwth-aachen.de/~pauldj/pubs/para-2008.pdf" }

abstractPDFbibtexGame and graphics processors are increasingly utilized for scientific computing applications and for signal processing in particular. This paper addresses the issue of efficiently mapping high-dimensional array operations for signal processing algorithms onto such computing platforms. Algorithms for fast Fourier transforms and convolutions are essential to many signal processing applications. Such algorithms entail fast high-dimensional data array operations. Game and graphics processors typically differ from general-purpose processors in memory hierarchy as well as in memory capacity and access patterns. We characterize the memory structures from the perspective of high-dimensional array operations, identify the mismatch between algorithmic dimension and architectural dimension and then describe the consequent penalty in memory latency. An architecture supports d-dimensional accesses if a d-dimensional data array can be accessed along one dimension as fast as along any other dimension. We introduce an approach to reduce latency and provide experimental results on the STI Cell Broadband Engine as supporting evidence.**Fast Computation of Local Correlation Coefficients**Proc. SPIE 7074, Advanced Signal Processing Algorithms, Architectures, and Implementations XVIII, Number 707405, 2008.@inproceedings{Bientinesi2008:478, author = "Paolo Bientinesi and Nikos Pitsianis and Xiaobai Sun", title = "Fast Computation of Local Correlation Coefficients", year = 2008, number = 707405, series = "Proc. SPIE 7074, Advanced Signal Processing Algorithms, Architectures, and Implementations XVIII" }

abstractwebbibtexThis paper presents an acceleration method, using both algorithmic and architectural means, for fast calculation of local correlation coefficients, which is a basic image-based information processing step for template or pattern matching, image registration, motion or change detection and estimation, compensation of changes, or compression of representations, among other information processing objectives. For real-time applications, the complexity in arithmetic operations as well as in programming and memory access latency had been a divisive issue between the so-called correction-based methods and the Fourier domain methods. In the presented method, the complexity in calculating local correlation coefficients is reduced via equivalent reformulation that leads to efficient array operations or enables the use of multi-dimensional fast Fourier transforms, without losing or sacrificing local and non-linear changes or characteristics. The computation time is further reduced by utilizing modern multi-core architectures, such as the Sony-Toshiba-IBM Cell processor, with high processing speed and low power consumption.**SuperMatrix: a Multithreaded Runtime Scheduling System for Algorithms-by-Blocks**Proceedings of ACM SIGPLAN 2008 Symposium on Principles and Practice of Parallel Programming (PPoPP'08), 2008.@inproceedings{Bientinesi2008:400, author = "Paolo Bientinesi and Ernie Chan and {Enrique S.} Quintana-Orti and Gregorio Quintana-Orti and Robert {van de Geijn}", title = "SuperMatrix: a Multithreaded Runtime Scheduling System for Algorithms-by-Blocks", booktitle = "Proceedings of ACM SIGPLAN 2008 Symposium on Principles and Practice of Parallel Programming (PPoPP'08)", year = 2008 }

abstractwebbibtexThis paper describes SuperMatrix, a runtime system that parallelizes matrix operations for SMP and/or multi-core architectures. We use this system to demonstrate how code described at a high level of abstraction can achieve high performance on such architectures while completely hiding the parallelism from the library programmer. The key insight entails viewing matrices hierarchically, consisting of blocks that serve as units of data where operations over those blocks are treated as units of computation. The implementation transparently enqueues the required operations, internally tracking dependencies, and then executes the operations utilizing out-of-order execution techniques inspired by superscalar microarchitectures. This separation of concerns allows library developers to implement algorithms without concerning themselves with the parallelization aspect of the problem. Different heuristics for scheduling operations can be implemented in the runtime system independent of the code that enqueues the operations. Results gathered on a 16 CPU ccNUMA Itanium2 server demonstrate excellent performance.**Sparse Direct Factorizations through Unassembled Hyper-Matrices**Proceedings of the International Congress on Industrial and Applied Mathematics (ICIAM'07), Proc. Appl. Math. Mech., Volume 7(1), pp. 1010901-1010902, December 2007.webbibtex@inproceedings{Bientinesi2007:254, author = "Paolo Bientinesi and Victor Eijkhout and Jason Kurtz and Robert {van de Geijn}", title = "Sparse Direct Factorizations through Unassembled Hyper-Matrices", booktitle = "Proceedings of the International Congress on Industrial and Applied Mathematics (ICIAM'07)", year = 2007, volume = 7, number = 1, series = "Proc. Appl. Math. Mech.", pages = "1010901--1010902", month = dec }

**Formal Correctness and Stability of Dense Linear Algebra Algorithms**Proceedings of 17th IMACS World Congress: Scientific Computation, Applied Mathematics and Simulation, 2005.@inproceedings{Bientinesi2005:110, author = "Paolo Bientinesi and Robert {van de Geijn}", title = "Formal Correctness and Stability of Dense Linear Algebra Algorithms", booktitle = "Proceedings of 17th IMACS World Congress: Scientific Computation, Applied Mathematics and Simulation", year = 2005, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/IMACS.pdf" }

abstractPDFbibtexThe Formal Linear Algebra Methods Environment (FLAME) project at UT-Austin pursues the mechanical derivation of algorithms for linear algebra operations. Rather than proving loop based algorithms correct a posteriori, a systematic methodology is employed that determines loop invariants from a mathematical specification of a given linear algebra operation. Algorithms and their correctness proofs are then constructively derived from this loop invariant. The process has been made mechanical via a prototype system implemented with Mathematica. Once an algorithm has been determined, a similarly systematic a posteriori process is used to determine the correctness in the presence of roundoff error (stability properties) of the algorithm. In this paper, we report progress towards the ultimate goal of full automation of the system.**Automatic Derivation of Linear Algebra Algorithms with Application to Control Theory**PARA'04 State-of-the-Art in Scientific Computing, June 2004.@inproceedings{Bientinesi2004:690, author = "Paolo Bientinesi and Sergey Kolos and Robert {van de Geijn}", title = "Automatic Derivation of Linear Algebra Algorithms with Application to Control Theory", booktitle = "PARA'04 State-of-the-Art in Scientific Computing", year = 2004, month = jun, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/PARA04-automsyst.pdf" }

abstractPDFbibtexIt is our belief that the ultimate automatic system for deriving linear algebra libraries should be able to generate a set of algorithms starting from the mathematical specification of the target operation only. Indeed, one should be able to visit a website, fill in a form with information about the operation to be performed and about the target architectures, click the SUBMIT button, and receive an optimized library routine for that operation even if the operation has not previously been implemented. In this paper we relate recent advances towards what is probably regarded as an unreachable dream. We discuss the steps necessary to automatically obtain an algorithm starting from the mathematical abstract description of the operation to be solved. We illustrate how these steps have been incorporated into two prototype systems and we show the application of one the two systems to a problem from Control Theory: The Sylvester Equation. The output of this system is a description of an algorithm that can then be directly translated into code via API’s that we have developed. The description can also be passed as input to a parallel performance analyzer to obtain optimized parallel routines.**Rapid Development of High-Performance Linear Algebra Libraries**PARA'04 State-of-the-Art in Scientific Computing, 2004.@inproceedings{Bientinesi2004:554, author = "Paolo Bientinesi and {John A.} Gunnels and {Fred G.} Gustavson and {Greg M.} Henry and {Margaret E.} Myers and {Enrique S.} Quintana-Orti and Robert {van de Geijn}", title = "Rapid Development of High-Performance Linear Algebra Libraries", booktitle = "PARA'04 State-of-the-Art in Scientific Computing", year = 2004, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/PARA04-worksheet.pdf" }

abstractPDFbibtexWe present a systematic methodology for deriving and implementing linear algebra libraries. It is quite common that an application requires a library of routines for the computation of linear algebra operations that are not (exactly) supported by commonly used libraries like LAPACK. In this situation, the application developer has the option of casting the operation into one supported by an existing library, often at the expense of performance, or implementing a custom library, often requiring considerable effort. Our recent discovery of a methodology based on formal derivation of algorithm allows such a user to quickly derive proven correct algorithms. Furthermore it provides an API that allows the so-derived algorithms to be quickly translated into high-performance implementations.**The Science of Programming High-Performance Linear Algebra Libraries**Proceedings of the Workshop on Performance Optimization for High-Level Languages and Libraries (POHLL-02), 2002.@inproceedings{Bientinesi2002:448, author = "Paolo Bientinesi and {John A.} Gunnels and {Fred G.} Gustavson and {Greg M.} Henry and {Margaret E.} Myers and {Enrique S.} Quintana-Orti and Robert {van de Geijn}", title = "The Science of Programming High-Performance Linear Algebra Libraries", booktitle = "Proceedings of the Workshop on Performance Optimization for High-Level Languages and Libraries (POHLL-02)", year = 2002, editor = "G. Baumgartner, J. Ramanujam, and P. Sadayappan " }

abstractbibtexWhen considering the unmanageable complexity of computer systems, Dijkstra recently made the following observations: 1. When exhaustive testing is impossible --i.e., almost always-- our trust can only be based on proof (be it mechanized or not). 2. A program for which it is not clear why we should trust it, is of dubious value. 3. A program should be structured in such a way that the argument for its correctness is feasible and not unnecessarily laborious. 4. Given the proof, deriving a program justified by it, is much easier than, given the program, constructing a proof justifying it. Over the last decade, our research in the area of the implementation of high performance sequential and parallel linear algebra libraries has made the wisdom of the above observations obvious. In this paper, we show how to apply formal derivation methods to linear algebra operations. By combining this approach with a high-level abstraction for coding such algorithms, a linear algebra library that is more desirable, as measured by the metric provided by the above observations, can be achieved. Moreover, such a library can include a richer array of algorithms and is, at the same time, more easily maintained and extended. Most surprisingly, the methodology results in more efficient implementations. The approach is sufficiently systematic that much of it can be, and has been, automated.

### Theses

**Mechanical Derivation and Systematic Analysis of Correct Linear Algebra Algorithms**Ph.D. Thesis, Department of Computer Sciences, University of Texas at Austin, July 2006.@phdthesis{Bientinesi2006:720, author = "Paolo Bientinesi", title = "Mechanical Derivation and Systematic Analysis of Correct Linear Algebra Algorithms", school = "Department of Computer Sciences, University of Texas at Austin", year = 2006, type = "Ph.D. Thesis", month = jul, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/thesis.pdf" }

abstractPDFbibtexWe consider the problem of developing formally correct dense linear algebra libraries. The problem would be solved convincingly if, starting from the mathe- matical specification of a target operation, it were possible to generate, implement and analyze a family of correct algorithms that compute the operation. This thesis presents evidence that for a class of dense linear operations, systematic and me- chanical development of algorithms is within reach. It describes and demonstrates an approach for deriving and implementing, systematically and even mechanically, proven correct algorithms. It also introduces a systematic procedure to analyze, in a modular fashion, numerical properties of the generated algorithms.**Computational Geometry Techniques for Approximation of Electrostatic Forces**Master's Thesis, University of Pisa, 1998.

### Others

**The Matrix Chain Algorithm to Compile Linear Algebra Expressions**Two-page abstract, 31 October 2016.

DSLDI 2016.webPDFbibtex@misc{Barthels2016:600, author = "Henrik Barthels and Paolo Bientinesi", title = "The Matrix Chain Algorithm to Compile Linear Algebra Expressions", month = oct, year = 2016, note = "DSLDI 2016", type = "Two-page abstract", institution = "RWTH Aachen", url = "https://arxiv.org/pdf/1611.05660" }

**HPC Sharing in the Cloud**August 2010.@misc{Napper2010:958, author = "Jeff Napper and Roman Iakymchuk and Paolo Bientinesi", title = "HPC Sharing in the Cloud", howpublished = "HPCWire.com", month = aug, year = 2010 }

abstractwebbibtexMany scientific applications can require significant coordination between large numbers of nodes. Massive effort is spent in the HPC arena to hide much of the latency from coordination with expensive low-latency networks and fine-tuned communication libraries. Such efforts have not yet been translated to the commercial cloud computing arena, which still typically provide systems with varying amounts of installed memory but rarely various quality interconnects.

### Technical Reports

**The ELAPS Framework: Experimental Linear Algebra Performance Studies**November 2016.@techreport{Peise2016:560, author = "Elmar Peise and Paolo Bientinesi", title = "The ELAPS Framework: Experimental Linear Algebra Performance Studies", year = 2016, month = nov, url = "http://arxiv.org/pdf/1504.08035v1" }

abstractwebPDFbibtexIn scientific computing, optimal use of computing resources comes at the cost of extensive coding, tuning and benchmarking. While the classic approach of “features first, performance later” is supported by a variety of tools such as Tau, Vampir, and Scalasca, the emerging performance-centric approach, in which both features and performance are primary objectives, is still lacking suitable development tools. For dense linear algebra applications, we fill this gap with the Experimental Linear Algebra Performance Studies framework (ELAPS), a multi-platform open-source environment for easy and fast, yet powerful performance experimentation and prototyping. In contrast to many existing tools, ELAPS targets the beginning of the development process, assisting application developers in both algorithmic and optimization decisions. With ELAPS, users construct experiments to investigate how performance and efficiency depend on factors such as caching, algorithmic parameters, problem size, and parallelism. Experiments are designed either through Python scripts or a specialized GUI, and run on a spectrum of architectures, ranging from laptops to accelerators and clusters. The resulting reports provide various metrics and statistics that can be analyzed both numerically and visually. In this paper, we introduce ELAPS and illustrate its practical value in guiding critical performance decisions already in early development stages.**A Note on Time Measurements in LAMMPS**Aachen Institute for Computational Engineering Science, RWTH Aachen, February 2016.

Technical Report AICES-2016/02-1.@techreport{Tameling2016:140, author = "Daniel Tameling and Paolo Bientinesi and {Ahmed E.} Ismail", title = "A Note on Time Measurements in LAMMPS", institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen", year = 2016, month = feb, note = "Technical Report AICES-2016/02-1", url = "http://arxiv.org/abs/1602.05566" }

abstractPDFbibtexWe examine the issue of assessing the efficiency of components of a parallel program at the example of the MD package LAMMPS. In particular, we look at how LAMMPS deals with the issue and explain why the approach adopted might lead to inaccurate conclusions. The misleading nature of this approach is subsequently verified experimentally with a case study. Afterwards, we demonstrate how one should correctly determine the efficiency of the components and show what changes to the code base of LAMMPS are necessary in order to get the correct behavior.**Cache-aware Performance Modeling and Prediction for Dense Linear Algebra**November 2014.@techreport{Peise2014:904, author = "Elmar Peise and Paolo Bientinesi", title = "Cache-aware Performance Modeling and Prediction for Dense Linear Algebra", year = 2014, month = nov, url = "http://arxiv.org/pdf/1409.8602v1" }

abstractPDFbibtexCountless applications cast their computational core in terms of dense linear algebra operations. These operations can usually be implemented by combining the routines offered by standard linear algebra libraries such as BLAS and LAPACK, and typically each operation can be obtained in many alternative ways. Interestingly, identifying the fastest implementation---without executing it---is a challenging task even for experts. An equally challenging task is that of tuning each routine to performance-optimal configurations. Indeed, the problem is so difficult that even the default values provided by the libraries are often considerably suboptimal; as a solution, normally one has to resort to executing and timing the routines, driven by some form of parameter search. In this paper, we discuss a methodology to solve both problems: identifying the best performing algorithm within a family of alternatives, and tuning algorithmic parameters for maximum performance; in both cases, we do not execute the algorithms themselves. Instead, our methodology relies on timing and modeling the computational kernels underlying the algorithms, and on a technique for tracking the contents of the CPU cache. In general, our performance predictions allow us to tune dense linear algebra algorithms within few percents from the best attainable results, thus allowing computational scientists and code developers alike to efficiently optimize their linear algebra routines and codes.**FLAME Derivation of the General Minimal Residual Method**Texas Advanced Computing Center, The University of Texas at Austin, November 2013.@techreport{Bientinesi2013:760, author = "Paolo Bientinesi and Victor Eijkhout", title = "FLAME Derivation of the General Minimal Residual Method", institution = "Texas Advanced Computing Center, The University of Texas at Austin", year = 2013, month = nov, url = "http://hpac.rwth-aachen.de/~pauldj/pubs/gmres.pdf" }

abstractPDFbibtexThe Conjugate Gradient method is found by constructing a sequence of residuals R that spans the Krylov space K and that is orthogonal. The GMRES method constructs another basis of the Krylov space, but the residuals S now satisfy 1) the residual is of minimum L2 length in each iteration, or equivalent, 2) the residuals are A-orthogonal. While it would be easy to construct the A-orthogonal basis of K, and in fact several methods do so, this construction can break down. For this reason, Saad and Schultz [2] proposed using a breakdown-free process, such as Arnoldi iteration, and constructing the basis by appropriate linear combinations.**Streaming Data from HDD to GPUs for Sustained Peak Performance**Aachen Institute for Computational Engineering Science, RWTH Aachen, February 2013.

Technical Report AICES-2013/02-1.@techreport{Beyer2013:398, author = "Lucas Beyer and Paolo Bientinesi", title = "Streaming Data from HDD to GPUs for Sustained Peak Performance", institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen", year = 2013, month = feb, note = "Technical Report AICES-2013/02-1" }

abstractwebbibtex**Improved Orthogonality for Dense Hermitian Eigensolvers based on the MRRR algorithm**Aachen Institute for Computational Engineering Science, RWTH Aachen, September 2012.

Technical Report AICES-2012/09-1.@techreport{Petschow2012:754, author = "Matthias Petschow and {Enrique S.} Quintana-Orti and Paolo Bientinesi", title = "Improved Orthogonality for Dense Hermitian Eigensolvers based on the MRRR algorithm", institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen", year = 2012, month = sep, note = "Technical Report AICES-2012/09-1", url = "http://www.aices.rwth-aachen.de:8080/%7Epetschow/pubs/mixed.pdf" }

abstractPDFbibtexThe dense Hermitian eigenproblem is of outstanding importance in numerical computations and a number of excellent algorithms for this problem exist. One of the fastest method is the MRRR algorithm, which is based on a reduction to real tridiagonal form. This approach, although fast, does not deliver the same accuracy (orthogonality) as competing methods like the Divide-and-Conquer or the QR algorithm. In this paper, we demonstrate how the use of mixed precisions in MRRR-based eigensolvers leads to improved orthogonality. At the same time, when compared to the classical use of the MRRR algorithm, our approach comes with no or only limited performance penalty, increases the robustness, and improves scalability.**High-Throughput Genome-Wide Association Analysis for Single and Multiple Phenotypes**Aachen Institute for Computational Engineering Science, RWTH Aachen, July 2012.

Technical Report AICES-2012/07-1.@techreport{Fabregat-Traver2012:20, author = "Diego Fabregat-Traver and {Yurii S.} Aulchenko and Paolo Bientinesi", title = "High-Throughput Genome-Wide Association Analysis for Single and Multiple Phenotypes", institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen", year = 2012, month = jul, note = "Technical Report AICES-2012/07-1", url = "http://arxiv.org/abs/1207.2169" }

abstractPDFbibtexThe variance component tests used in genomewide association studies of thousands of individuals become computationally exhaustive when multiple traits are analysed in the context of omics studies. We introduce two high-throughput algorithms -- CLAK-CHOL and CLAK-EIG -- for single and multiple phenotype genome-wide association studies (GWAS). The algorithms, generated with the help of an expert system, reduce the computational complexity to the point that thousands of traits can be analyzed for association with millions of polymorphisms in a course of days on a standard workstation. By taking advantage of problem specific knowledge, CLAK-CHOL and CLAK-EIG significantly outperform the current state-of-the-art tools in both single and multiple trait analysis.**Solving Dense Generalized Eigenproblems on Multi-Threaded Architectures**Aachen Institute for Computational Engineering Science, RWTH Aachen, November 2011.

Technical Report AICES-2011/11-3.@techreport{Aliaga2011:348, author = "Jose' Aliaga and Paolo Bientinesi and Davor Davidovic and Edoardo {Di Napoli} and Francisco Igual and {Enrique S.} Quintana-Orti", title = "Solving Dense Generalized Eigenproblems on Multi-Threaded Architectures", institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen", year = 2011, month = nov, note = "Technical Report AICES-2011/11-3" }

abstractbibtex**Proof-Driven Derivation of Krylov Solver Libraries**Aachen Institute for Computational Engineering Science, RWTH Aachen, June 2010.

Technical Report AICES-2010/06-3.PDFbibtex@techreport{Eijkhout2010:0, author = "Victor Eijkhout and Paolo Bientinesi and Robert {van de Geijn}", title = "Proof-Driven Derivation of Krylov Solver Libraries ", institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen", year = 2010, month = jun, note = "Technical Report AICES-2010/06-3", url = "http://www.aices.rwth-aachen.de:8080/~pauldj/pubs/Krylov-TR.pdf" }

**Automation in Dense Linear Algebra**Aachen Institute for Computational Engineering Science, RWTH Aachen, October 2008.

Technical Report AICES-2008-2.PDFbibtex@techreport{Bientinesi2008:748, author = "Paolo Bientinesi and Robert {van de Geijn}", title = "Automation in Dense Linear Algebra", institution = "Aachen Institute for Computational Engineering Science, RWTH Aachen", year = 2008, month = oct, note = "Technical Report AICES-2008-2", url = "http://www.aices.rwth-aachen.de:8080/~pauldj/pubs/CC-2009.pdf" }

**Multi-dimensional Array Memory Accesses for FFTs on Parallel Architectures.**Department of Computer Science, Duke University, December 2007.

Technical Report CS-2007-10.bibtex@techreport{Bientinesi2007:250, author = "Paolo Bientinesi and Nikos Pitsianis and Xiaobai Sun", title = "Multi-dimensional Array Memory Accesses for FFTs on Parallel Architectures. ", institution = "Department of Computer Science, Duke University", year = 2007, month = dec, note = "Technical Report CS-2007-10" }

**Sparse Direct Factorizations through Unassembled Hyper-Matrices**Texas Advanced Computing Center (TACC), The University of Texas at Austin, October 2007.

Technical Report TR-07-02.PDFbibtex@techreport{Bientinesi2007:178, author = "Paolo Bientinesi and Victor Eijkhout and Kyungjoo Kim and Jason Kurtz and Robert {van de Geijn}", title = "Sparse Direct Factorizations through Unassembled Hyper-Matrices", institution = "Texas Advanced Computing Center (TACC), The University of Texas at Austin", year = 2007, month = oct, note = "Technical Report TR-07-02", url = "http://www.aices.rwth-aachen.de:8080/~pauldj/pubs/uhmreport.pdf" }

**Parallel 2D FFTs on the Cell Broadband Engine**Department of Computer Science, Duke University, April 2007.

Technical Report CS-2007-03.bibtex@techreport{Bientinesi2007:4, author = "Paolo Bientinesi and Nikos Pitsianis and Xiaobai Sun", title = "Parallel 2D FFTs on the Cell Broadband Engine", institution = "Department of Computer Science, Duke University", year = 2007, month = apr, note = "Technical Report CS-2007-03" }

**Mechanical Derivation and Systematic Analysis of Correct Linear Algebra Algorithms**The University of Texas at Austin, Department of Computer Sciences, July 2006.

Technical Report TR-06-46.@techreport{Bientinesi2006:4, author = "Paolo Bientinesi", title = "Mechanical Derivation and Systematic Analysis of Correct Linear Algebra Algorithms", institution = "The University of Texas at Austin, Department of Computer Sciences", year = 2006, month = jul, note = "Technical Report TR-06-46", url = "http://www.aices.rwth-aachen.de:8080/~pauldj/pubs/thesis.pdf" }

abstractPDFbibtex**Families of Algorithms Related to the Inversion of a Symmetric Positive Definite Matrix**The University of Texas at Austin, Department of Computer Sciences, April 2006.

FLAME Working Note #19. Technical Report TR-06-20.bibtex@techreport{Bientinesi2006:610, author = "Paolo Bientinesi and Brian Gunter and Robert {van de Geijn}", title = "Families of Algorithms Related to the Inversion of a Symmetric Positive Definite Matrix", institution = "The University of Texas at Austin, Department of Computer Sciences", year = 2006, month = apr, note = "FLAME Working Note #19. Technical Report TR-06-20" }

**Representing Dense Linear Algebra Algorithms: A Farewell to Indices**The University of Texas at Austin, Department of Computer Sciences, February 2006.

FLAME Working Note #17. Technical Report TR-06-10.@techreport{Bientinesi2006:304, author = "Paolo Bientinesi and Robert {van de Geijn}", title = "Representing Dense Linear Algebra Algorithms: A Farewell to Indices", institution = "The University of Texas at Austin, Department of Computer Sciences", year = 2006, month = feb, note = "FLAME Working Note #17. Technical Report TR-06-10", url = "http://hpac.rwth-aachen.de/~pauldj/pubs/farewell.pdf" }

abstractPDFbibtexWe present a notation that allows a dense linear algebra algorithm to be represented in a way that is visually recognizable. The primary value of the notation is that it exposes subvectors and submatrices allowing the details of the algorithm to be the focus while hiding the intricate indices related to the arrays in which the vectors and matrices are stored. The applicability of the notation is illustrated through a succession of progressively complex case studies ranging from matrix-vector operations to the chasing of the bulge of the symmetric QR iteration. The notation facilitates comparing and contrasting different algorithms for the same operation as well as similar algorithms for different operations. Finally, we point out how algorithms represented with this notation can be directly translated into high-performance code.**FLAME 2005 Prospectus: Towards the Final Generation of Dense Linear Algebra Libraries**The University of Texas at Austin, Department of Computer Sciences, April 2005.

FLAME Working Note #16. Technical Report TR-05-15.bibtex@techreport{Bientinesi2005:218, author = "Paolo Bientinesi and Kazushige Goto and Tze {Meng Low} and {Enrique S.} Quintana-Orti and Robert {van de Geijn} and Field {Van Zee}", title = "FLAME 2005 Prospectus: Towards the Final Generation of Dense Linear Algebra Libraries", institution = "The University of Texas at Austin, Department of Computer Sciences", year = 2005, month = apr, note = "FLAME Working Note #16. Technical Report TR-05-15" }

**FLAME@Lab: A Farewell to Indices**The University of Texas at Austin, Department of Computer Sciences, April 2003.

FLAME Working Note #11. Technical Report TR-03-11.bibtex@techreport{Bientinesi2003:828, author = "Paolo Bientinesi and {Enrique S.} Quintana-Orti and Robert {van de Geijn}", title = "FLAME@Lab: A Farewell to Indices", institution = "The University of Texas at Austin, Department of Computer Sciences", year = 2003, month = apr, note = "FLAME Working Note #11. Technical Report TR-03-11" }

**The Science of Deriving Dense Linear Algebra Algorithms**The University of Texas at Austin, Department of Computer Sciences, September 2002.

FLAME Working Note #8. Technical Report TR-02-53.bibtex@techreport{Bientinesi2002:440, author = "Paolo Bientinesi and {John A.} Gunnels and {Margaret E.} Myers and {Enrique S.} Quintana-Orti and Robert {van de Geijn}", title = "The Science of Deriving Dense Linear Algebra Algorithms", institution = "The University of Texas at Austin, Department of Computer Sciences", year = 2002, month = sep, note = "FLAME Working Note #8. Technical Report TR-02-53" }

**A Parallel Eigensolver for Dense Symmetric Matrices Based on Multiple Relatively Robust Representations**The University of Texas at Austin, Department of Computer Sciences, September 2002.

Technical Report TR-03-26.bibtex@techreport{Bientinesi2002:54, author = "Paolo Bientinesi and Inderjit Dhillon and Robert {van de Geijn}", title = "A Parallel Eigensolver for Dense Symmetric Matrices Based on Multiple Relatively Robust Representations", institution = "The University of Texas at Austin, Department of Computer Sciences", year = 2002, month = sep, note = "Technical Report TR-03-26" }

**Electrostatic Fields Without Singularities: Implementation and Experiments**Institute for Computational Mathematics, CNR, Pisa, 1997.

Technical Report TR-B4-16-97.PDFbibtex@techreport{Bientinesi1997:760, author = "Paolo Bientinesi and Marco Pellegrini", title = "Electrostatic Fields Without Singularities: Implementation and Experiments", institution = "Institute for Computational Mathematics, CNR, Pisa", year = 1997, note = "Technical Report TR-B4-16-97", url = "http://www.aices.rwth-aachen.de:8080/~pauldj/pubs/report.pdf" }