scholarly journals ScalaLab and GroovyLab: Comparing Scala and Groovy for Scientific Computing

2015 ◽  
Vol 2015 ◽  
pp. 1-13
Author(s):  
Stergios Papadimitriou ◽  
Kirsten Schwark ◽  
Seferina Mavroudi ◽  
Kostas Theofilatos ◽  
Spiridon Likothanasis
Keyword(s):  
Programming Language ◽  
User Interfaces ◽  
High Performance ◽  
Scientific Computing ◽  
Point Of View ◽  
Java Virtual Machine ◽  
Programming Environment ◽  
Fast Pace ◽  
Native Code ◽  
Performance Computing

ScalaLab and GroovyLab are both MATLAB-like environments for the Java Virtual Machine. ScalaLab is based on the Scala programming language and GroovyLab is based on the Groovy programming language. They present similar user interfaces and functionality to the user. They also share the same set of Java scientific libraries and of native code libraries. From the programmer's point of view though, they have significant differences. This paper compares some aspects of the two environments and highlights some of the strengths and weaknesses of Scala versus Groovy for scientific computing. The discussion also examines some aspects of the dilemma of using dynamic typing versus static typing for scientific programming. The performance of the Java platform is continuously improved at a fast pace. Today Java can effectively support demanding high-performance computing and scales well on multicore platforms. Thus, both systems can challenge the performance of the traditional C/C++/Fortran scientific code with an easier to use and more productive programming environment.

The design of JVM and native libraries in ScalaLab for efficient scientific computation

2018 ◽  
Vol 09 (05) ◽  
pp. 1850037 ◽  
Author(s):  
Stergios Papadimitriou ◽  
Lefteris Moussiades
Keyword(s):  
High Performance ◽  
Scientific Computing ◽  
Java Virtual Machine ◽  
Just In Time ◽  
Instruction Sets ◽  
Fast Pace ◽  
Native Code ◽  
Scientific Libraries ◽  
Java Native Interface ◽  
Performance Computing

ScalaLab is a MATLAB-like environment for the Java Virtual Machine (JVM). ScalaLab is based on the Scala programming language. It utilizes an extensive set of Java and Scala scientific libraries and also has access to many native C/C[Formula: see text] scientific libraries by using mainly the Java Native Interface (JNI). The performance of the JVM platform is continuously improved at a fast pace. Today JVM can effectively support demanding high-performance computing and scales well on multicore platforms. However, sometimes optimized native C/[Formula: see text] code can yield even better performance, by exploiting low-level programming issues, such as optimization of caches and architecture-dependent instruction sets. The present work reports some of the experiences that we gained with experiments with both Just in Time (JIT) JVM code and native code. We compare some aspects of Scala and C[Formula: see text] that concern the requirements of scientific computing and highlight some strong features of the Scala language that facilitate the implementation of scientific scripting. This paper describes how ScalaLab tries to combine the best features of the JVM with those of the C/C[Formula: see text] technology, in order to implement an effective scientific computing environment.

scholarly journals High-performance Python for crystallographic computing

2019 ◽  
Vol 52 (4) ◽  
pp. 882-897 ◽  
Author(s):  
A. Boulle ◽  
J. Kieffer
Keyword(s):  
Programming Language ◽  
High Performance ◽  
Scientific Computing ◽  
State Of The Art ◽  
Third Party ◽  
Improve Performance ◽  
Python Language ◽  
Python Programming Language ◽  
Numerical Computing ◽  
Python Programming

The Python programming language, combined with the numerical computing library NumPy and the scientific computing library SciPy, has become the de facto standard for scientific computing in a variety of fields. This popularity is mainly due to the ease with which a Python program can be written and executed (easy syntax, dynamical typing, no compilation etc.), coupled with the existence of a large number of specialized third-party libraries that aim to lift all the limitations of the raw Python language. NumPy introduces vector programming, improving execution speeds, whereas SciPy brings a wealth of highly optimized and reliable scientific functions. There are cases, however, where vector programming alone is not sufficient to reach optimal performance. This issue is addressed with dedicated compilers that aim to translate Python code into native and statically typed code with support for the multi-core architectures of modern processors. In the present article it is shown how these approaches can be efficiently used to tackle different problems, with increasing complexity, that are relevant to crystallography: the 2D Laue function, scattering from a strained 2D crystal, scattering from 3D nanocrystals and, finally, diffraction from films and multilayers. For each case, detailed implementations and explanations of the functioning of the algorithms are provided. Different Python compilers (namely NumExpr, Numba, Pythran and Cython) are used to improve performance and are benchmarked against state-of-the-art NumPy implementations. All examples are also provided as commented and didactic Python (Jupyter) notebooks that can be used as starting points for crystallographers curious to enter the Python ecosystem or wishing to accelerate their existing codes.

Estimating the overhead and coupling of scientific computing clusters

SIMULATION ◽  
2021 ◽  
pp. 003754972110641
Author(s):  
Aurelio Vivas ◽  
Harold Castro
Keyword(s):  
High Performance ◽  
Scientific Computing ◽  
Virtual Machines ◽  
Building Blocks ◽  
Scientific Applications ◽  
Computing Systems ◽  
The Third ◽  
Cluster Of Workstations ◽  
Computer Aided ◽  
Performance Computing

Since simulation became the third pillar of scientific research, several forms of computers have become available to drive computer aided simulations, and nowadays, clusters are the most popular type of computers supporting these tasks. For instance, cluster settings, such as the so-called supercomputers, cluster of workstations (COW), cluster of desktops (COD), and cluster of virtual machines (COV) have been considered in literature to embrace a variety of scientific applications. However, those scientific applications categorized as high-performance computing (HPC) are conceptually restricted to be addressed only by supercomputers. In this aspect, we introduce the notions of cluster overhead and cluster coupling to assess the capacity of non-HPC systems to handle HPC applications. We also compare the cluster overhead with an existing measure of overhead in computing systems, the total parallel overhead, to explain the correctness of our methodology. The evaluation of capacity considers the seven dwarfs of scientific computing, which are well-known, scientific computing building blocks considered in the development of HPC applications. The evaluation of these building blocks provides insights regarding the strengths and weaknesses of non-HPC systems to deal with future HPC applications developed with one or a combination of these algorithmic building blocks.

scholarly journals HPC resource integration into CMS Computing via HEPCloud

2019 ◽  
Vol 214 ◽  
pp. 03031
Author(s):  
Dirk Hufnagel ◽  
Burt Holzman ◽  
David Mason ◽  
Parag Mhashilkar ◽  
Steven Timm ◽  
...  
Keyword(s):  
High Performance Computing ◽  
Performance Studies ◽  
High Performance ◽  
Scientific Computing ◽  
Current Model ◽  
Scaling Up ◽  
Resource Integration ◽  
Present Experience ◽  
Performance Computing ◽  
Increased Pressure

The higher energy and luminosity from the LHC in Run 2 have put increased pressure on CMS computing resources. Extrapolating to even higher luminosities (and thus higher event complexities and trigger rates) beyond Run 3, it becomes clear that simply scaling up the the current model of CMS computing alone will become economically unfeasible. High Performance Computing (HPC) facilities, widely used in scientific computing outside of HEP, have the potential to help fill the gap. Here we describe the U.S.CMS efforts to integrate US HPC resources into CMS Computing via the HEPCloud project at Fermilab. We present advancements in our ability to use NERSC resources at scale and efforts to integrate other HPC sites as well. We present experience in the elastic use of HPC resources, quickly scaling up use when so required by CMS workflows. We also present performance studies of the CMS multi-threaded framework on both Haswell and KNL HPC resources.

scholarly journals Understanding the landscape of scientific software used on high-performance computing platforms

2020 ◽  
Vol 34 (4) ◽  
pp. 465-477
Author(s):  
A Grannan ◽  
K Sood ◽  
B Norris ◽  
A Dubey
Keyword(s):  
High Performance Computing ◽  
High Performance ◽  
Scientific Computing ◽  
Scientific Discovery ◽  
Simulation Software ◽  
Scientific Software ◽  
Survey Paper ◽  
Software Productivity ◽  
Computing Platforms ◽  
Performance Computing

Scientific discovery increasingly relies on computation through simulations, analytics, and machine and deep learning. Of these, simulations on high-performance computing (HPC) platforms have been the cornerstone of scientific computing for more than two decades. However, the development of simulation software has, in general, occurred through accretion, with a few exceptions. With an increase in scientific understanding, models have become more complex, rendering an accretion mode untenable to the point where software productivity and sustainability have become active concerns in scientific computing. In this survey paper, we examine a modest set of HPC scientific simulation applications that are already using cutting-edge HPC platforms. Several have been in existence for a decade or more. Our objective in this survey is twofold: first, to understand the landscape of scientific computing on HPC platforms in order to distill the currently scattered knowledge about software practices that have helped both developer and software productivity, and second, to understand the kind of tools and methodologies that need attention for continued productivity.

scholarly journals UTOPIA—User-Friendly Tools for Operating Informatics Applications

2004 ◽  
Vol 5 (1) ◽  
pp. 56-60 ◽  
Author(s):  
S. R. Pettifer ◽  
J. R. Sinnott ◽  
T. K. Attwood
Keyword(s):  
Real Time ◽  
User Interfaces ◽  
High Performance ◽  
Ad Hoc ◽  
Point Of View ◽  
Cognitive Capacity ◽  
End User ◽  
Time Interaction ◽  
Data Files ◽  
Visualization Systems

Bioinformaticians routinely analyse vast amounts of information held both in large remote databases and in flat data files hosted on local machines. The contemporary toolkit available for this purpose consists of anad hoccollection of data manipulation tools, scripting languages and visualization systems; these must often be combined in complex and bespoke ways, the result frequently being an unwieldy artefact capable of one specific task, which cannot easily be exploited or extended by other practitioners. Owing to the sizes of current databases and the scale of the analyses necessary, routine bioinformatics tasks are often automated, but many still require the unique experience and intuition of human researchers: this requires tools that support real-time interaction with complex datasets. Many existing tools have poor user interfaces and limited real-time performance when applied to realistically large datasets; much of the user's cognitive capacity is therefore focused on controlling the tool rather than on performing the research. The UTOPIA project is addressing some of these issues by building reusable software components that can be combined to make useful applications in the field of bioinformatics. Expertise in the fields of human computer interaction, high-performance rendering, and distributed systems is being guided by bioinformaticians and end-user biologists to create a toolkit that is both architecturally sound from a computing point of view, and directly addresses end-user and application-developer requirements.

EXECUTION OF SEQUENTIAL AND PARALLEL JAVA BYTECODE IN A METACOMPUTING SYSTEM

2003 ◽  
Vol 13 (01) ◽  
pp. 53-64 ◽  
Author(s):  
ERIC GAMESS
Keyword(s):  
Linear Algebra ◽  
Virtual Machine ◽  
Message Passing ◽  
High Performance ◽  
Scientific Computing ◽  
Message Passing Interface ◽  
Java Virtual Machine ◽  
Parallel Applications ◽  
Beowulf Cluster ◽  
Java Bytecode

In this paper, we address the goal of executing Java parallel applications in a group of nodes of a Beowulf cluster transparently chosen by a metacomputing system oriented to efficient execution of Java bytecode, with support for scientific computing. To this end, we extend the Java virtual machine by providing a message passing interface and quick access to distributed high performance resources. Also, we introduce the execution of parallel linear algebra methods for large objects from sequential Java applications by invoking SPLAM, our parallel linear algebra package.

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