Ralph Müller-Pfefferkorn

The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations

The MoSGrid portal offers an approach to carry out high-quality molecular simulations on distributed compute infrastructures to scientists with all kinds of background and experience levels. A user-friendly Web interface guarantees the ease-of-use of modern chemical simulation applications well established in the field. The usage of well-defined workflows annotated with metadata largely improves the reproducibility of simulations in the sense of good lab practice. The MoSGrid science gateway supports applications in the domains quantum chemistry (QC), molecular dynamics (MD), and docking. This paper presents the open-source MoSGrid architecture as well as lessons learned from its design.

A Single Sign-On Infrastructure for Science Gateways on a Use Case for Structural Bioinformatics

Structural bioinformatics applies computational methods to analyze and model three-dimensional molecular structures. There is a huge number of applications available to work with structural data on large scale. Using these tools on distributed computing infrastructures (DCIs), however, is often complicated due to a lack of suitable interfaces. The MoSGrid (Molecular Simulation Grid) science gateway provides an intuitive user interface to several widely-used applications for structural bioinformatics, molecular modeling, and quantum chemistry. It ensures the confidentiality, integrity, and availability of data via a granular security concept, which covers all layers of the infrastructure. The security concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the Grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled Grid portal WS-PGRADE (Web Services Parallel Grid Runtime and Developer Environment), the gUSE (Grid User Support Environment) DCI services, and the cloud file system XtreemFS. The presented security infrastructure allows a single sign-on process to all involved DCI components and, therefore, lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics.

Standards-based metadata management for molecular simulations

State‐of‐the‐art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high‐performance computing. The MoSGrid (molecular simulation grid) infrastructure relieves this burden from scientists by providing a science gateway, which eases access to and usage of computational chemistry applications. One of its cornerstones is the molecular simulations markup language (MSML), an extension of the chemical markup language. MSML abstracts all chemical as well as computational aspects of simulations. An application and its results can be described with common semantics. Using such application, independent descriptions users can easily switch between different applications or compare them. This paper introduces MSML, its integration into a science gateway, and its usage for molecular dynamics, quantum chemistry, and protein docking. Copyright

Scout: a source-to-source transformator for SIMD-Optimizations

We present Scout, a configurable source-to-source transformation tool designed to automatically vectorize C source code. Scout provides the means to vectorize loops using SIMD instructions at source level. Our main focus during the development of Scout is a maximum flexibility of the tool in two ways: being capable of vectorizing a wide range of loop constructs and being capable of targeting various modern SIMD architectures. Scout supports several SIMD instructions sets like SSE or AVX and is easily extensible to upcoming ones. In the second part of the paper we present results of applying Scouts vectorizing capabilities to CFD production codes of the German Aerospace Center. The complex loops used in these codes often inhibit the automatic vectorization of usual C compilers. In contrast, Scout is able to vectorize most of these loops. We measured the resulting speedup for SSE and AVX platforms.

Managing large datasets with iRODS—A performance analysis

The integrated Rule Orientated Data System (iRODS) is a Grid data management system that organizes distributed data and their metadata. A Rule Engine allows a flexible definition of data storage, data access and data processing. This paper presents scenarios implemented in a benchmark tool to measure the performance of an iRODS environment as well as results of measurements with large datasets. The scenarios concentrate on data transfers, metadata transfers and stress tests. The user has the possibility to influence the scenarios to adapt them to his own use case. The results show the possibility to find bottlenecks and potential to optimize the settings of an iRODS environment.

Optimizing cache access: A tool for source-to-source transformations and real-life compiler tests

Loop transformations are well known to be a very useful tool for performance improvements by optimizing cache access. Nevertheless, the automatic application is a complex and challenging task especially for parallel codes. Since the end of the 1980’s it has been promised by most compiler vendors that these features will be implemented – in the next release. We tested current FORTRAN90 compilers (on IBM, Intel and SGI hardware) for their capabilities in this field. This paper shows the results of our analysis. Motivated by this experience we have developed the optimization environment Goofi to assist programmers in applying loop transformations to their code thus gaining better performance for parallel codes even today.

GASPI – A Partitioned Global Address Space Programming Interface

At the threshold to exascale computing, limitations of the MPI programming model become more and more pronounced. HPC programmers have to design codes that can run and scale on systems with hundreds of thousands of cores. Setting up accordingly many communication buffers, point-to-point communication links, and using bulk-synchronous communication phases is contradicting scalability in these dimensions. Moreover, the reliability of upcoming systems will worsen.

Job monitoring and steering in D-Grid's High Energy Physics Community Grid

In the High Energy Physics Comunity Grid (HEPCG) of Germanys D-Grid initiative, a suite of tools supporting the user in monitoring his jobs was developed. In the HEP community many users submit large numbers of jobs. A considerable fraction of these jobs fail for various reasons. Until now, it has been hard or even impossible for the user to find the reason for the job failure. The AMon tool supports the user with a graphical web-based overview on status and resource usage of his jobs. The script wrapper JEM (Job Execution Monitor) monitors a jobs environment giving detailed information about the job execution. Finally, once the job itself is running, a computational steering tool allows the user to interact with his job at runtime, to visualize intermediate results, and to modify job parameters.

HICFD: Highly Efficient Implementation of CFD Codes for HPC Many-Core Architectures

The objective of the German BMBF research project Highly Efficient Implementation of CFD Codes for HPC Many-Core Architectures (HICFD) is to develop new methods and tools for the analysis and optimization of the performance of parallel computational fluid dynamics (CFD) codes on high performance computer systems with many-core processors. In the work packages of the project it is investigated how the performance of parallel CFD codes written in C can be increased by the optimal use of all parallelism levels. On the highest level Message Passing Interface (MPI) is utilized. Furthermore, on the level of the many-core architecture, highly scaling, hybrid OpenMP/MPI methods are implemented. On the level of the processor cores the parallel Single Instruction Multiple Data (SIMD) units provided by modern CPUs are exploited.

User- and job-centric monitoring: Analysing and presenting large amounts of monitoring data

For data analysis or simulations (e.g. in particle physics) single users submit hundreds or thousands of jobs to the Grid. This puts a new burden on the users side - keeping an overview on the status and performance of the jobs in a distributed environment. In this paper, a user- and job-centric monitoring system is presented. It collects job and system specific information, analyses them and presents them graphically to the user. In the analysis of the monitoring data job problems are classified to give hints to the user. The graphical and interactive presentation allows the user to easily keep an overview as well as to dig into more detailed monitoring data.