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Linking Scientific Instruments and HPC: Patterns, Technologies, Experiences [article]

Rafael Vescovi, Ryan Chard, Nickolaus Saint, Ben Blaiszik, Jim Pruyne, Tekin Bicer, Alex Lavens, Zhengchun Liu, Michael E. Papka, Suresh Narayanan, Nicholas Schwarz, Kyle Chard (+1 others)
2022 arXiv   pre-print
We also present experiences with the application of these methods to the processing of data from five different scientific instruments, each of which engages HPC resources for data inversion, machine learning  ...  Such online analyses require methods for configuring and running high-performance distributed computing pipelines--what we call flows--linking instruments, HPC (e.g., for analysis, simulation, AI model  ...  APPLICATION EXPERIENCES We use five instrument+HPC applications to illustrate how the patterns and technologies described in preceding sections are realized and applied in practice.  ... 
arXiv:2204.05128v2 fatcat:nyjb3rf3angqpbh5ox4sojfegy

HPC Infrastructures Workshop #10

Huub Stoffers, Norbert Meyer, Gert Svensson, Andreas Johansson, Susanna Salminen, Hayk Shoukourian, François Robin
2019 Zenodo  
bringing technologies to the market relevant for energy-efficient HPC and energy-efficient HPC facility management in particular.  ...  The workshop covered a broad range of topics, ranging from cooling technologies to the provisioning of electricity, and from overviews of standards and certification to the management, storage, and analyses  ...  Acknowledgements This work was financially supported by the PRACE project funded in part by the EU's Horizon 2020 Research and Innovation programme (2014-2020) under grant agreement 730913.  ... 
doi:10.5281/zenodo.3773754 fatcat:dngi5432szcuvb4vm57ieqqywq

D7.5: HPC Programming Techniques

Cevdet Aykanat, Antun Balaz, Iris Christadler, Ivan Girotto, Jose Gracia, Vladimir Slavnic, Andy Sunderland, Ata Türk
2012 Zenodo  
Task 7.5 worked on five different areas to increase performance and scalability of user codes: Scalable algorithms Scalable libraries Multi-core/many core systems Accelerators Novel HPC languages Overall  ...  , more than 30 projects were carried out by 25 different partners and third parties.  ...  TAU instruments the source code with lightweight timers and then compiles and links. Both MPI functions and user functions are profiled with TAU, this profiling has negligible overhead.  ... 
doi:10.5281/zenodo.6552939 fatcat:z2gdhmnojrh6bj2lordyl7lmnq

Breaking HPC Barriers with the 56GbE Cloud

Muhammad Atif, Rika Kobayashi, Benjamin J. Menadue, Ching Yeh Lin, Matthew Sanderson, Allan Williams
2016 Procedia Computer Science  
This cloud is targeted at high-performance scientific applications, and enables scientists to build their own clusters when their demands and software stacks conflict with traditional bare-metal HPC environments  ...  A detailed analysis of these metrics in the context of micro-benchmarks and scientific applications is presented, including the affects of using TCP and RDMA on scientific applications.  ...  Where applicable, instrumented performance data obtained using IPM 9,10 are presented and detailed performance analysis is performed.  ... 
doi:10.1016/j.procs.2016.07.174 fatcat:7nym2pkzrndkpagvtx2ujkscje

HPC and Grid Computing for Integrative Biomedical Research

Tahsin Kurc, Shannon Hastings, Vijay Kumar, Stephen Langella, Ashish Sharma, Tony Pan, Scott Oster, David Ervin, Justin Permar, Sivaramakrishnan Narayanan, Yolanda Gil, Ewa Deelman (+4 others)
2009 The international journal of high performance computing applications  
With the increasing availability of high-throughput and high-resolution instruments, the integrative biomedical research imposes many challenging requirements on software middleware systems.  ...  In this paper, we look at some of these requirements using example research pattern templates.  ...  AGMT TECH-04049, and the NIH through grants #R24 HL085343, #R01 LM009239, and #79077CBS10.  ... 
doi:10.1177/1094342009106192 pmid:20107625 pmcid:PMC2811341 fatcat:5p26dv5uwnbqtjjhn3lnugmqly

Main Memory in HPC

Darko Zivanovic, Milan Pavlovic, Milan Radulovic, Hyunsung Shin, Jongpil Son, Sally A. Mckee, Paul M. Carpenter, Petar Radojković, Eduard Ayguadé
2017 ACM Transactions on Architecture and Code Optimization (TACO)  
Overall, the study identifies the HPC applications and use cases with memory footprints that could be provided by 3D-stacked memory chiplets, making a first step towards adoption of this novel technology  ...  This study analyzes the memory capacity requirements of important HPC benchmarks and applications.  ...  technology in the HPC domain.  ... 
doi:10.1145/3023362 fatcat:465twr4fzncxtjyqvdhj2cjx4m

HPC Infrastructures Workshop 2021

Gert Svensson
2021 Zenodo  
the latest trends in HPC infrastructure and supporting technologies for supercomputing centres.  ...  The 11th EWHPC event was held on the 18th and 19th of May 2021 and was followed, as usual, by a PRACE session on HPC infrastructures.  ...  Acknowledgements This work was financially supported by the PRACE project funded in part by the EU's Horizon 2020 Research and Innovation programme (2014-2020) under grant agreement 823767.  ... 
doi:10.5281/zenodo.5794766 fatcat:p3phw2u6vzfjxoutydphkf4x3m

Scaling Spark on HPC Systems

Nicholas Chaimov, Allen Malony, Shane Canon, Costin Iancu, Khaled Z. Ibrahim, Jay Srinivasan
2016 Proceedings of the 25th ACM International Symposium on High-Performance Parallel and Distributed Computing - HPDC '16  
We report our experiences porting Spark to large production HPC systems.  ...  Overall, our results indicate that scalability is currently limited to O(10 2 ) cores in a HPC installation with Lustre and default Spark.  ...  This work has been partially supported by the US Department of Defense and by Intel through an Intel Parallel Computing Center grant to LBNL.  ... 
doi:10.1145/2907294.2907310 dblp:conf/hpdc/ChaimovMCIIS16 fatcat:cuske3juqbd3rdq7nzkeuvnf7a

D4.4: Collaboration plan with non-European HPC stakeholders Final

Andrew Emerson, Giovanni Erbacci, Georgi Prangov, Nelly Stoyanova, Ana Bela Dias
2011 Zenodo  
Regions not including the USA and Europe, but with high HPC investments include Russia, S.E.  ...  The challenges facing the development and exploitation of HPC can only be addressed in partnership with its stakeholders.  ...  HPC will increasingly depend upon economic instruments complementary to conventional technological and scientific inputs.  ... 
doi:10.5281/zenodo.6552866 fatcat:bcet5yhrf5amlizok54zk237jm

HPC Benchmarking: Problem Size Matters

Vladimir Marjanovic, Jose Gracia, Colin W. Glass
2016 2016 7th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS)  
Lately, two benchmarks, arguably more representative of typical modern workloads, have been proposed: HPCG and HPGMG.  ...  However, we refrain from proposing the specific way to best compose such an aggregate and invite the community to open the discussion on the topic.  ...  ACKNOWLEDGMENT The authors would like to thank Peter Kogge for the encouragement and insightful discussion on the topics of this paper, Ryusuke Egawa and staff at Tohoku University for helping setting  ... 
doi:10.1109/pmbs.2016.006 dblp:conf/sc/MarjanovicGG16 fatcat:r6v6zngdcbhv3kuryz2u6c22uy

Eurolab-4-HPC Long-Term Vision on High-Performance Computing [article]

Theo Ungerer, Paul Carpenter
2018 arXiv   pre-print
Because of the long-term perspective and its speculative nature, the authors started with an assessment of future computing technologies that could influence HPC hardware and software.  ...  , software, and applications in High-Performance Computing (HPC).  ...  Typically, funding instruments and calls focus on basic technologies and specific modules and in some cases towards point-topoint links as a final objective (e.g. optical cables).  ... 
arXiv:1807.04521v1 fatcat:5neetrgubjhnvcajcktpkohrzq

D5.4: HPC Infrastructures Workshop #9

Huub Stoffers
2018 Zenodo  
for HPC centres.  ...  The workshop brought together experts from the vendor side and experts from the HPC datacentre facility management side.  ...  In summary, the prototype was considered a successful demonstration of porting relevant scientific HPC applications to an FPGA-accelerated architecture.  ... 
doi:10.5281/zenodo.6805973 fatcat:o2kwdb7xcvd3vc7lxurvesmrpa

Construction of an Intelligent Arrangement Model for Vocal Music Based on HPC Cluster Programming

Tianzhuo Gong, Chunli Han, Sheng Bin
2022 Scientific Programming  
The rapid development of HPC technology has promoted the study of automatic music generation technology, which effectively avoids the traditional machine learning method of music.  ...  We model in this paper the HPC cluster programming structure and perform a multidimensional computational analysis to design a vocal intelligent arrangement model based on HPC cluster programming using  ...  Figure 8 :Figure 9 : 89 Figure 8: Instrumental song style analysis. Scientific Programming  ... 
doi:10.1155/2022/9728085 fatcat:ecnul5nopzezlnd2xqfbjiwpzi

DARPA's HPCS Program: History, Models, Tools, Languages [chapter]

Jack Dongarra, Robert Graybill, William Harrod, Robert Lucas, Ewing Lusk, Piotr Luszczek, Janice Mcmahon, Allan Snavely, Jeffrey Vetter, Katherine Yelick, Sadaf Alam, Roy Campbell (+5 others)
2008 Advances in Computers  
government agencies to address HPC technology and application challenges for the next decade.  ...  Patterns of activity were used to generate a representative workflow for HPC code development.  ... 
doi:10.1016/s0065-2458(08)00001-6 fatcat:ilchf26s2fgkzlnqplxt243u7m

D3.3.1: Survey of HPC education and training needs

Tim Stitt, Tim Robinson
2008 Zenodo  
In this report we present the outcome of a comprehensive survey of HPC training and educational needs amongst the top-tier users across all PRACE partner sites.  ...  Furthermore, it is revealed that users would significantly benefit from a centralised European repository of training material and HPC knowledge dissemination.  ...  experience in the HPC field, and the scientific domains in which they carry out their computational research.  ... 
doi:10.5281/zenodo.6543230 fatcat:67kvbjhnt5hl5isho4s2kx5osu
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