T. Scogland, Jonathan J. Azose, D. Rohr, Suzanne Rivoire, Natalie J. Bates, D. Hackenberg
The last decade has seen power consumption move from an afterthought to the foremost design constraint of new supercomputers. Measuring the power of a supercomputer can be a daunting proposition, and as a result, many published measurements are extrapolated. This paper explores the validity of these extrapolations in the context of inter-node power variability and power variations over time within a run. We characterize power variability across nodes in systems at eight supercomputer centers across the globe. This characterization shows that the current requirement for measurements submitted to the Green500 and others is insufficient, allowing variations of up to 20% due to measurement timing and a further 10--15% due to insufficient sample sizes. This paper proposes new power and energy measurement requirements for supercomputers, some of which have been accepted for use by the Green500 and Top500, to ensure consistent accuracy.
{"title":"Node variability in large-scale power measurements: perspectives from the Green500, Top500 and EEHPCWG","authors":"T. Scogland, Jonathan J. Azose, D. Rohr, Suzanne Rivoire, Natalie J. Bates, D. Hackenberg","doi":"10.1145/2807591.2807653","DOIUrl":"https://doi.org/10.1145/2807591.2807653","url":null,"abstract":"The last decade has seen power consumption move from an afterthought to the foremost design constraint of new supercomputers. Measuring the power of a supercomputer can be a daunting proposition, and as a result, many published measurements are extrapolated. This paper explores the validity of these extrapolations in the context of inter-node power variability and power variations over time within a run. We characterize power variability across nodes in systems at eight supercomputer centers across the globe. This characterization shows that the current requirement for measurements submitted to the Green500 and others is insufficient, allowing variations of up to 20% due to measurement timing and a further 10--15% due to insufficient sample sizes. This paper proposes new power and energy measurement requirements for supercomputers, some of which have been accepted for use by the Green500 and Top500, to ensure consistent accuracy.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125412529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Marc Gamell, K. Teranishi, M. Heroux, J. Mayo, H. Kolla, Jacqueline H. Chen, M. Parashar
Application resilience is a key challenge that has to be addressed to realize the exascale vision. Online recovery, even when it involves all processes, can dramatically reduce the overhead of failures as compared to the more traditional approach where the job is terminated and restarted from the last checkpoint. In this paper we explore how local recovery can be used for certain classes of applications to further reduce overheads due to resilience. Specifically we develop programming support and scalable runtime mechanisms to enable online and transparent local recovery for stencil-based parallel applications on current leadership class systems. We also show how multiple independent failures can be masked to effectively reduce the impact on the total time to solution. We integrate these mechanisms with the S3D combustion simulation, and experimentally demonstrate (using the Titan Cray-XK7 system at ORNL) the ability to tolerate high failure rates (i.e., node failures every 5 seconds) with low overhead while sustaining performance, at scales up to 262144 cores.
{"title":"Local recovery and failure masking for stencil-based applications at extreme scales","authors":"Marc Gamell, K. Teranishi, M. Heroux, J. Mayo, H. Kolla, Jacqueline H. Chen, M. Parashar","doi":"10.1145/2807591.2807672","DOIUrl":"https://doi.org/10.1145/2807591.2807672","url":null,"abstract":"Application resilience is a key challenge that has to be addressed to realize the exascale vision. Online recovery, even when it involves all processes, can dramatically reduce the overhead of failures as compared to the more traditional approach where the job is terminated and restarted from the last checkpoint. In this paper we explore how local recovery can be used for certain classes of applications to further reduce overheads due to resilience. Specifically we develop programming support and scalable runtime mechanisms to enable online and transparent local recovery for stencil-based parallel applications on current leadership class systems. We also show how multiple independent failures can be masked to effectively reduce the impact on the total time to solution. We integrate these mechanisms with the S3D combustion simulation, and experimentally demonstrate (using the Titan Cray-XK7 system at ORNL) the ability to tolerate high failure rates (i.e., node failures every 5 seconds) with low overhead while sustaining performance, at scales up to 262144 cores.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128235949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. Kathareios, C. Minkenberg, B. Prisacari, G. Rodríguez, T. Hoefler
HPC network topology design is currently shifting from high-performance, higher-cost Fat-Trees to more cost-effective architectures. Three diameter-two designs, the Slim Fly, Multi-Layer Full-Mesh, and Two-Level Orthogonal Fat-Tree excel in this, exhibiting a cost per endpoint of only 2 links and 3 router ports with lower end-to-end latency and higher scalability than traditional networks of the same total cost. However, other than for the Slim Fly, there is currently no clear understanding of the performance and routing of these emerging topologies. For each network, we discuss minimal, indirect random, and adaptive routing algorithms along with deadlock-avoidance mechanisms. Using these, we evaluate the performance of a series of representative workloads, from global uniform and worst-case traffic to the all-to-all and near-neighbor exchange patterns prevalent in HPC applications. We show that while all three topologies have similar performance, OFTs scale to twice as many endpoints at the same cost as the others.
{"title":"Cost-effective diameter-two topologies: analysis and evaluation","authors":"G. Kathareios, C. Minkenberg, B. Prisacari, G. Rodríguez, T. Hoefler","doi":"10.1145/2807591.2807652","DOIUrl":"https://doi.org/10.1145/2807591.2807652","url":null,"abstract":"HPC network topology design is currently shifting from high-performance, higher-cost Fat-Trees to more cost-effective architectures. Three diameter-two designs, the Slim Fly, Multi-Layer Full-Mesh, and Two-Level Orthogonal Fat-Tree excel in this, exhibiting a cost per endpoint of only 2 links and 3 router ports with lower end-to-end latency and higher scalability than traditional networks of the same total cost. However, other than for the Slim Fly, there is currently no clear understanding of the performance and routing of these emerging topologies. For each network, we discuss minimal, indirect random, and adaptive routing algorithms along with deadlock-avoidance mechanisms. Using these, we evaluate the performance of a series of representative workloads, from global uniform and worst-case traffic to the all-to-all and near-neighbor exchange patterns prevalent in HPC applications. We show that while all three topologies have similar performance, OFTs scale to twice as many endpoints at the same cost as the others.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131366510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dramatic advances in DNA sequencing technology have made it possible to study microbial environments by direct sequencing of environmental DNA samples. Yet, due to the huge volume and high data complexity, current de novo assemblers cannot handle large metagenomic datasets or fail to perform assembly with acceptable quality. This paper presents the first parallel solution for decomposing the metagenomic assembly problem without compromising the post-assembly quality. We transform this problem into that of finding weakly connected components in the de Bruijn graph. We propose a novel distributed memory algorithm to identify the connected subgraphs, and present strategies to minimize the communication volume. We demonstrate the scalability of our algorithm on a soil metagenome dataset with 1.8 billion reads. Our approach achieves a runtime of 22 minutes using 1280 Intel Xeon cores for a 421 GB uncompressed FASTQ dataset. Moreover, our solution is generalizable to finding connected components in arbitrary undirected graphs.
{"title":"A parallel connectivity algorithm for de Bruijn graphs in metagenomic applications","authors":"P. Flick, Chirag Jain, Tony Pan, S. Aluru","doi":"10.1145/2807591.2807619","DOIUrl":"https://doi.org/10.1145/2807591.2807619","url":null,"abstract":"Dramatic advances in DNA sequencing technology have made it possible to study microbial environments by direct sequencing of environmental DNA samples. Yet, due to the huge volume and high data complexity, current de novo assemblers cannot handle large metagenomic datasets or fail to perform assembly with acceptable quality. This paper presents the first parallel solution for decomposing the metagenomic assembly problem without compromising the post-assembly quality. We transform this problem into that of finding weakly connected components in the de Bruijn graph. We propose a novel distributed memory algorithm to identify the connected subgraphs, and present strategies to minimize the communication volume. We demonstrate the scalability of our algorithm on a soil metagenome dataset with 1.8 billion reads. Our approach achieves a runtime of 22 minutes using 1280 Intel Xeon cores for a 421 GB uncompressed FASTQ dataset. Moreover, our solution is generalizable to finding connected components in arbitrary undirected graphs.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133071999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Graphics processing units (GPUs) are increasingly utilized as throughput engines in the modern computer systems. GPUs rely on fast context switching between thousands of threads to hide long latency operations, however, they still stall due to the memory operations. To minimize the stalls, memory operations should be overlapped with other operations as much as possible to maximize memory-level parallelism (MLP). In this paper, we propose Earliest Load First (ELF) warp scheduling, which maximizes the MLP by giving higher priority to the warps that have the fewest instructions to the next memory load. ELF utilizes the same warp priority for the fetch scheduling so that both are coordinated. We also show that ELF reveals its full benefits when there are fewer memory conflicts and fetch stalls. Evaluations show that ELF can improve the performance by 4.1% and achieve total improvement of 11.9% when used with other techniques over commonly-used greedy-then-oldest scheduling.
{"title":"ELF: maximizing memory-level parallelism for GPUs with coordinated warp and fetch scheduling","authors":"Jason Jong Kyu Park, Yongjun Park, S. Mahlke","doi":"10.1145/2807591.2807598","DOIUrl":"https://doi.org/10.1145/2807591.2807598","url":null,"abstract":"Graphics processing units (GPUs) are increasingly utilized as throughput engines in the modern computer systems. GPUs rely on fast context switching between thousands of threads to hide long latency operations, however, they still stall due to the memory operations. To minimize the stalls, memory operations should be overlapped with other operations as much as possible to maximize memory-level parallelism (MLP). In this paper, we propose Earliest Load First (ELF) warp scheduling, which maximizes the MLP by giving higher priority to the warps that have the fewest instructions to the next memory load. ELF utilizes the same warp priority for the fetch scheduling so that both are coordinated. We also show that ELF reveals its full benefits when there are fewer memory conflicts and fetch stalls. Evaluations show that ELF can improve the performance by 4.1% and achieve total improvement of 11.9% when used with other techniques over commonly-used greedy-then-oldest scheduling.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"180 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133489577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Rudi, A. Malossi, T. Isaac, G. Stadler, M. Gurnis, P. Staar, Y. Ineichen, C. Bekas, A. Curioni, O. Ghattas
Mantle convection is the fundamental physical process within earth's interior responsible for the thermal and geological evolution of the planet, including plate tectonics. The mantle is modeled as a viscous, incompressible, non-Newtonian fluid. The wide range of spatial scales, extreme variability and anisotropy in material properties, and severely nonlinear rheology have made global mantle convection modeling with realistic parameters prohibitive. Here we present a new implicit solver that exhibits optimal algorithmic performance and is capable of extreme scaling for hard PDE problems, such as mantle convection. To maximize accuracy and minimize runtime, the solver incorporates a number of advances, including aggressive multi-octree adaptivity, mixed continuous-discontinuous discretization, arbitrarily-high-order accuracy, hybrid spectral/geometric/algebraic multigrid, and novel Schur-complement preconditioning. These features present enormous challenges for extreme scalability. We demonstrate that---contrary to conventional wisdom---algorithmically optimal implicit solvers can be designed that scale out to 1.5 million cores for severely nonlinear, ill-conditioned, heterogeneous, and anisotropic PDEs.
{"title":"An extreme-scale implicit solver for complex PDEs: highly heterogeneous flow in earth's mantle","authors":"J. Rudi, A. Malossi, T. Isaac, G. Stadler, M. Gurnis, P. Staar, Y. Ineichen, C. Bekas, A. Curioni, O. Ghattas","doi":"10.1145/2807591.2807675","DOIUrl":"https://doi.org/10.1145/2807591.2807675","url":null,"abstract":"Mantle convection is the fundamental physical process within earth's interior responsible for the thermal and geological evolution of the planet, including plate tectonics. The mantle is modeled as a viscous, incompressible, non-Newtonian fluid. The wide range of spatial scales, extreme variability and anisotropy in material properties, and severely nonlinear rheology have made global mantle convection modeling with realistic parameters prohibitive. Here we present a new implicit solver that exhibits optimal algorithmic performance and is capable of extreme scaling for hard PDE problems, such as mantle convection. To maximize accuracy and minimize runtime, the solver incorporates a number of advances, including aggressive multi-octree adaptivity, mixed continuous-discontinuous discretization, arbitrarily-high-order accuracy, hybrid spectral/geometric/algebraic multigrid, and novel Schur-complement preconditioning. These features present enormous challenges for extreme scalability. We demonstrate that---contrary to conventional wisdom---algorithmically optimal implicit solvers can be designed that scale out to 1.5 million cores for severely nonlinear, ill-conditioned, heterogeneous, and anisotropic PDEs.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127644031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
H. Kabir, J. Booth, G. Aupy, A. Benoit, Y. Robert, P. Raghavan
We consider techniques to improve the performance of parallel sparse triangular solution on non-uniform memory architecture multicores by extending earlier coloring and level set schemes for single-core multiprocessors. We develop STS-k, where k represents a small number of transformations for latency reduction from increased spatial and temporal locality of data accesses. We propose a graph model of data reuse to inform the development of STS-k and to prove that computing an optimal cost schedule is NP-complete. We observe significant speed-ups with STS-3 on 32-core Intel Westmere-Ex and 24-core AMD `MagnyCours' processors. Incremental gains solely from the 3-level transformations in STS-3 for a fixed ordering, correspond to reductions in execution times by factors of 1.4(Intel) and 1.5(AMD) for level sets and 2(Intel) and 2.2(AMD) for coloring. On average, execution times are reduced by a factor of 6(Intel) and 4(AMD) for STS-3 with coloring compared to a reference implementation using level sets.
{"title":"STS-k: a multilevel sparse triangular solution scheme for NUMA multicores","authors":"H. Kabir, J. Booth, G. Aupy, A. Benoit, Y. Robert, P. Raghavan","doi":"10.1145/2807591.2807667","DOIUrl":"https://doi.org/10.1145/2807591.2807667","url":null,"abstract":"We consider techniques to improve the performance of parallel sparse triangular solution on non-uniform memory architecture multicores by extending earlier coloring and level set schemes for single-core multiprocessors. We develop STS-k, where k represents a small number of transformations for latency reduction from increased spatial and temporal locality of data accesses. We propose a graph model of data reuse to inform the development of STS-k and to prove that computing an optimal cost schedule is NP-complete. We observe significant speed-ups with STS-3 on 32-core Intel Westmere-Ex and 24-core AMD `MagnyCours' processors. Incremental gains solely from the 3-level transformations in STS-3 for a fixed ordering, correspond to reductions in execution times by factors of 1.4(Intel) and 1.5(AMD) for level sets and 2(Intel) and 2.2(AMD) for coloring. On average, execution times are reduced by a factor of 6(Intel) and 4(AMD) for STS-3 with coloring compared to a reference implementation using level sets.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115388985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Randles, E. Draeger, T. Oppelstrup, L. Krauss, John A. Gunnels
The potential impact of blood flow simulations on the diagnosis and treatment of patients suffering from vascular disease is tremendous. Empowering models of the full arterial tree can provide insight into diseases such as arterial hypertension and enables the study of the influence of local factors on global hemodynamics. We present a new, highly scalable implementation of the lattice Boltzmann method which addresses key challenges such as multiscale coupling, limited memory capacity and bandwidth, and robust load balancing in complex geometries. We demonstrate the strong scaling of a three-dimensional, high-resolution simulation of hemodynamics in the systemic arterial tree on 1,572,864 cores of Blue Gene/Q. Faster calculation of flow in full arterial networks enables unprecedented risk stratification on a perpatient basis. In pursuit of this goal, we have introduced computational advances that significantly reduce time-to-solution for biofluidic simulations.
{"title":"Massively parallel models of the human circulatory system","authors":"A. Randles, E. Draeger, T. Oppelstrup, L. Krauss, John A. Gunnels","doi":"10.1145/2807591.2807676","DOIUrl":"https://doi.org/10.1145/2807591.2807676","url":null,"abstract":"The potential impact of blood flow simulations on the diagnosis and treatment of patients suffering from vascular disease is tremendous. Empowering models of the full arterial tree can provide insight into diseases such as arterial hypertension and enables the study of the influence of local factors on global hemodynamics. We present a new, highly scalable implementation of the lattice Boltzmann method which addresses key challenges such as multiscale coupling, limited memory capacity and bandwidth, and robust load balancing in complex geometries. We demonstrate the strong scaling of a three-dimensional, high-resolution simulation of hemodynamics in the systemic arterial tree on 1,572,864 cores of Blue Gene/Q. Faster calculation of flow in full arterial networks enables unprecedented risk stratification on a perpatient basis. In pursuit of this goal, we have introduced computational advances that significantly reduce time-to-solution for biofluidic simulations.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125992550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jongsoo Park, M. Smelyanskiy, U. Yang, Dheevatsa Mudigere, P. Dubey
Algebraic Multigrid (AMG) is a linear solver, well known for its linear computational complexity and excellent parallelization scalability. As a result, AMG is expected to be a solver of choice for emerging extreme scale systems capable of delivering hundred Pflops and beyond. While node level performance of AMG is generally limited by memory bandwidth, achieving high bandwidth efficiency is challenging due to highly sparse irregular computation, such as triple sparse matrix products, sparse-matrix dense-vector multiplications, independent set coarsening algorithms, and smoothers such as Gauss-Seidel. We develop and analyze a highly optimized AMG implementation, based on the well-known HYPRE library. Compared to the HYPRE baseline implementation, our optimized implementation achieves 2.0x speedup on a recent Intel® Xeon® Haswell processor. Combined with our other multi-node optimizations, this translates into similarly high speedups when weak-scaled multiple nodes. In addition, our implementation achieves 1.3x speedup compared to AmgX, NVIDIA's high-performance implementation of AMG, running on K40c.
{"title":"High-performance algebraic multigrid solver optimized for multi-core based distributed parallel systems","authors":"Jongsoo Park, M. Smelyanskiy, U. Yang, Dheevatsa Mudigere, P. Dubey","doi":"10.1145/2807591.2807603","DOIUrl":"https://doi.org/10.1145/2807591.2807603","url":null,"abstract":"Algebraic Multigrid (AMG) is a linear solver, well known for its linear computational complexity and excellent parallelization scalability. As a result, AMG is expected to be a solver of choice for emerging extreme scale systems capable of delivering hundred Pflops and beyond. While node level performance of AMG is generally limited by memory bandwidth, achieving high bandwidth efficiency is challenging due to highly sparse irregular computation, such as triple sparse matrix products, sparse-matrix dense-vector multiplications, independent set coarsening algorithms, and smoothers such as Gauss-Seidel. We develop and analyze a highly optimized AMG implementation, based on the well-known HYPRE library. Compared to the HYPRE baseline implementation, our optimized implementation achieves 2.0x speedup on a recent Intel® Xeon® Haswell processor. Combined with our other multi-node optimizations, this translates into similarly high speedups when weak-scaled multiple nodes. In addition, our implementation achieves 1.3x speedup compared to AmgX, NVIDIA's high-performance implementation of AMG, running on K40c.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"34-35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131844446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrew Schoenrock, Daniel J. Burnside, H. Moteshareie, A. Wong, A. Golshani, F. Dehne
Engineered proteins are synthetic novel proteins (not found in nature) that are designed to fulfill a predetermined biological function. Such proteins can be used as molecular markers, inhibitory agents, or drugs. For example, a synthetic protein could bind to a critical protein of a pathogen, thereby inhibiting the function of the target protein and potentially reducing the impact of the pathogen. In this paper we present the In-Silico Protein Synthesizer (InSiPS), a massively parallel computational tool for the IBM Blue Gene/Q that is aimed at designing inhibitory proteins. More precisely, InSiPS designs proteins that are predicted to interact with a given target protein (and may inhibit the target's cellular functions) while leaving non-target proteins unaffected (to minimize side-effects). As proof-of-concepts, two InSiPS designed proteins have been synthesized in the lab and their inhibitory properties have been experimentally verified through wet-lab experimentation.
工程蛋白是合成的新型蛋白质(不存在于自然界中)，旨在实现预定的生物功能。这些蛋白质可用作分子标记、抑制剂或药物。例如，合成蛋白可以与病原体的关键蛋白结合，从而抑制目标蛋白的功能并潜在地减少病原体的影响。在本文中，我们介绍了In- silicon Protein Synthesizer (insps)，这是IBM Blue Gene/Q的大规模并行计算工具，旨在设计抑制蛋白。更准确地说，insps设计的蛋白质可以与给定的靶蛋白相互作用(并可能抑制靶蛋白的细胞功能)，而不影响非靶蛋白(以减少副作用)。作为概念验证，两种insps设计的蛋白质已经在实验室合成，并通过湿实验室实验验证了它们的抑制特性。
{"title":"Engineering inhibitory proteins with InSiPS: the in-silico protein synthesizer","authors":"Andrew Schoenrock, Daniel J. Burnside, H. Moteshareie, A. Wong, A. Golshani, F. Dehne","doi":"10.1145/2807591.2807630","DOIUrl":"https://doi.org/10.1145/2807591.2807630","url":null,"abstract":"Engineered proteins are synthetic novel proteins (not found in nature) that are designed to fulfill a predetermined biological function. Such proteins can be used as molecular markers, inhibitory agents, or drugs. For example, a synthetic protein could bind to a critical protein of a pathogen, thereby inhibiting the function of the target protein and potentially reducing the impact of the pathogen. In this paper we present the In-Silico Protein Synthesizer (InSiPS), a massively parallel computational tool for the IBM Blue Gene/Q that is aimed at designing inhibitory proteins. More precisely, InSiPS designs proteins that are predicted to interact with a given target protein (and may inhibit the target's cellular functions) while leaving non-target proteins unaffected (to minimize side-effects). As proof-of-concepts, two InSiPS designed proteins have been synthesized in the lab and their inhibitory properties have been experimentally verified through wet-lab experimentation.","PeriodicalId":117494,"journal":{"name":"SC15: International Conference for High Performance Computing, Networking, Storage and Analysis","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125344488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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