10,787 research outputs found
Improving the scalability of parallel N-body applications with an event driven constraint based execution model
The scalability and efficiency of graph applications are significantly
constrained by conventional systems and their supporting programming models.
Technology trends like multicore, manycore, and heterogeneous system
architectures are introducing further challenges and possibilities for emerging
application domains such as graph applications. This paper explores the space
of effective parallel execution of ephemeral graphs that are dynamically
generated using the Barnes-Hut algorithm to exemplify dynamic workloads. The
workloads are expressed using the semantics of an Exascale computing execution
model called ParalleX. For comparison, results using conventional execution
model semantics are also presented. We find improved load balancing during
runtime and automatic parallelism discovery improving efficiency using the
advanced semantics for Exascale computing.Comment: 11 figure
The End of a Myth: Distributed Transactions Can Scale
The common wisdom is that distributed transactions do not scale. But what if
distributed transactions could be made scalable using the next generation of
networks and a redesign of distributed databases? There would be no need for
developers anymore to worry about co-partitioning schemes to achieve decent
performance. Application development would become easier as data placement
would no longer determine how scalable an application is. Hardware provisioning
would be simplified as the system administrator can expect a linear scale-out
when adding more machines rather than some complex sub-linear function, which
is highly application specific.
In this paper, we present the design of our novel scalable database system
NAM-DB and show that distributed transactions with the very common Snapshot
Isolation guarantee can indeed scale using the next generation of RDMA-enabled
network technology without any inherent bottlenecks. Our experiments with the
TPC-C benchmark show that our system scales linearly to over 6.5 million
new-order (14.5 million total) distributed transactions per second on 56
machines.Comment: 12 page
Improving the Performance and Endurance of Persistent Memory with Loose-Ordering Consistency
Persistent memory provides high-performance data persistence at main memory.
Memory writes need to be performed in strict order to satisfy storage
consistency requirements and enable correct recovery from system crashes.
Unfortunately, adhering to such a strict order significantly degrades system
performance and persistent memory endurance. This paper introduces a new
mechanism, Loose-Ordering Consistency (LOC), that satisfies the ordering
requirements at significantly lower performance and endurance loss. LOC
consists of two key techniques. First, Eager Commit eliminates the need to
perform a persistent commit record write within a transaction. We do so by
ensuring that we can determine the status of all committed transactions during
recovery by storing necessary metadata information statically with blocks of
data written to memory. Second, Speculative Persistence relaxes the write
ordering between transactions by allowing writes to be speculatively written to
persistent memory. A speculative write is made visible to software only after
its associated transaction commits. To enable this, our mechanism supports the
tracking of committed transaction ID and multi-versioning in the CPU cache. Our
evaluations show that LOC reduces the average performance overhead of memory
persistence from 66.9% to 34.9% and the memory write traffic overhead from
17.1% to 3.4% on a variety of workloads.Comment: This paper has been accepted by IEEE Transactions on Parallel and
Distributed System
Extreme Scale De Novo Metagenome Assembly
Metagenome assembly is the process of transforming a set of short,
overlapping, and potentially erroneous DNA segments from environmental samples
into the accurate representation of the underlying microbiomes's genomes.
State-of-the-art tools require big shared memory machines and cannot handle
contemporary metagenome datasets that exceed Terabytes in size. In this paper,
we introduce the MetaHipMer pipeline, a high-quality and high-performance
metagenome assembler that employs an iterative de Bruijn graph approach.
MetaHipMer leverages a specialized scaffolding algorithm that produces long
scaffolds and accommodates the idiosyncrasies of metagenomes. MetaHipMer is
end-to-end parallelized using the Unified Parallel C language and therefore can
run seamlessly on shared and distributed-memory systems. Experimental results
show that MetaHipMer matches or outperforms the state-of-the-art tools in terms
of accuracy. Moreover, MetaHipMer scales efficiently to large concurrencies and
is able to assemble previously intractable grand challenge metagenomes. We
demonstrate the unprecedented capability of MetaHipMer by computing the first
full assembly of the Twitchell Wetlands dataset, consisting of 7.5 billion
reads - size 2.6 TBytes.Comment: Accepted to SC1
LogBase: A Scalable Log-structured Database System in the Cloud
Numerous applications such as financial transactions (e.g., stock trading)
are write-heavy in nature. The shift from reads to writes in web applications
has also been accelerating in recent years. Write-ahead-logging is a common
approach for providing recovery capability while improving performance in most
storage systems. However, the separation of log and application data incurs
write overheads observed in write-heavy environments and hence adversely
affects the write throughput and recovery time in the system. In this paper, we
introduce LogBase - a scalable log-structured database system that adopts
log-only storage for removing the write bottleneck and supporting fast system
recovery. LogBase is designed to be dynamically deployed on commodity clusters
to take advantage of elastic scaling property of cloud environments. LogBase
provides in-memory multiversion indexes for supporting efficient access to data
maintained in the log. LogBase also supports transactions that bundle read and
write operations spanning across multiple records. We implemented the proposed
system and compared it with HBase and a disk-based log-structured
record-oriented system modeled after RAMCloud. The experimental results show
that LogBase is able to provide sustained write throughput, efficient data
access out of the cache, and effective system recovery.Comment: VLDB201
- …