Achieving high performance on many-core accelerators is a complex task, even for experienced programmers. This task is made even more challenging by the fact that, to achieve high performance, code optimization is not enough, and auto-tuning is often necessary. The reason for this is that computational kernels running on many-core accelerators need ad-hoc configurations that are a function of kernel, input, and accelerator characteristics to achieve high performance. However, tuning kernels in isolation may not be the best strategy for all scenarios.
Imagine having a pipeline that is composed by a certain number of computational kernels. You can tune each of these kernels in isolation, and find the optimal configuration for each of them. Then you can use these configurations in the pipeline, and achieve some level of performance. But these kernels may depend on each other, and may also influence each other. What if the choice of a certain memory layout for one kernel causes performance degradation on another kernel?
One of the existing optimization strategies to deal with pipelines is to fuse kernels together, to simplify execution patterns and decrease overhead. In this project we aim to measure the performance of accelerated pipelines in three different tuning scenarios: (1) tuning each component in isolation, (2) tuning the pipeline as a whole, and (3) tuning the fused kernel. Measuring the performance of one or more pipelines in these scenarios we hope to, on one level, being able to determine which is the best strategy for the specific pipelines on different hardware platform, and on another level we hope to better understand which are the characteristics that influence this behavior.
Genotype and single nucleotide polymorphism calling (SNP) is a technique to find bases in next-generation sequencing data that differ from a reference genome. This technique is commonly used in (plant) genetic research. However, most algorithms focus on allowing calling in diploid heterozygous organisms (specifically human) only. Within the realm of plant breeding, many species are of polyploid nature (e.g. potato with 4 copies, wheat with 6 copies and strawberry with eight copies). For genotype and SNP calling in these organisms, only a few algorithms exist, such as freebayes (https://github.com/ekg/freebayes). However, with the increasing amount of next generation sequencing data being generated, we are noticing limits to the scalability of this methodology, both in compute time and memory consumption (>100Gb).
We are looking for a student with a background in computer science, who will perform the following tasks:
- Examine the current implementation of the freebayes algorithm
- Identify bottlenecks in memory consumption and compute performance
- Come up with an improved strategy to reduce memory consumption of the freebayes algorithm
- Come up with an improved strategy to execute this algorithm on a cluster with multiple CPU’s or on GPU/s (using the memory of multiple compute nodes)
- Implement an improved version of freebayes, according to the guidelines established above
- Test the improved algorithm on real datasets of potato.
This is a challenging master thesis project on an important food crop (potato) on a problem which is relevant for both science and industry. As part of the thesis, you will be given the opportunity to present your progress/results to relevant industrial partners for the Dutch breeding industry.
Occasional traveling to Wageningen will be required.
Humanities researchers and literary scholars commonly struggle to make sense of, and extract information from patterns in large document collections. Computational techniques for finding similarities between documents in such collections continue to be developed and are invaluable in understanding these collections as single entities.
Topic modelling is a text processing tool widely used to identify structure in document collections. It has been successfully used for a wide range of applications. However, it suffers from several weaknesses which make it difficult to use and may lead to unreliable results: It is dependent on preprocessing for removal of stop-words and other text features: this is a common first step on many NLP applications; results produced are highly dependent on the quality of the selection at this stage:
- The number of topics typically needs to be determined a priori: ideally the number of topics could be inferred from the data itself.
- Interpretation of resulting topics is difficult: topics are normally represented by a set of most representative words for the topic, but these words do not relate directly to human experience.
- Visualization of produced topics is not intuitive: the optimal way of visualizing topics is current area of active research.
- Incorporating additional dimensions to a model (e.g. evolution of topics over time) is a feature which is not easily incorporated.
- Topic models scale poorly for large document collections: this is mainly due to the computational complexity of the algorithm.
There have been various efforts to overcome such limitations with varying degrees of success.
However solutions to these issues are not yet common practice and require additional knowledge and effort in order to take full advantage of them.
The aim of this project is to develop topic modelling tools which can help humanities researchers and literary scholars to make sense of large document collections without requiring extensive expertise in tuning model parameters.
Auto-tuning is a well-known optimization technique in computer science. It has been used to ease the manual optimization process that is traditionally performed by programmers, and to maximize the performance portability. Auto-tuning works by just executing the code that has to be tuned many times on a small problem set, with different tuning parameters. The best performing version is than subsequently used for the real problems. Tuning can be done with application-specific parameters (different algorithms, granularity, convergence heuristics, etc) or platform parameters (number of parallel threads used, compiler flags, etc).
For this project, we apply auto-tuning on GPUs. We have several GPU applications where the absolute performance is not the most important bottleneck for the application in the real world. Instead the power dissipation of the total system is critical. This can be due to the enormous scale of the application, or because the application must run in an embedded device. An example of the first is the Square Kilometre Array, a large radio telescope that currently is under construction. With current technology, it will need more power than all of the Netherlands combined. In embedded systems, power usage can be critical as well. For instance, we have GPU codes that make images for radar systems in drones. The weight and power limitations are an important bottleneck (batteries are heavy).
In this project, we use power dissipation as the evaluation function for the auto-tuning system. Earlier work by others investigated this, but only for a single compute-bound application. However, many realistic applications are memory-bound. This is a problem, because loading a value from the L1 cache can already take 7-15x more energy than an instruction that only performs a computation (e.g., multiply).
There also are interesting platform parameters than can be changed in this context. It is possible to change both core and memory clock frequencies, for instance. It will be interesting to if we can at runtime, achieve the optimal balance between these frequencies.
We want to perform auto-tuning on a set of GPU benchmark applications that we developed.
Apache Spark is a system for large-scale data processing used for Big Data applications business applications, but also in many scientific applications. Spark uses Java (or Scala) object serialization to transfer data over the network. Especially if data fits in memory, the performance of serialization is the most important bottleneck in Spark applications. Spark currently offers two mechanisms for serialization: Standard Java object serialization and Kryo serialization.
In the Ibis project (www.cs.vu.nl/ibis), we have developed an alternative serialization mechanism for high-performance computing applications that relies on compile-time code generation and zero-copy networking for increased performance. Performance of JVM serialization can also be compared with benchmarks: https://github.com/eishay/jvm-serializers/wiki. However, we also want to evaluate if we can increase Spark performance at the application level by using out improved object serialization system. In addition, our Ibis implementation can use fast local networks such as Infiniband transparently. We also want to investigate if using specialized networks increases application performance. Therefore, this project involves extending Spark with our serialization and networking methods (based on existing libraries), and on analyzing the performance of several real-world Spark applications.
TIDA is a library for high-level programming of parallel applications, focusing on data locality. TIDA has been shown to work well for grid-based operations, like stencils and convolutions. These are in an important building block for many simulations in astrophysics, climate simulations and water management, for instance. The TIDA paper gives more details on the programming model.
This projects aims to achieve several things and answer several research questions:
- TIDA currently only works with up to 3D. In many applications we have, higher dimensionalities are needed. Can we generalize the model to N dimensions?
- The model currently only supports a two-level hierarchy of data locality. However, modern memory systems often have many more levels, both on CPUs and GPUs (e.g., L1, L2 and L3 cache, main memory, memory banks coupled to a different core, etc). Can we generalize the model to support N-level memory hierarchies?
- The current implementation only works on CPUs, can we generalize to GPUs as well?
- Given the above generalizations, can we still implement the model efficiently? How should we perform the mapping from the abstract hierarchical model to a real physical memory system?
We want to test the new extended model on a real application. We have examples available in many domains. The student can pick one that is of interest to her/him.