RELION is a widely-used software suite for cryoelectron microscopy (cryo-EM) single-particle analysis (SPA), yet its performance optimization has primarily focused on x86 CPUs and NVIDIA GPUs. In this work, we present the first systematic effort to optimize RELION on modern many-core CPUs. Through detailed performance analysis, we identify critical bottlenecks across RELION's major computational stages. We then apply a set of software- and hardware-aware optimizations, including vectorization optimization, process and thread configurations tuning, algorithm optimization, lock optimization, memory affinity optimization, and computation redundancy optimization. Our optimized version achieves significant speedups and exhibits better scalability than the original RELION across all stages. Notably, it outperforms a single NVIDIA A100 GPU on the complete SPA workflow, achieving a$2.22 \times$speedup on the SPA dataset and a$1.13 \times$speedup on the RELION Benchmark dataset. Validation experiments further confirm that our optimizations preserve the reconstruction accuracy, demonstrating the potential of specific CPU architectures as a competitive and efficient platform for cryo-EM data processing.

Sparse Matrix-Vector Multiplication (SpMV) is a key operation in many applications, and optimizing its performance is crucial for achieving high computational efficiency. Existing efforts have optimized SpMV performance on CPUs with corresponding sparse matrix formats adopted. However, the performance of existing SpMV implementations primarily focuses on maximizing hardware’s vector unit usage, neglecting the potential for exploiting idle scalar units simultaneously. To address such limitation, we propose OVERT, a new storage format of sparse matrix designed to exploit both vector and scalar execution units on modern CPUs for accelerating SpMV performance. OVERT, containing two format variants (OVERT-S and OVERT-E), outperforms existing formats by partitioning the matrix into multiple data panels, which can efficiently utilize vector and scalar units. Moreover, we propose an effective format selection model that dynamically chooses the optimal format variant from OVERT according to the characteristics of the input matrix. Experimental results on SuiteSparse show that OVERT achieves an average speedup of 3.91 × against Intel MKL on X86 CPU and an average speedup of 1.24 × against ArmPL on ARM CPU.

Zero-value propagation is a common phenomenon in modern programs, where redundant operations caused by zero-values can severely impact performance. Since zero-values are often generated dynamically at runtime, eliminating such redundancies through static analysis alone is challenging. In this paper, we propose an efficient static control data flow analysis algorithm to identify redundancies resulting from zero-value propagation. Based on this algorithm, we design and implement ZeroSpec, a fully automated profile-guided code optimizer that detects zero-values at runtime and specializes fast paths for them. To maximize performance gains, ZeroSpec also employs a fine-grained cost model that evaluates the optimization potential of individual zero-value instructions to guide the construction of targeted optimization regions. Evaluation on SPEC CPU2017, NPB and real-world applications demonstrates the effectiveness of ZeroSpec, achieving a maximum performance speedup of 1.31 ×.

Modern optimizing compilers are able to exploit memory access or computation patterns to generate vectorized codes. However, such patterns in irregular programs are unknown until runtime due to the input dependence. Thus, either compiler’s static optimization or profile-guided optimization cannot represent the patterns for any common input, which leads to suboptimal vectorization. To address the above drawback, we propose DynVec , 1 a framework to automatically exploit regular patterns buried deeply inside irregular programs and apply corresponding optimizations for better vectorization. Due to the integration of workload distribution and the ability to represent instruction features and identify regular patterns with effective feature extraction and data re-arranging methods, DynVec can generate highly efficient vectorized codes for both serial and parallel irregular programs by replacing gather / scatter / reduction operations with optimized operation groups. We evaluate DynVec on optimizing irregular programs such as SpMV and graph programs with representative sparse matrix datasets. The experiment results show that DynVec achieves significant speedup compared to the state-of-the-art implementations across a range of X86 and ARM platforms.

Fine-grained value profilers reveal a promising way to accurately detect value-related software inefficiencies with binary instrumentation. Due to the architecture-dependent implementation details of binary instrumentation, existing value profilers suffer from poor portability as well as high engineering efforts to achieve efficiency across platforms. In this paper, we propose VClinic, a portable and efficient fine-grained value profiling framework for analyzing highly optimized binaries on both X86 and ARM platforms. VClinic exploits operand-centric two-level designs in its implementation to provide the common building blocks required for value profilers. By constructing four representative value profilers with VClinic, we demonstrate that VClinic can ease the development of value profilers with portability and efficiency across platforms. Guided by the value profilers built upon VClinic, we can achieve up to 89.94% and 74.66% speedup for real-world programs on X86 and ARM platforms, respectively.

Big data applications are widely adopted to mine valuable information from a tremendous amount of industry data, which is commonly represented as a series of map-reduce operations. Among various map-reduce frameworks, Hadoop is most commonly adopted for data processing at large scale. Although Hadoop eases the development of highly scalable distributed big data applications, inefficient implementation due to poor coding practice and deep software abstractions can cause severe performance issues such as unreasonable slowdown, high response latency, and waste of computing resources, which can lead to unsatisfactory serving delay or significant maintenance cost. In this paper, we first categorize three common types of redundant patterns in big data applications. Then we propose a tool-assisted optimization workflow to detect the redundant patterns automatically, which profiles the application by sampling hardware performance monitoring units. Moreover, we present a profiling visualization method that can help to pinpoint the redundant codes. Based on these approaches, we optimize several big data applications by eliminating redundancies, yielding up to 14.8% performance improvement.

Function interception of fully-optimized binaries is widely used for optimization with its ability to accurately collect runtime information and detect inefficiencies at the function level. However, the implementation of function interception with existing binary rewriting techniques still suffers from limited reliability and performance on ARM platform. In this paper, we propose BiRFIA, an efficient selective binary rewriting framework for function interception targeting highly optimized binaries on ARM platforms. BiRFIA performs static binary rewriting of specific functions and intercepts them through well-formed trampoline sections and external instrumentation libraries. Besides, BiRFIA places complex instrumentation code in the trampoline section and jumps to the trampoline section via an adaptive instruction eviction strategy, which significantly reduces the probability of unexpected errors. For evaluation, we develop two function interception tools based on BiRFIA, including a function performance event counter collector and a function parameter tracer. Guided by these tools, we optimize several benchmarks and real-world programs, yielding up to 8% performance speedup. Our evaluation result demonstrates that BiRFIA incurs negligible runtime overhead of 1.006× on average.

Trivial operations cause software inefficiencies that waste functional units and memory bandwidth for executing useless instructions. Although previous works have identified a significant amount of trivial operations in widely used programs, the proposed solutions only provide useful observations, other than actionable guidance to eliminate trivial operations for better performance. In this paper, we propose TrivialSpy - a fine-grained and dataflow-based value profiler to effectively identify software triviality with optimization potential estimation. With the help of dataflow analysis, TrivialSpy can detect software trivialities of heavy operation, trivial chain, and redundant backward slice. In addition, TrivialSpy can identify trivial breakpoints that combine multiple trivial conditions for more optimization opportunities. The evaluation results demonstrate TrivialSpy is capable of identifying software triviality in highly optimized programs. Based on the optimization guidance provided by TrivialSpy, we can achieve 52.09% performance speedup at maximum after eliminating trivial operations.