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In this work, we present an efficient Processing in MRAM-Accelerated De Bruijn Graph-based DNA Assembly platform, named PANDA, based on an optimized and hardware-friendly genome assembly algorithm. PANDA is able to assemble large-scale DNA sequence datasets from all-pair overlaps. We first design a PANDA platform that exploits MRAM as computational memory and converts it to a potent processing unit for genome assembly. PANDA can not only execute efficient bulk bit-wise X(N)OR-based comparison/addition operations heavily required for the genome assembly task but also a full set of 2-/3-input logic operations inside the MRAM chip. We then develop a highly parallel and step-by-step hardware-friendly DNA assembly algorithm for PANDA that only requires the developed in-memory logic operations. The platform is then configured with a novel data partitioning and mapping technique that provides local storage and processing to utilize the algorithm level’s parallelism fully. The cross-layer simulation results demonstrate that PANDA reduces the run time and power by a factor of 18 and 11, respectively, compared with CPU. Moreover, speed-ups of up to 2.5 to 10× can be obtained over other recent processing in-memory platforms to perform the same task, like STT-MRAM, ReRAM, and DRAM.
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PyPANDA: Taming the PANDAmonium of Whole System Dynamic Analysis
When working with real world programs, dynamic analyses often must be run on a whole-system instead of just a single binary. Existing whole-system dynamic analysis platforms generally require analyses to be written in compiled languages, a suboptimal choice for many iterative analysis tasks. Furthermore, these platforms leave analysts with a split view between the behavior of the system under analysis and the analysis itself---in particular the system being analyzed must commonly be controlled manually while analysis scripts are run. To improve this process, we designed and implemented PyPANDA, a Python interface to the PANDA dynamic analysis platform. PyPANDA unifies the gap between guest virtual machines behavior and analysis tasks; enables painless integrations with other program analysis tools; and greatly lowers the barrier of entry to whole-system dynamic analysis. The capabilities of PyPANDA are demonstrated by using it to dynamically evaluate the accuracy of three binary analysis frameworks, track heap allocations across multiple processes, and synchronize state between PANDA and a binary analysis platform. Significant challenges were overcome to integrate a scripting language into PANDA with minimal performance impact.
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- Award ID(s):
- 1657199
- PAR ID:
- 10251208
- Date Published:
- Journal Name:
- NDSS Binary Analysis Research Workshop
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.14722/bar.2021.23001
