Interview with Damla Senol Cali: about her work, experience in SAFARI, and her future directions

Damla Senol Cali is a PhD student with SAFARI at CMU co-advised by Onur Mutlu and Saugata Ghose.
We recently interviewed Damla about her work, her experience as a PhD student in SAFARI, and her future directions.  Damla’s interview appears as the first video contribution to the SAFARI Meet our Members section in our January 2021 newsletter.

Watch Damla’s video interview here    |    Read the transcript here 

Damla Senol Cali, Gurpreet S. Kalsi, Zulal Bingol, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu, GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence AnalysisProceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.

Full paper link | Talk Video (18 mins) | Talk Slides (pptx) (pdf) |
Lecture Video (37 mins) | Lecture Slides (pptx) (pdf) | GenASM Source Code |
More information here

Damla Senol Cali, Jeremie Kim, Saugata Ghose, Can Alkan, and Onur Mutlu, Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future DirectionsBriefings in Bioinformatics (BIB), 2018.

Paper link | Paper PDF | AACBB’19 Talk Video | Slides (ppt) (pdf) |
More information here

Read the latest edition of our SAFARI Newsletter

Dear SAFARI friends,

Happy New Year!  We are excited to share our group highlights with you in this second edition of the SAFARI newsletter: https://safari.ethz.ch/safari-newsletter-january-2021/

In this second edition of the SAFARI newsletter, we share our research, teaching and outreach highlights from 2020, and look ahead to a new and inspiring future in 2021.

We wish you a wonderful 2021, in all aspects of your lives!

Onur Mutlu

Radio Interview: Onur Mutlu discusses the review process

Listen to Onur Mutlu’s interview as he discusses the review process in the “ORF Dimensionen” broadcast on “Peer Review and Open Science”

How well does peer review work?
Interviewer: Mariann Unterluggauer
11 November 2020

The idea of using an assessment process to control the quality and efficiency of scientific work emerged in the middle of the 20th century. Since then, publishers have been using this “peer review” as a basis for making decisions about what should appear in their specialist journals. And anyone who wants to be awarded funding for their research projects must first go through and pass such an assessment process. However, this does not always work properly, as misjudgments and sloppiness have shown in the past. In addition, a positive “peer review” does not automatically mean that there is good or relevant science in a publication. – So what’s the point of peer review? Does the procedure have to be evaluated itself? Above all, the discussion about open science has stimulated the discussion about the review process of science.

Some useful related videos:

  • https://youtu.be/HvswnsfG3oQ?t=1800 (Onur Mutlu, Computer Architecture – Lecture 5c: Secure and Reliable Memory (ETH Zürich, Fall 2020): discussing the review process of RowHammer)
  • https://youtu.be/FYwOyapck3M?t=5421 (Onur Mutlu, Seminar in Computer Architecture – Lecture 2: RowClone – In-Memory Data Copy (ETH Zürich, Fall 2020): discussing the review process of RowClone)
  • https://youtu.be/yEYEzFwAY9g?t=4445 (Onur, Mutlu, Seminar in Computer Architecture – Lecture 3: Memory Channel Partitioning (ETH Zürich, Fall 2020): discussing the review process of Memory Channel Partitioning)

We are at MICRO 2020 this week! Join Lois Orosa for his talk on FIGARO, Monday, October 19 6:30PM CEST

Our new paper: FIGARO: Improving System Performance via Fine-Grained In-DRAM Data Relocation and Caching will be presented by Lois Orosa at MICRO 2020 on Monday, October 19 at 6:30 PM CEST.  Join us at MICRO 2020 online!

Authors: Yaohua Wang, Lois Orosa, Xiangjun Peng, Yang Guo, Saugata Ghose, Minesh Patel, Jeremie S. Kim, Juan Gómez Luna, Mohammad Sadrosadati, Nika Mansouri Ghiasi, and Onur Mutlu

Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
[Slides (pptx) (pdf)]
[Lightning Talk Slides (pptx) (pdf)]
[Talk Video (16 minutes)]
[Lightning Talk Video (1.5 minutes)]

Best Paper Award MICRO 2020: Congratulations Minesh Patel and co-authors!

Our new paper: Bit-Exact ECC Recovery (BEER): Determining DRAM On-Die ECC Functions by Exploiting DRAM Data Retention Characteristics  will be presented by Minesh Patel at MICRO 2020 on Monday, October 19 at 6:00 PM CEST.  Join us at MICRO 2020 online!

Update: This paper won the Best Paper Award!  Congratulations to Minesh Patel and co-authors: Jeremie S. Kim, Taha Shahroodi, Hasan Hassan, and Onur Mutlu,

We asked Minesh a couple questions about his paper, here’s what he had to say:

You recently won the Best Paper Award at MICRO.  Can you tell us more about the
significance of this paper?
This paper addresses the larger problem that hidden proprietary features
implemented by DRAM manufacturers impede end-users from bringing out the best of
DRAM technology. We believe BEER takes an important step towards bridging the
gap between industry and end-users, starting by focusing on a key example of
such features: on-die ECC. Our work discusses how and why on-die ECC limits
third-party DRAM consumers and then introduces techniques that the consumers can
use to overcome these limitations.

What were the biggest challenges for you during the writing and review process?I would say that the biggest challenge we faced when writing this paper was to
clearly articulate the problem of on-die ECC limiting third-party users. This
includes both (i) describing how and why this limitation arises and (ii)
providing concrete examples that the reader can relate to. We spent considerable
effort in crafting these arguments such that both we and the reader have a clear
understanding of the problem we tackle, our goal in this work, and the final
value of our contributions.

Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
[Slides (pptx) (pdf)]
[Short Talk Slides (pptx) (pdf)]
[Lightning Talk Slides (pptx) (pdf)]
[Talk Video (15 minutes)]
[Short Talk Video (5.5 minutes)]
[Lightning Talk Video (1.5 minutes)]
[BEER Source Code]

Paper MICRO 2020: Join Damla Senol Cali for her talk on Wednesday, October 21, 7PM CEST

Damla Senol Cali will present: GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis, Wednesday, October 21 at 7:00 PM CEST.

Authors: Damla Senol Cali, Gurpreet S. Kalsi, Zulal Bingol, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu,

Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
[ARM Research Summit Talk Video (21 minutes)]
[ARM Research Summit Short Talk Video (15 minutes)]
[ARM Research Summit Short Talk Video and Q&A (31 minutes)]
[ARM Research Summit Talk Slides (pptx) (pdf)]
[ARM Research Summit Short Talk Slides (pptx) (pdf)]
[Lighting Talk Video (1.5 minutes)]
[Lightning Talk Slides (pptx) (pdf)]
[Talk Video (18 minutes)]
[Slides (pptx) (pdf)]

Paper MICRO 2020: Join Jawad Haj-Yahya for his talk Wednesday, October 21, 7:30PM CEST

Join Jawad Haj-Yahya for his MICRO 2020 talk where he will present our paper: FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors, Wednesday October 21 at 7:30 PM CEST.

Authors: Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Lois Orosa, Efraim Rotem, Avi Mendelson, Anupam Chattopadhyay, and Onur Mutlu,

Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
[Slides (pptx) (pdf)]
[Lightning Talk Slides (pptx) (pdf)]
[Talk Video (15 minutes)]
[Lightning Talk Video (1.5 minutes)]

Talk: Intelligent Architectures for Intelligent Machines Oct 7

Join Onur for his online talk in the HKUST Engineering x HKSTP Distinguished Speaker Series on Oct 7 at 11:00 CEST (Zurich time).

You can register here: https://calendar.ust.hk/events/hkust-engineering-x-hkstp-distinguished-speaker-series-webinar-intelligent-architectures

Computing is bottlenecked by data. Large amounts of application data overwhelm storage capability, communication capability, and computation capability of the modern machines we design today. As a result, many key applications’ performance, efficiency and scalability are bottlenecked by data movement.

Jointly hosted by SENG, HKUST AI Chip Center for Emerging Smart Systems and Hong Kong Science and Technology Parks Corporation, this webinar features a renowned computer architecture expert, Prof. Onur Mutlu from ETH Zurich. We will discuss the major shortcomings of modern architectures, the recent research that could enable computation close to data, as well as the guiding principles for future computing architecture and system designs. (Please click here for more information.)

Moderated by Prof. Tim Cheng, Dean of Engineering, register to get more insights on how intelligent architecture could be designed to handle data well.

Paper: Accelerating Genome Analysis: A Primer on an Ongoing Journey

In our new paper, we describe the ongoing journey in significantly improving the performance of read mapping: Accelerating Genome Analysis: A Primer on an Ongoing Journey

Mohammed AlserZülal BingölDamla Senol CaliJeremie KimSaugata GhoseCan AlkanOnur Mutlu

Paper, arXiv: https://people.inf.ethz.ch/omutlu/pub/AcceleratingGenomeAnalysis_ieeemicro20.pdf
Paper, IEEE Micro: https://www.computer.org/csdl/magazine/mi/2020/05/09154510/1lZzYVaH7lC

Invited Talks

Mohammed Alser:
A Roadmap for Fast and Efficient Genome Analysis, Univ. of Tokyo, Shirokanedai:
https://www.youtube.com/watch?v=DTfNzcYIgOI&feature=youtu.be

Mohammed Alser:
Accelerating Genome Analysis Using New Algorithms and Hardware Designs, Univ. of Tokyo: https://www.youtube.com/watch…

Onur Mutlu:
AACBB 2019 Keynote Talk: https://www.youtube.com/watch?v=hPnSmfwu2-A

Paper: NERO: A Near High-Bandwidth Memory Stencil Accelerator for Weather Prediction Modeling

Gagandeep Singh presented his work on “NERO: A Near High-Bandwidth Memory Stencil Accelerator for Weather Prediction Modeling” yesterday at the International Conference on Field-Programmable Logic and Applications (FPL) 2020.

Co-authors: Dionysios Diamantopoulos, Christoph Hagleitner, Juan Gómez Luna, Onur Mutlu, Sander Stuijk, Henk Corporaal

This work has also been nominated for the Stamatis Vassiliadis Memorial Award at #FPL2020!

Gagandeep Singh, Dionysios Diamantopoulos, Christoph Hagleitner, Juan Gómez-Luna, Sander Stuijk, Onur Mutlu, and Henk Corporaal,
“NERO: A Near High-Bandwidth Memory Stencil Accelerator for Weather Prediction Modeling”
Proceedings of the 30th International Conference on Field-Programmable Logic and Applications (FPL), Gothenburg, Sweden, September 2020.
[Slides (pptx) (pdf)]
[Lightning Talk Slides (pptx) (pdf)]
[Talk Video (23 minutes)]
Nominated for the Stamatis Vassiliadis Memorial Award.