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Tom Friend

Oct 20, 2021

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What types of storage are needed for different aspects of AI? That was one of the many topics covered in our SNIA Networking Storage Forum (NSF) webcast “Storage for AI Applications.” It was a fascinating discussion and I encourage you to check it out on-demand. Our panel of experts answered many questions during the live roundtable Q&A. Here are answers to those questions, as well as the ones we didn’t have time to address. Q. What are the different data set sizes and workloads in AI/ML in terms of data set size, sequential/ random, write/read mix? A. Data sets will vary incredibly from use case to use case. They may be GBs to possibly 100s of PB. In general, the workloads are very heavily reads maybe 95%+. While it would be better to have sequential reads, in general the patterns tend to be closer to random. In addition, different use cases will have very different data sizes. Some may be GBs large, while others may be <1 KB. The different sizes have a direct impact on performance in storage and may change how you decide to store the data. Q. More details on the risks associated with the use of online databases? A. The biggest risk with using an online DB is that you will be adding an additional workload to an important central system. In particular, you may find that the load is not as predictable as you think and it may impact the database performance of the transactional system. In some cases, this is not a problem, but when it is intended for actual transactions, you could be hurting your business. Q. What is the difference between a DPU and a RAID / storage controller? A. A Data Processing Unit or DPU is intended to process the actual data passing through it. A RAID/storage controller is only intended to handle functions such as data resiliency around the data, but not the data itself. A RAID controller might take a CSV file and break it down for storage in different drives. However, it does not actually analyze the data. A DPU might take that same CSV and look at the different rows and columns to analyze the data. While the distinction may seem small, there is a big difference in the software. A RAID controller does not need to know anything about the data, whereas a DPU must be programmed to deal with it. Another important aspect is whether or not the data will be encrypted. If the data will encrypted, a DPU will have to have additional security mechanisms to deal with decryption of the data. However, a RAID-based system will not be affected. Q. Is a CPU-bypass device the same as a SmartNIC? A. Not entirely. They are often discussed together, but a DPU is intended to process data, whereas a SmartNIC may only process how the data is handled (such as encryption, handle TCP/IP functions, etc.).  It is possible for a SmartNIC to also act as a DPU where the data itself is processed. There are new NVMe-oF™ technologies that are beginning to allow FPGA, TPD, DPU, GPU and other devices direct access to other servers’ storage directly over a high-speed local area network without having to access the CPU of that system. Q. What work is being done to accelerate S3 performance with regard to AI? A. A number of companies are working to accelerate the S3 protocol. Presto and a number of Big Data technologies use it natively. For AI workloads there are a number of caching technologies to handle the re-reads of training on a local system. Minimizing the performance penalty Q. From a storage perspective, how do I take different types of data from different storage systems to develop a model? A. Work with your project team to find the data you need and ensure it can be served to the ML/DL training (or inference) environment in a timely manner. You may need to copy (or clone) data on to a faster medium to achieve your goals. But look at the process as a whole. Do not underestimate the data cleansing/normalization steps in your storage analysis as it can prove to be a bottleneck. Q. Do I have to “normalize” that data to the same type, or can a model accommodate different data types? A. In general, yes. Models can be very sensitive. A model trained on one set of data with one set of normalizations may not be accurate if data that was taken from a different set with different normalizations is used for inference. This does depend on the model, but you should be aware not only of the model, but also the details of how the data was prepared prior to training. Q. If I have to change the data type, do I then need to store it separately? A. It depends on your data, “do other systems need it in the old format?” Q. Are storage solutions that are right for one form of AI also the best for others? A. No. While it may be possible to use a single solution for multiple AIs, in general there are differences in the data that can necessitate different storage. A relatively simple example is large data (MBs) vs. small data (~1KB). Data in that multiple MBs large example can be easily erasure coded and stored more cost effectively. However, for small data, Erasure Coding is not practical and you generally will have to go with replication. Q. How do features like CPU bypass impact performance of storage? A. CPU bypass is essential for those times when all you need to do is transfer data from one peripheral to another without processing. For example, if you are trying to take data from a NIC and transfer it to a GPU, but not process the data in any way, CPU bypass works very well. It prevents the CPU and system memory from becoming a bottleneck. Likewise, on a storage server, if you simply need to take data from an SSD and pass it to a NIC during a read, CPU bypass can really help boost system performance. One important note: if you are well under the limits of the CPU, the benefits of bypass are small. So, think carefully about your system design and whether or not the CPU is a bottleneck. In some cases, people will use system memory as a cache and in these cases, bypassing CPU isn’t possible. Q. How important is it to use All-Flash storage compared to HDD or hybrid? A. Of course, It depends on your workloads. For any single model, you may be able to make due with HDD. However, another consideration for many of the AI/ML systems is that their use can quite suddenly expand. Once there is some amount of success, you may find that more people will want access to the data and the system may experience more load. So beware of the success of these early projects as you may find your need for creation of multiple models from the same data could overload your system. Q. Will storage for AI/ML necessarily be different from standard enterprise storage today? A. Not necessarily. It may be possible for enterprise solutions today to meet your requirements. However, a key consideration is that if your current solution is barely able to handle its current requirements, then adding an AI/ML training workload may push it over the edge. In addition, even if your current solution is adequate, the size of many ML/DL models are growing exponentially every year.  So, what you provision today may not be adequate in a year or even several months.  Understanding the direction of the work your data scientists are pursuing is important for capacity and performance planning.

Olivia Rhye

Product Manager, SNIA

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Automating Discovery for NVMe IP-based SANs

Erik Smith

Oct 6, 2021

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NVMe® IP-based SANs (including transports such as TCP, RoCE, and iWARP) have the potential to provide significant benefits in application environments ranging from the Edge to the Data Center. However, before we can fully unlock the potential of the NVMe IP-based SAN, we first need to address the manual and error prone process that is currently used to establish connectivity between NVMe Hosts and NVM subsystems.  This process includes administrators explicitly configuring each Host to access the appropriate NVM subsystems in their environment. In addition, any time an NVM Subsystem interface is added or removed, a Host administrator may need to explicitly update the configuration of impacted hosts to reflect this change. 

Due to the decentralized nature of this configuration process, using it to manage connectivity for more than a few Host and NVM subsystem interfaces is impractical and adds complexity when deploying an NVMe IP-based SAN in environments that require a high-degrees of automation.

For these and other reasons, several companies have been collaborating on innovations that simplify and automate the discovery process used with NVMe IP-based SANs. This will be the topic of our live webcast on November 4, 2021 “NVMe-oF: Discovery Automation for IP-based SANs.”

During this session we will explain:

  • The NVMe IP-based SAN discovery problem
  • The types of network topologies that can support the automated discovery of NVMe-oF Discovery controllers
  • Direct Discovery versus Centralized Discovery
  • An overview of the discovery protocol

We hope you will join us. The experts working to address this limitation with NVME IP-based SANs will be on-hand to directly answer your questions on November 4th. Register today.

Olivia Rhye

Product Manager, SNIA

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Automating Discovery for NVMe IP-based SANs

Erik Smith

Oct 6, 2021

title of post
NVMe® IP-based SANs (including transports such as TCP, RoCE, and iWARP) have the potential to provide significant benefits in application environments ranging from the Edge to the Data Center. However, before we can fully unlock the potential of the NVMe IP-based SAN, we first need to address the manual and error prone process that is currently used to establish connectivity between NVMe Hosts and NVM subsystems.  This process includes administrators explicitly configuring each Host to access the appropriate NVM subsystems in their environment. In addition, any time an NVM Subsystem interface is added or removed, a Host administrator may need to explicitly update the configuration of impacted hosts to reflect this change. Due to the decentralized nature of this configuration process, using it to manage connectivity for more than a few Host and NVM subsystem interfaces is impractical and adds complexity when deploying an NVMe IP-based SAN in environments that require a high-degrees of automation. For these and other reasons, several companies have been collaborating on innovations that simplify and automate the discovery process used with NVMe IP-based SANs. This will be the topic of our live webcast on November 4, 2021 “NVMe-oF: Discovery Automation for IP-based SANs.” During this session we will explain:
  • The NVMe IP-based SAN discovery problem
  • The types of network topologies that can support the automated discovery of NVMe-oF Discovery controllers
  • Direct Discovery versus Centralized Discovery
  • An overview of the discovery protocol
We hope you will join us. The experts working to address this limitation with NVME IP-based SANs will be on-hand to directly answer your questions on November 4th. Register today.

Olivia Rhye

Product Manager, SNIA

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Q&A (Part 2) from “Storage Trends for 2021 and Beyond” Webcast

Andee Wilcott

Oct 4, 2021

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Questions from “Storage Trends for 2021 and Beyond” Webcast Answered

This is part two of the Q&A portion of the roundtable talk between Rick Kutcipal, board director, SCSI Trade Association (STA); Jeff Janukowicz, Research vice president at IDC; and Chris Preimesberger, former editor-in-chief of eWeek, where they discussed prominent data storage technologies shaping the market. If you missed this webcast titled “Storage Trends for 2021 and Beyond,” it’s available on demand here. Part One of the Q&A can be found at https://www.scsita.org/library/qa-part-1-from-storage-trends-for-2021-and-beyond-webcast/. Q1. What are your views around NVMe over Fabrics? A1. NVMe technology enables the benefits of flash-based storage to be realized at a much larger scale and not limited to the confines of PCIe backplane-based systems. With NVMe-oF technology, it’s possible to attach many SSDs in a network — generally far more than the number that can be accommodated via PCIe backplane-based systems. With NVMe-oF technology, high performance, low latency flash-based storage resources can be disaggregated from the servers and pooled into a network-attached, shared resource. With this pooling, the ability to provision just the right amount of storage for each workload on each server within the data center is achievable. This highly resembles SAN technology that SAS/SCSI has been implementing for decades. SAS inherently scales from direct-attach topologies to large-scale storage systems with hundreds (if not thousands) of drives. Q2. Where can we get the 24G SAS specs? A2. The T10 Technical Committee of the InterNational Committee for Information Technology Standards (INCITS) develops the technical standards concerning the SAS specifications. INCITS is accredited by, and operates under rules that are approved by, the American National Standards Institute (ANSI). These rules are designed to ensure that voluntary standards are developed by the consensus of industry groups. Please visit the T10 Working Drafts site for the most comprehensive list of documents for the SAS technical specifications. Anyone can access the drafts until they are published by ANSI, after which they are available for purchase from the ANSI eStandards Store at https://webstore.ansi.org/SDO/INCITS. Q3. Do you see any effort going into optical SAS? Will it get any coverage at the next plugfest? A3. Optical 24G SAS cable samples are available today and have been tested during the 24G SAS plugfest. We are seeing an increased interest in active 24G SAS cables, both optical and copper, and expect the trend to continue. Q4. Do you have any report or study about Intel DC Persistent Memory usage for the next 5 years? A4. Per the Emerging Non-Volatile Memory report, Market and Technology Report 2020 (Yole Developpement, www.yole.fr):
  • The stand-alone emerging NVM market is dynamic and is expected to grow with a CAGR (2019-2025) of ~42%, reaching more than $4B by 2025. 3D XPoint-based products for the datacenter space will play a key role in sustaining this growth.
  • The stand-alone STT-MRAM market will be driven by adoption in low-latency storage (e.g., SSD caching), while RRAM could experience a resurgence thanks to the introduction of new low-latency RRAM-based drives by Japanese players.
Q5. Do you see NVMe/TCP becoming the dominant NVMe-oF protocol? A5. Yes, NVMe-oF using TCP will likely become the preferred highly scalable NVMe protocol as it matures. Today, while NVMe-oF using TCP is not yet fully mature, recent demonstrations have shown comparable throughput, compared to RDMA-based protocols, but there is a need for more efficient processing implementations. Q6. Why has there been such a delay in getting NVMe Hardware RAID controllers out into the mainstream market? I finally see some tri-mode (SAS/SATA/NVMe) controllers becoming available – do you see these being widely adopted in the server market? A6. Implementation of hardware RAID is difficult and requires a very intricate interaction between the HW RAID engine and the storage protocol. Today’s RAID engines have been developed and hardened over many generations of products and to introduce a new storage protocol will take time. Innovations to align with the requirements of NVMe hardware RAID will begin to emerge in the near future. Q7. What do you see as the crossover timeline for NVMe replacing SATA SSDs? A7. NVMe has already replaced SATA in PC and mobile compute systems. In the enterprise, value SAS is replacing a lot of SATA SSDs due to its near price parity with SATA. Q8.1 Can you please share with us the roadmap of 24G SAS Disk Drives? A8.1 The next generation of 24G SAS drives are available now and should become mainstream in 2022. It is expected that the next generation of SAS technology will include improvements made to the drives and to 24G SAS infrastructure, rather than turning the speed crank to 48G SAS. Q8.2 Can you please share with us the current status of 24G SAS RAID controllers, JBOD Expanders? A8.2 With a second 24G SAS Plugfest to be concluded in Q4’2021, the SAS ecosystem will reach a major milestone for production readiness. The specification is done, and most major system integrators are investing in it today. 24G SAS RAID/HBA controllers and adapter cards, SSDs, and analyzer products have already been announced, with PCIe 4.0 based servers deploying 24G SAS solutions shipping now. Further product introductions are expected to continue into 2022. Going forward, 24G SAS storage systems are expected within a few quarters after server launches. Q8.3 In terms of the SAS spec, can you please list the major changes to 24G SAS from 12Gb/s SAS? A8.3 In addition to doubling the effective bandwidth from 12Gb/s SAS, 24G SAS improvements over 12Gb/s SAS include:
  • 20-bit Forward Error Correction (FEC)
  • 128b/130b encoding
  • Active PHY Transmitter Adjustment (APTA)
  • Fairness and persistent connection enhancements
  • Storage intelligence to optimize SSD performance
Q9. The IDC slide does not show much SATA SSDs at all…SATA SSDs share was quite prevalent 2015-2020. Agree? A9. The IDC slide shows enterprise storage capacity shipped, and while SAS and SATA represent a large portion of the storage shipped in 2015-2020, the vast majority of that capacity was in SAS and SATA HDDs, not SSDs.

Olivia Rhye

Product Manager, SNIA

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See You – Virtually – at SDC 2021

Marty Foltyn

Sep 23, 2021

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SNIA Storage Developer Conference goes virtual September 28-29 2021, and compute, memory, and storage are important topics.  SNIA Compute, Memory, and Storage Initiative is a sponsor of SDC 2021 – so visit our booth for the latest information and a chance to chat with our experts.  With over 120 sessions available to watch live during the event and later on-demand, live Birds of a Feather chats, and a Persistent Memory Bootcamp and Hackathon accessing new systems in the cloud, we want to make sure you don’t miss anything!  Register here to see sessions live – or on demand to your schedule. Agenda highlights include: LIVE Birds of a Feather Sessions are OPEN to all – SDC registration not required. Here is your chance, via zoom, to ask your questions of the SNIA experts.  Registration links will go live on September 28 and 29 at this page link. Computational Storage Talks A great video provides an overview of sessions. Watch it here.
  • Computational Storage APIs – how the SNIA Computational Storage TWG is leading the way with new interface definitions with Computational Storage APIs that work across different hardware architectures.
  • NVMe Computational Storage Update – Learn what is happening in NVMe to support Computational Storage devices, including a high level architecture that is being defined in NVMe for Computational Storage. The architecture provides for programs based on a standardized eBPF. (Check out our blog on eBPF.)
Persistent Memory Presentations A great video provides an overview of sessions. Watch it here. The post See You – Virtually – at SDC 2021 first appeared on SNIA Compute, Memory and Storage Blog.

Olivia Rhye

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Storage at the Edge Q&A

Alex McDonald

Sep 15, 2021

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The ability to run analytics from the data center to the Edge, where the data is generated and lives creates new use cases for nearly every business. The impact of Edge computing on storage strategy was the topic at our recent SNIA Cloud Storage Technologies Initiative (CSTI) webcast, “Extending Storage to the Edge – How It Should Affect Your Storage Strategy.” If you missed the live event, it’s available on-demand. Our experts, Erin Farr, Senior Technical Staff Member, IBM Storage CTO Innovation Team and Vincent Hsu, IBM Fellow, VP & CTO for Storage received several interesting questions during the live event. As promised, here are answers to them all. Q. What is the core principle of Edge computing technology? A. Edge computing is an industry trend rather than a standardized architecture, though there are organizations like LF EDGE with the objective of establishing an open, interoperable framework. Edge computing is generally about moving the workloads closer to where the data is generated and creating new innovative workloads due to that proximity. Common principles often include the ability to manage Edge devices at scale, using open technologies to create portable solutions, and of ultimately doing all of this with enterprise levels of security. Reference architectures exist for guidance, though implementations can vary greatly by industry vertical. Q. We all know connectivity is not guaranteed – how does that affect these different use cases? What are the HA implications? A. Assuming the requisite retry logic is in place at the various layers (e.g. network, storage, platform, application) as needed, it comes down to a question of how much can each of these use cases tolerate delays until connectivity is obtained again. The cloud bursting use case would likely be impacted by connectivity delays if the workload burst to the cloud for availability reasons or because it needed time-sensitive additional resources. When bursting for performance, the impact depends on the length of the delay vs. the length of the average time savings gained when bursting. Delays in the federated learning use case might only impact how soon a model gets refreshed with updated data. The query engine use case might avoid being impacted if the data has been pre-fetched before the connectivity loss occurred. In all of these cases it is important that the storage fabric resynchronizes the data to be a single unified view (when configured to do so.) Q. Heterogeneity of devices is a challenge in Edge computing, right? A. It is one of the challenges of Edge computing. How the data from Edge devices is stored on an Edge server may also vary depending on how that data gets shared (e.g. MQTT, NFS, REST). Storage software that can virtualize accessing data on an Edge server across different file protocols could simplify application complexity and data management. Q. Can we say Edge computing is an opposite of cloud computing? A. From our perspective, Edge computing is an extension of hybrid cloud. Edge computing can also be viewed as complementary to cloud computing since some workloads are more suitable for Cloud and some are more suitable for Edge. Q. What assumptions are you making about WAN bandwidth? Even when caching data locally the transit time for large amounts of data or large amounts of metadata could be prohibitive. A. Each of these use cases should be assessed under the lens of your industry, business, and data volumes to understand whether any potential latency that’s part of any segment of these flows would be acceptable to you. WAN acceleration, which can be used to ensure certain workloads are prioritized for guaranteed qualities of service, could also be explored to improve or ensure transit times. Integration with Software Defined Networking solutions may also provide mechanisms to mitigate or avoid bandwidth problems. Q. How about the situation where data resides in on-premises data center and machine learning tools are in the cloud to build the model and the goal is not to move the data (security) to cloud, but run and test model only on-premises and score and improve and finally implement? A. The Federated Learning use case allows you to keep the data in the on-premises data center while only moving the model updates to the cloud.  If you also cannot move model updates and if the ML tools are containerized and/or the on-premises site can act as a satellite location for your cloud, it may be possible to run the ML tools in your on-premises data center.

Olivia Rhye

Product Manager, SNIA

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Next-generation Interconnects: The Critical Importance of Connectors and Cables

Tim Lustig

Sep 14, 2021

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Modern data centers consist of hundreds of subsystems connected with optical transceivers, copper cables, and industry standards-based connectors. As data demands escalate, it drives the throughput of these interconnects to increase rapidly, making the maximum reach of copper cabling very short. At the same time, data centers are expanding in size, with nodes stretching further apart. This is making longer-reach optical technologies much more popular. However, optical interconnect technologies are more costly and complex than copper with many new buzz-words and technology concepts.

The rate of change from the vast uptick in data demand accelerates new product development at an incredible pace. While much of the enterprise is still on 10/40/100GbE and 128GFC speeds, the optical standards bodies are beginning to deliver 800G, with 1.6Tb transceivers in discussion! The introduction of new technologies creates a paradigm shift that requires changes and adjustments throughout the network.

There’s a lot to keep up with. That’s why on October 19, 2021 the SNIA Network Storage Forum is hosting a live webcast, “Next-generation Interconnects: The Critical Importance of Connectors and Cables.” In this session, our experts will cover the latest in the impressive array of data center infrastructure components designed to address expanding requirements for higher-bandwidth and lower-power. Including defining new terminology and addressing the next-generation copper and optics solutions required to deliver high signal integrity, lower-latency, and lower insertion loss to achieve maximum efficiency, speed, and density. Register today. We look forward to seeing you on October 19th.

Olivia Rhye

Product Manager, SNIA

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Next-generation Interconnects: The Critical Importance of Connectors and Cables

Tim Lustig

Sep 14, 2021

title of post
Modern data centers consist of hundreds of subsystems connected with optical transceivers, copper cables, and industry standards-based connectors. As data demands escalate, it drives the throughput of these interconnects to increase rapidly, making the maximum reach of copper cabling very short. At the same time, data centers are expanding in size, with nodes stretching further apart. This is making longer-reach optical technologies much more popular. However, optical interconnect technologies are more costly and complex than copper with many new buzz-words and technology concepts. The rate of change from the vast uptick in data demand accelerates new product development at an incredible pace. While much of the enterprise is still on 10/40/100GbE and 128GFC speeds, the optical standards bodies are beginning to deliver 800G, with 1.6Tb transceivers in discussion! The introduction of new technologies creates a paradigm shift that requires changes and adjustments throughout the network. There’s a lot to keep up with. That’s why on October 19, 2021 the SNIA Network Storage Forum is hosting a live webcast, “Next-generation Interconnects: The Critical Importance of Connectors and Cables.” In this session, our experts will cover the latest in the impressive array of data center infrastructure components designed to address expanding requirements for higher-bandwidth and lower-power. Including defining new terminology and addressing the next-generation copper and optics solutions required to deliver high signal integrity, lower-latency, and lower insertion loss to achieve maximum efficiency, speed, and density. Register today. We look forward to seeing you on October 19th.

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Product Manager, SNIA

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Genomics Compute, Storage & Data Management Q&A

Alex McDonald

Sep 13, 2021

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Everyone knows data is growing at exponential rates. In fact, the numbers can be mind-numbing. That’s certainly the case when it comes to genomic data where 40,000PB of storage each year will be needed by 2025. Understanding, managing and storing this massive amount of data was the topic at our SNIA Cloud Storage Technologies Initiative webcast “Moving Genomics to the Cloud: Compute and Storage Considerations.” If you missed the live presentation, it’s available on-demand along with presentation slides. Our live audience asked many interesting questions during the webcast, but we did not have time to answer them all. As promised, our experts, Michael McManus, Torben Kling Petersen and Christopher Davidson have answered them all here. Q. Human genomes differ only by 1% or so, there’s an immediate 100x improvement in terms of data compression, 2743EB could become 27430PB, that’s 2.743M HDDs of 10TB each. We have ~200 countries for the 7.8B people, and each country could have 10 sequencing centers on average, each center would need a mere 1.4K HDDs, is there really a big challenge here? A. The problem is not that simple unfortunately. The location of genetic differences and the size of the genetic differences vary a lot across people. Still, there are compression methods like CRAM and PetaGene that can save a lot of space. Also consider all of the sequencing for rare disease, cancer, single cell sequencing, etc. plus sequencing for agricultural products. Q. What’s the best compression ratio for human genome data? A. CRAM states 30-60% compression, PetaGene cites up to 87% compression, but there are a lot of variables to consider and it depends on the use case (e.g., is this compression for archive or for withing run computing). Lustre can compress data by roughly half (compression ratio of 2), though this does not usually include compression of metadata. We have tested PetaGene in our lab and achieved a compression ratio of 2 without any impact on the wall clock. Q. What is the structure of the Genome processed file? It is one large file or multiple small files and what type of IO workload do they have? A. The addendum at the end of this presentation covers file formats for genome files, e.g. FASTQ, BAM, VCF, etc. Q. It’s not just capacity, it’s also about performance. Analysis of genomic data sets is very often hard on large-scale storage systems. Are there prospects for developing methods like in-memory processing, etc., to offload some of the analysis and/or ways to optimize performance of I/O in storage systems for genomic applications? A. At Intel, we are using HPC systems that are using an IB or OPA fabric (or RoCE over Ethernet) with Lustre. We are running in a “throughput” mode versus focusing on individual sample processing speed. Multiple samples are processed in parallel versus sequentially on a compute node. We use a sizing methodology to rate a specific compute node config to provide, for example, our benchmark on our 2nd Gen Scalable processors. This benchmark is 6.4 30x whole genomes per compute node per day. Benchmarks on our 3rd Gen Scalable processors are underway. This sizing methodology allows for the most efficient use of compute resources, which in turn can alleviate storage bottlenecks. Q. What is the typical access pattern of a 350G sequence? Is full traversal most common, or are there usually focal points or hot spots? A. The 350GB is comprised of two possible input file types and 2 output file types. For input file types they can be either a FASTQ file, which is an uncompressed, raw text file, or a compressed version called a uBAM (u=unaligned). The output file types are a compressed “aligned” version called a BAM file, output of the alignment process; and a gVCF file which is the output of the secondary analysis. This 350GB number is highly dependent on data retention policies, compression tools, genome coverage, etc. Q. What is the size of a sequence and how many sequence are we looking at? A. If you are asking about an actual sequence of 6 billion DNA bases (3 billion base pairs) then each base is represented by 1 byte so you have 6 GB.  However, the way the current “short read” sequencers work is using the concept of coverage. This means you run the sequence multiple times, for example 30 times, which is referred to as “30x”. So, 30 times 6GB = 180GB. In terms of My “thought experiment” I considered 7.8B sequences, one for each person on the planet at 30x coverage. This analysis use the ~350GB number which all the files mentioned above. Q. Can you please help with the IO pattern question? A. IO patterns are dependent on the applications used in the pipeline. Applications like GATK baserecal and SAMtools have a lot of random IO and can benefit from the use of SSDs. On the flipside, many of the applications are sequential in nature. Another thing to consider is the amount of IO in relation to the overall pipeline, as the existence of random IO does not inherently mean the existence of a bottleneck. Q. You talked about Prefetch the data before compute which needs a compressed file signature of the actual data and referencing of it. Can you please share some details of what is used now to do this? A. The current implementation of Prefetch via workload manager directives (WLM) is based on metadata queries done using standard SQL on distributed index files in the system. This way, any metadata recorded for a specific file can be used as a search criterion. We’re also working on being able to access and process the index in large concatenated file formats such as NetCDF and others which will extend the capabilities to find the right data at the right time. Q. For Genome and the quantum of data do you see Quartz Glass a better replacement to tape? A. Quartz Glass is an interesting concept but one of many new long term storage technologies being researched. Back in 2012 when this was originally announced by Hitachi, I thought it would most definitely replace many storage technologies, but it’s gone very quiet the last 5+ years so I’m wondering whether this particular technology survived.

Olivia Rhye

Product Manager, SNIA

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Genomics Compute, Storage & Data Management Q&A

Alex McDonald

Sep 13, 2021

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Everyone knows data is growing at exponential rates. In fact, the numbers can be mind-numbing. That’s certainly the case when it comes to genomic data where 40,000PB of storage each year will be needed by 2025. Understanding, managing and storing this massive amount of data was the topic at our SNIA Cloud Storage Technologies Initiative webcast “Moving Genomics to the Cloud: Compute and Storage Considerations.” If you missed the live presentation, it’s available on-demand along with presentation slides. Our live audience asked many interesting questions during the webcast, but we did not have time to answer them all. As promised, our experts, Michael McManus, Torben Kling Petersen and Christopher Davidson have answered them all here. Q. Human genomes differ only by 1% or so, there’s an immediate 100x improvement in terms of data compression, 2743EB could become 27430PB, that’s 2.743M HDDs of 10TB each. We have ~200 countries for the 7.8B people, and each country could have 10 sequencing centers on average, each center would need a mere 1.4K HDDs, is there really a big challenge here? A. The problem is not that simple unfortunately. The location of genetic differences and the size of the genetic differences vary a lot across people. Still, there are compression methods like CRAM and PetaGene that can save a lot of space. Also consider all of the sequencing for rare disease, cancer, single cell sequencing, etc. plus sequencing for agricultural products. Q. What’s the best compression ratio for human genome data? A. CRAM states 30-60% compression, PetaGene cites up to 87% compression, but there are a lot of variables to consider and it depends on the use case (e.g., is this compression for archive or for withing run computing). Lustre can compress data by roughly half (compression ratio of 2), though this does not usually include compression of metadata. We have tested PetaGene in our lab and achieved a compression ratio of 2 without any impact on the wall clock. Q. What is the structure of the Genome processed file? It is one large file or multiple small files and what type of IO workload do they have? A. The addendum at the end of this presentation covers file formats for genome files, e.g. FASTQ, BAM, VCF, etc. Q. It’s not just capacity, it’s also about performance. Analysis of genomic data sets is very often hard on large-scale storage systems. Are there prospects for developing methods like in-memory processing, etc., to offload some of the analysis and/or ways to optimize performance of I/O in storage systems for genomic applications? A. At Intel, we are using HPC systems that are using an IB or OPA fabric (or RoCE over Ethernet) with Lustre. We are running in a “throughput” mode versus focusing on individual sample processing speed. Multiple samples are processed in parallel versus sequentially on a compute node. We use a sizing methodology to rate a specific compute node config to provide, for example, our benchmark on our 2nd Gen Scalable processors. This benchmark is 6.4 30x whole genomes per compute node per day. Benchmarks on our 3rd Gen Scalable processors are underway. This sizing methodology allows for the most efficient use of compute resources, which in turn can alleviate storage bottlenecks. Q. What is the typical access pattern of a 350G sequence? Is full traversal most common, or are there usually focal points or hot spots? A. The 350GB is comprised of two possible input file types and 2 output file types. For input file types they can be either a FASTQ file, which is an uncompressed, raw text file, or a compressed version called a uBAM (u=unaligned). The output file types are a compressed “aligned” version called a BAM file, output of the alignment process; and a gVCF file which is the output of the secondary analysis. This 350GB number is highly dependent on data retention policies, compression tools, genome coverage, etc. Q. What is the size of a sequence and how many sequence are we looking at? A. If you are asking about an actual sequence of 6 billion DNA bases (3 billion base pairs) then each base is represented by 1 byte so you have 6 GB.  However, the way the current “short read” sequencers work is using the concept of coverage. This means you run the sequence multiple times, for example 30 times, which is referred to as “30x”. So, 30 times 6GB = 180GB. In terms of My “thought experiment” I considered 7.8B sequences, one for each person on the planet at 30x coverage. This analysis use the ~350GB number which all the files mentioned above. Q. Can you please help with the IO pattern question? A. IO patterns are dependent on the applications used in the pipeline. Applications like GATK baserecal and SAMtools have a lot of random IO and can benefit from the use of SSDs. On the flipside, many of the applications are sequential in nature. Another thing to consider is the amount of IO in relation to the overall pipeline, as the existence of random IO does not inherently mean the existence of a bottleneck. Q. You talked about Prefetch the data before compute which needs a compressed file signature of the actual data and referencing of it. Can you please share some details of what is used now to do this? A. The current implementation of Prefetch via workload manager directives (WLM) is based on metadata queries done using standard SQL on distributed index files in the system. This way, any metadata recorded for a specific file can be used as a search criterion. We’re also working on being able to access and process the index in large concatenated file formats such as NetCDF and others which will extend the capabilities to find the right data at the right time. Q. For Genome and the quantum of data do you see Quartz Glass a better replacement to tape? A. Quartz Glass is an interesting concept but one of many new long term storage technologies being researched. Back in 2012 when this was originally announced by Hitachi, I thought it would most definitely replace many storage technologies, but it’s gone very quiet the last 5+ years so I’m wondering whether this particular technology survived.

Olivia Rhye

Product Manager, SNIA

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