AI inferencing using light alone

Researchers at UCLA have taken a trained DL neural network and implemented it into a series of passive optical only, 3D printed diffraction gratings to perform fashion MNIST object classification. And did the same with a MNIST handwritten digit and ImageNet DL neural network classifiers.

But first please take our new poll:

Experimental testing of 3D-printed D2NNs.(A and B) After the training phase, the final designs of five different layers (L1, L2, …, L5) of the handwritten digit classifier, fashion product classifier, and the imager D2NNs are shown. To the right of the network layers, an illustration of the corresponding 3D-printed D2NN is shown. (C and D) Schematic (C) and photo (D) of the experimental terahertz setup. An amplifier-multiplier chain was used to generate continuous-wave radiation at 0.4 THz, and a mixer-amplifier-multiplier chain was used for the detection at the output plane of the network. RF, radio frequency; f, frequency.

See the article on SlashGear, 3D printed all-optical diffractive deep learning neural network…. The research article is only available on Optical Society of America’s website/magazine (see Residual D2NN: training diffractive deep neural networks via learnable light shortcuts behind hard paywall). However, I did find a follow on article on ArchivX (see Analysis of Diffractive Optical Neural Networks and Their Integration with Electronic Neural Networks) that discussed how to integrate D2NN approaches with an electronic NN to create a hybrid inference engine. And another earlier Science article (see All-optical machine learning using diffractive deep neural networks) that was available which described earlier versions of D2NN technology for MNIST digit classification, fashion MNIST classification and ImageNet object classification.

How does it work

Apparently the researchers trained a normal (electronic based) deep learning neural network on the MNIST, Fashion MNIST and ImageNet and then converted the resultant trained NNs into a set of multiple diffraction grids. They did some computer simulation of the D2NN and once satisfied it worked and achieved decent accuracy, 3D printed the diffraction plates.

All-optical D2NN-based classifiers. These D2NN designs were based on spatially and temporally coherent illumination and linear optical materials/layers. (a) D2NN setup for the task of classification of handwritten digits (MNIST), where the input information is encoded in the amplitude channel of the input plane. (b) Final design of a 5-layer, phase-only classifier for handwritten digits. (c) Amplitude distribution at the input plane for a test sample (digit ‘0’). (d-e) Intensity patterns at the output plane for the input in (c); (d) is for MSE-based, and (e) is softmax- cross-entropy (SCE)-based designs. (f) D2NN setup for the task of classification of fashion products (Fashion-MNIST), where the input information is encoded in the phase channel of the input plane. (g) Same as (b), except for fashion product dataset. (h) Phase distribution at the input plane for a test sample. (i-j) Same as (d) and (e) for the input in (h),  refers to the illumination source wavelength. Input plane represents the plane of the input object or its data, which can also be generated by another optical imaging system or a lens, projecting an image of the object data onto this plane.

In their D2NN, they start with coherent (laser) light in the THz spectrum, used this to illuminate the input plane (I assume an image of the object/digit/fashion accessory) and passed this through multiple plates of diffraction grids onto THz detector which was used to detect the illuminated spot that indicated the classification.

The article in science has a supplementary materials download that show how the researchers converted NN weights into a diffraction grating. Essentially each pixel on the diffraction grating either transmits, refracts, or reflects a light path. And this represents the connections between layers. It’s unclear whether the 5 or 6 plates used in the D2NN correspond to the NN layers but it’s certainly possible.

And to the life of me I can’t understand what they mean by “Residual D2NN”, other than if it means using a trained (residual) NN and converting this to D2NN.

Some advantages of D2NN

3D printing diffraction gratings means anyone/lab could do this. The 3D printers they used had a spatial accuracy of 600 dpi, with 0.1mm accuracy, almost consumer grade 3D printers. In any case, being able to print these in a matter of hours, while not as easy as changing an all digital NN, seems like an easy way to try out the approach.

For example, for the MNIST digit classifier they used a pixel size of 400um and each diffraction layer they created was equivalent to 200X200 neural weights. Which means that 5 layer D2NN could handle about 0.2M neural weights which were completely connected to one another. This meant they could have (200×200)**2*5=8B connections in the MNIST D2NN. In the image classifier, each diffraction layer had 300×300 neural weights. So D2NN’s seem to scale very well.

Being an all passive optical device, the system is operates entirely in parallel, That is, the researchers indicated that the D2NN devices operate at the speed of light and would perform the inferencing activity in the time it takes a camera to capture the image.

Also the device uses very little energy (I assume just the energy for the THz generator, the input plane detector and the THz detector at the end.

And the researchers also claimed the device was cheap to manufacture, it could be created for less than $50. (Unclear if this included all the electronics or just the D2NN diffraction gratings and holder). And once you have locked into a D2NN that you wanted to use, could be manufactured in volume, very cheaply (sort of like stamping out CD platters). Finally, the number of neural network nodes and layers can be scaled up to a large number of layers and nodes per layer while still fitting on the diffraction gratings. In contrast, all electronic NN require more compute power as you scale up network layers and nodes per layer.

The other article (ArchivX) talked about potentially using a hybrid optical-electronic DNN approach with some layers being D2NN and others being purely digital (electronics). Such a system could potentially be used where some portion of the NN was more stable/more compute intensive than others and where the final output classification layer(s) was more changeable and much smaller/less compute intensive. Such a hybrid system could make use of the best of of the all optical D2NN to efficiently and quickly compress the input space and then have the electronic final classification layer provide the final classification step.

The Oracle

Combining a handful of D2NNs into a device that accepts speech input and provides speech output with the addition of say an offline copy of Wikipedia, Google Books etc. with a search engine that could be used to retrieve responses to questions asked would create an oracle device. Where you would ask a question and the device would respond with the best answer it could find (in it’s databases).

If this could be made out of an all passive optical components and use natural sunlight/electronic illumination to perform it’s functionality, such an all optical, question to answer oracle would be very useful to the populations of the world. And could be manufactured in volume very cheaply and would cost almost nothing to operate.

A couple of other tweaks, if we could collapse the multiple grating D2NNs into a single multi-layer plate/platter and make these replaceable in the device that would allow the oracle’s information base to be updated periodically.

Then if we could embed such a device into a Long Now Clock that would reflect sunlight onto the disk every Solstice, or Equinox, then we could have a quarterly oracle device that could last for 1000 of years. That would provide answers to queries one day every quarter. And that would be quite the oracle…

Photo credit(s):

The birth of biocomputing (on paper)

Read an article this past week discussing how researchers in Barcelona Spain have constructed a biological computing device on paper (see Biocomputer built with cells printed on paper). Their research was written up in a Nature Article (see 2D printed multi-cellular devices performing digital or analog computations).

We’ve written about DNA computing and storage before (see DNA IT …, DNA Computing… posts and our GBoS podcast on DNA storage…). But this technology takes all that to another level.

2-bit_ALU (from wikimedia.org)
2-bit_ALU (from wikimedia.org)

The challenges with biological computing previously had been how to perform the input processing and output within a single cell or when using multiple cells for computations, how to wire the cells together to provide the combinational logic required for the circuit.

The researchers in Spain seemed to have solved the wiring problems by using diffusion across a porous surface (like paper) to create a carrier signal (wire equivalent) and having cell groups at different locations along this diffusion path either enhance or block that diffusion, amplify/reduce that diffusion or transform that diffusion into something different

Analog (combinatorial circuitry types of) computation for this biocomputer are performed based on the location of sets of cells along this carrier signal. So spatial positioning is central to the device and the computation it performs. Not unlike digital or combinatorial circuitry, different computations can be performed just by altering the position along the wire (carrier signal) that gates (cells) are placed.

Their process seems to start with designing multiple cell groups to provide the processing desired, i.e., enhancing, blocking, transforming of the diffusion along the carrier signal, etc. Once they have the cells required to transform the diffusion process along the carrier signal, they then determine the spatial layout for the cells to be used in the logical circuit to perform the computation desired. Then they create a stamp which has wells (or indentations) which can be filled in with the cells required for the computation. Then they fill these wells with cells and nutrients for their operation and then stamp the circuit onto a porous surface.

The carrier signal the research team uses is a small molecule, the bacterial 3OC6HSL acyl homoserine lactone (AHL) which seems to be naturally used in a sort of biologic quorum sensing. And the computational cells produce an enzyme that enhances or degrades the AHL flow along the carrier signal. The AHL diffuses across the paper and encounters these computational cells along the way and compute whatever it is that’s required to be computed. At some point a cell transforms AHL levels to something externally available

They created:

  • Source cells (Sn) that take a substance as input (say mercury) and converts this into AHL
  • .Gate cells (M) that provide a switch on the solution of AHL difusing across the substrate.
  • Carrier reporter cells (CR) which can be used to report on concentrations of AHL.

The CR cells produce green florescent reporter proteins (GFP). Moreover, each gate cell expresses red florescent reporter proteins (RFP) as well for sort of a diagnostic tap into its individual activity.

Mapping of a general transistor architecture on a cellular printed pattern obtained using a stamping template. Similar to the transistor architecture, the cellular pattern is composed of three main components: source (S1 cells), gate (M cells) that responds to external inputs and a drain (CR cells) as the final output responding to the presence of the carrying signal (CS). b Stamping template used to create the circuit made of PLA with a layer of synthetic fibre (green). Cellular inks (yellow) are in their corresponding containers. Before stamping, the synthetic fibre is soaked with the different cell types. Finally, the stamping template is pressed against the paper surface, depositing all cells. c Circuit response. In the absence of external input, i.e. arabinose, the CS encoded in the production of AHL molecules by S1 cells diffuses along the surface, inducing GFP expression in reporter cells CR. In the presence of 10−3 M arabinose (Ara), the modulatory element Mara produces the AHL cleaving enzyme Aiia, which degrades the CS. Error bars are the standard deviation (SD) of three independent experiments. Data are presented as mean values ± SD. Experiments are performed on paper strips. The average fold change is 5.6x. d Photography of the device. Source data are provided as a Source Data file.

Using S, M and CR cells they are able to create any type of gate needed. This includes OR, AND, NOR and XNOR gates and just about any truth table needed. With this level of logic they could potentially implement any analog circuit on a piece of paper (if it was big enough).

a Schematic representation of the multi-branch implementation of a truth table. bImplementation of different logic gates. A schematic representation of the cells used in each paper strip and their corresponding distance points is given (Left). Gates with two sources of S1 (OR and XNOR gates) are circuits carrying two branches, while the other gates (NOR and AND gates) can be implemented with just one branch. Input concentrations are Ara = 10−3 M and aTc = 10−6 M. M+aTc and MaTc are, respectively, positive and negative modulatory cells responding to aTc. M+ara and Mara are, respectively, positive and negative modulatory cells responding to arabinose. S1 cells produce AHL constitutively and CR are the reporter cells. Error bars are the standard deviation (SD) of three independent experiments. The average fold change has been obtained from the mean of ON and OFF states from each circuit. OR gate 14.31x, AND gate 6.21x, NOR gate 6.58x, XNOR gate 5.6x. Source data are provided as a Source Data file.

As we learn in circuits class, any digital logic can be reduced to one of a few gates, such as NAND or NOR.

As an example of uses of the biocomputing, they implemented a mercury level sensing device. Once the device is dipped in a solution with mercury, the device will display a number of green florescent dots indicating the mercury levels of the solution

The bio-logical computer can be stamped onto any surface that supports agent diffusion, even flexible surfaces such as paper. The process can create a single use bio-logic computer, sort of smart litmus paper that could be used once and then recycled.

The computational cells stay “alive” during operation by metabolizing nutrients they were stamped with. As the biocomputer uses biological cells and paper (or any flexible diffusible substrate) as variable inputs and cells can be reproduced ad-infinitum for almost no cost, biocomputers like this can be made very inexpensively and once designed (and the input cells and stamp created) they can be manufactured like a printing press churns out magazines.

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Now I’d like to see some sort of biological clock capability that could be used to transform this combinatorial logic into digital logic. And then combine all this with DNA based storage and I think we have all the parts needed for a biological, ARM/RISC V/POWER/X86 based server.

And a capacitor would be a nice addition, then maybe they could design a DRAM device.

Its one off nature, or single use will be a problem. But maybe we can figure out a way to feed all the S, M, and CR cells that make up all the gates (and storage) for the device. Sort of supplying biological power (food) to the device so that it could perform computations continuously.

Ok, maybe it will be glacially slow (as diffusion takes time). We could potentially speed it up by optimizing the diffusion/enzymatic processes. But it will never be the speed of modern computers.

However, it can be made very cheap, and very height dense. Just imagine a stack of these devices 40in tall that would potentially consist of 4000-8000 or more processing elements with immense amounts of storage. And slowness may not be as much of a problem.

Now if we could just figure out how to plug it into an ethernet network, then we’d have something.

Photo credit(s):

  • 2 Bit alu from Wikipedia
  • Figures 1 & 3 from Nature article 2D printed multi-cellular devices performing digital and analog computation

Storageless data!?

I (virtually) attended SFD21 earlier this year and a company called Hammerspace presented discussing their vision for storageless data (see videos of their session at SFD21).

We’ve talked them before but now they have something to offer the enterprise – data mobility or storageless data.

The white board after David Flynn’s session at SFD8

In essence, customers want to be able to run their workloads wherever it makes the most sense, on prem, in private cloud, and in the public cloud among other places. Historically, it’s been relatively painless to transfer an application’s binary from one to another data center, to a managed service provider or to the public cloud.

And with VMware Cloud Foundation, Kubernetes, Docker and Linux operating everywhere, the runtime environment and other OS services that applications depend on are pretty much available in any of those locations. So now customers have 2 out of 3, what’s left?

It’s all about the Data

Data can take a very long time to move around a data center, let alone across the web between locations. MBs and even GBs of data may be relatively painless to move, but TBs of data can be take days, and moving PBs of data is suicidal.

For instance, when we signed up for a globally accessible file synch and share storage service, I probably had 75GB or so of data I wanted managed. It took literally several days of time to upload this. Yes, I didn’t have data center class internet access, but even that might have only sped this up 2-5X. Ok, now try this with 1TB or more and it’s pretty much going to take days, and you can easily multiple that by 10 to do a PB or more. And that’s if it happens to continue to perform the transfer without disruption.

So what’s Hammerspace storageless data got to do with any of this.

Hammerspace’s idea

It’s been sort of a ground truth of storage, since I’ve been in the industry (40+ years now), that not all random IO data is accessed at the same frequency. That is, some data is accessed a lot and other data accessed hardly at all. That’s why DRAM caching of data can be so important to a host or storage system.

Similarly for sequential access, if you can get the first blocks of data to the host and then stream the rest in time, a storage system can appear to read fast.

Now I won’t go into all the tricks of doing good data caching, (the secret sauce to every vendor’s enterprise storage), but if you can appear to cache data well, you don’t actually need to transfer all the data associated with an application to a location it’s running in, you can appear as if all the data is there, when actually only some of it is present.

Essentially, Hammerspace creates a global file system for your data, across any locations you wish to use it, with great caching, optimized data transfer and with real storage behind it. Servers running your applications mount a Hammerspace file system/share that stitches together all the file storage behind it, across all the locations it’s operating in.

An application request goes to Hammerspace and if the data is not present there, Hammerspace goes and fetches and caches blocks of data as fast as it can. This will let the application start performing IO while the rest of the data is being cached and if allowed, moved to the new location.

Storage can be not managed by Hammerspace, read-write managed by Hammerspace or read-only managed by Hammerspace. For customers who want the whole Hammerspace storageless data functionality they would use read-write mode. For those who just want to access data elsewhere read-only would suffice. Customers who want to continue to access data directly but want read access globally, would use the read-only mode.

Once read-write storage is assigned to Hammerspace grabs all the file metadata information on the storage system. Once this process completes, customers no longer access this file data directly, but rather must access it through Hammerspace. At that point, this data is essentially storageless and can be accessed wherever Hammerspace services are available.

How does Hammerspace do it

Behind the scenes is a lot of technology. Some of which is discussed in the SFD21 sessions (see video’s above). Hammerspace is not in the data path but rather in the control path of data access. But it does orchestrate data movement, and it does route data IO requests from an application to where the data (currently) resides.

Hammerspace also supports Service Level Objectives (SLOs) for performance, geolocation, security, data protection options,, etc. These can be used to keep data in particular regions, to encrypt data (using KMIP), ensure high performance, high data availability, etc.

Hammerspace can manage data across 32 separate sites. It takes a couple of hours to deploy. per site. Each site has a Hammerspace metadata service with standalone access to all data within that site. For example, standalone access could be used, in the event of a network loss.

At the moment, they support eventual consistency and don’t support a global lock service. Rather, Hammerspace uses a conflict resolution service in the event data is overwritten by two or more applications. For any file that was being updated in two or more locations, that file would be flagged as in conflict, Hammerspace would provide snapshots of the various versions of the file(s) and it would require some sort of manual intervention to resolve the conflict. Each location would have (temporary) access to the data it had written directly, but at some point the conflict would need resolution.

They also support NFS and SMB file access for the front end and use object storage services for backend data. Data is copied on demand to the local site’s storage when accessed based on the SLO policies in effect for it. During data movement it is copied up, temporarily into objects on AWS, Microsoft Azure, or GCP, and then copied down to the location it’s being moved to. I believe this temporary object data is encrypted and compressed. Hammerspace support KMIP key providers.

Pricing for Hammerspace is on a managed capacity basis. But anyone can use Hammerspace for up to 10TB for free. Hammerspace is available in AWS marketplace for configuration there.

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Well it’s been a long time coming, but it appears to be here. Any customers wanting hybrid-cloud operations or global access to their data would be remiss to not check out Hammerspace.

[Edited after posting, The Eds.]

Tattoos that light up

Read an article the other day, titled Light-emitting tattoo engineered in ScienceDaily. Which was reporting on research done by University College London and Istituto Italiano di Tecnologia (Italian Institute of Technology) (Ultrathin, ultra-comfortable and free-standing, tattooable LEDs – behind paywall).

The new technology out of their research can construct OLEDs, found in TVs, phones, and other displays, and apply them as temporary tattoos. The tattoos will eventually degrade, wash off but while present on the skin they can light up and display information.

According to the Nanowerk news article reporting on the research, (see Light emitting tattoos engineered for the 1st time), the OLEDs are printed onto paper which can then be transferred to skin by the application of water. The picture above shows a number of the OLED tattoos ready for application.

The vision is that OLED tattoos along with other flexible electronics could provide wearable sensors of bio-chemical activity of a person. Such sensors could be used in hospitals and in the home to display dehydration, glucose status, oxygenation, etc. as well as be able to display heart and breath rates. But in order to get to that vision there’s a few steps that are needed.

Flexible, stretchable electronics

There have been a number of articles about creating flexible electronics, (e.g., see A design to improve the resilience and electrical performance thin metal film based electrodes). This article was reporting on research done at the University of Illinois, Champaign-Urbana reported in Nature (behind paywall) but one of the researchers blogged about in NaturePortfolio Devices & Materials (see: An atom-thick interlayer enables the electrical ductility of thin-film metal electrodes).

Flexible electronics can be constructed by creating a thin metal film with the electronics embedded in it placed on top of a flexible substrate. However, when that flexible substrate starts to deform or stretch it induces cracks in the thin metal films which lead to loss of conductivity, or loss of electronics function.

The research cited in the article above showed videos of cracking that takes place during deformation and stretching which would lead to loss of conductivity.

But the researchers at UofI found out that if you place a thin layer of graphene or other 2D sheet of material between the electronic thin film and the flexible substrate, the cracks that eventually happen are much less harmful to electronic conduction or functioning or provide electronic ductability. To add ductablity to an electronic circuit using LEDs the team applied an atomically thin (<1nm), 2D layer of graphene between it and the flexible substrate.

Somehow the graphene provided a mechanical buffer between the flexible substrate and the thin film electronics that allowed the circuits to have much more ductility. It appears that this mechanical buffer changed the type of cracking that occurs on the thin metal film such that they are shorter and more varied in direction rather than straight across and this helped them retain functioning longer than without the

The researchers at U of I actually created a led display that could be bent without failure. See a video of them comparing the thin film vs thin film with 2D substrate.

Skin sensors

Moreover, there have been a number of articles discussing new wearable technologies that could be used to sense a persons bio-chemical state. For example, research reported on recently (see Do Sweat It! Wearable Microfluidic Sensor to Measure Lactate Concentration in Real Time) done at the Tokyo University of Science, published in Electochimica Acta (behind paywall) talks about a sweat sensor that can be applied to skin to determine when athletes or others are getting dehydrated.

This sensor uses a micro-fluidics device which printed with electronic ink. Such a device could be manufactured in volume and be readily printed onto surfaces, that could be applied to the skin, anywhere sweat was being produced.

Future tattoos

Wearable sensors already surround us. We have watches that can tell our heart rates, walk/running speed/rates, step counts, etc. It doesn’t take much to imagine that most if not all of these could be fabricated on a thin film and with the proper 2D substrate layer be applied as a tattoo to a person while in the hospital but all these sensors have lacked a read out or display up until now. With OLED readouts wearable sensors now have a reasonable display capability.

The sweat sensor above uses microfluidics to do a lactate assay of sweat. The motion sensors in my watch uses MEMs and onboard IMU/GPS to determine speed and direction of movement. Electronic temperature sensors use thermoelectric effects. Blood oxygen sensors use LEDs and light sensors. None of these appears unable to be fabricated, miniaturized and printed on thin films. Adding OLEDs and why do we need a watch anymore?

What seems to be the most glaring omission is gas sensors (although the lactate micro-fluidic sensor is close). If we could somehow miniaturize gas sensors with enough sensitivity to glucose levels, immunological load, specific diseases (COVID19), then maybe there’d be a mass market for such devices, outside of a hospital or smart watch users.

Then with OLED and electronics that can be temporarily tattooed onto a person skin., why couldn’t this be a fashion accessory. I can imagine lot’s of people would have interest in lighting up messages, iconography or other data on their arms, hands, or other areas of a person’s body. I wonder if it could be used to display hair on the top of my head :)?

And of course these OLED-electronics based tattoos are temporary. But if they are all made from electronic ink, it seems to me that such tattoos could be permanently printed (implanted?) onto a persons skin.

Maybe at some future point a permanent OLED-electronics based tattoo could provide an electronic display and input device that could be used in conjunction with a phone or a smart-watch. All it would take would be blue-tooth.

Comments?

Photo credits:

Data Science storage with NetApp’s Python Toolkit

I’ve got a book someplace (yet to be read completely) with the title Data science with Python. At a recent Storage Field Day 21 last month, NetApp was there discussing a number of their product offerings one of which was their Python SDK to manage NetApp storage for data scientists and AI researchers (see videos of their sessions here).

I’m not a data science expert but a Python SDK for storage management just makes so much sense to me I just had to take a look. Their GitHub repo is available online and they call it the NetApp Data Science Toolkit.

But first please take our new poll:

The challenge for data science and AI researchers is that it’s all about the data. How do you find the data, gain access to it, clean it, and process it quickly so you can do it all over again. Having some sort of Python SDK that allows you to do some rudimentary storage volume configuration, access, snapshotting etc. can make these sorts of pipelines be self-serviced rather than going back and forth with operations to get volumes configured, mounted, and services established.

NetApp Data Science Toolkit

The NetApp Data Science Toolkit can be PIP installed into anything with Python 3.5 or later and can be invoked via a command line or as a library of Python functions that can be invoked. The command line utility and the Python calls appear to be functionally equivalent.

pip3 install netapp-ontap pandas tabulate requests boto3

The Toolkit must be configured for your environment and NetApp storage but once that’s done your ready to rock and roll.

MLOps pipeline from Google

The command line is invoked with

./ntap_dsutil.py

following that command are subcommands and parameters specifying what ONTAP operation you want to perform and how it is to be done. Python function calls seem to follow the same parameterization as the CLI.

The CLI and Python function calls can run on MacOS or any Linux distribution. There’s a paper that discusses how to use the SDK to accelerate AI pipelines as well as another ReadMe that describes it’s use in Kubernetes with NetApp’s Trident CSI plugin.

The functionality supports NetApp AFF, FAS, Cloud Volumes and Select that are running ONTAP 9.7 or later. For a current list of ONTAP functions available, check out the toolkit. But for a overview these ONTAP functions were available.

  • For Volume Management – cloning, creating, listing all, deleting or mounting a volume,
  • For Snapshot Management – creating, deleting, listing and restoring snapshots (of volumes)
  • For Data Fabric Management – listing all cloud sync relationships, triggering a cloud sync operation, multi-thread pulling a bucket down from S3 storage (into a NetApp volume directory), pulling a single object down from S3 into a file, pushing the contents of a directory to bucket on S3 and pushing a file into an object on S3.
  • For Advanced Data Fabric Management – listing all SnapMirror relationships and triggering a sync operation for an existing SnapMirror relationship.

This is a pretty comprehensive list of NetApp ONTAP storage functionality. Having all this under control of Python and CLI for data scientist or AI researcher seems pretty impressive.

Of course not every option for all those functions are supported but it’s just a start (V1.1 of the toolkit). I’m sure there’s more to come, especially if customers demand it.

However, it would be nice to have an ONTAP simulator available with the toolkit that could be used to test out your Python code and CLI commands before using real NetApp storage. This would be very useful for those of us lacking our own test ONTAP storage, just hanging around on prem or in the cloud.

As Python becomes the language of choice for AI and now data science, it seems only natural that storage and data protection companies would start releasing Python SDKs/APIs for their product functionality. That way AI and data science researchers could embed any storage functionality they needed directly into their Python code or Jupyter Notebook application.

Having a Python SDK for NetApp ONTAP storage, means using data storage for your MLops or data science pipelines is that much easier.

Great move by NetApp. Ok where’s the rest of the industry?

Picture credit(s):

New DRAM can be layered on top of CPU cores

At the last IEDM (IEEE International ElectronDevices Meenting), there were two sessions devoted to a new type of DRAM cell that consists or 2 transistors and no capacitors (2TOC) that can be built in layers on top of a micro processor which doesn’t disturb the microprocessor silicon. I couldn’t access (behind paywalls) the actual research but one of the research groups was from Belgium (IMEC) and the other from the US (Notre Dame and R.I.T). This was written up in a couple of teaser articles in the tech press (see IEEE Spectrum tech talk article).

DRAM today is built using 1 transistor and 1 capacitor (1T1C). And it appears that capacitors and logic used for microprocessors aren’t very compatible. As such, most DRAM lives outside the CPU (or microprocessor cores) chip and is attached over a memory bus.

New 2T0C DRAM Bit Cell: Data is written by appliying current to the WBL and WWL and bit’s are read by seeing if acurrent can pass through the RWL RBL

Memory busses have gotten faster in order to allow faster access to DRAM but this to is starting to reach fundamental physical limits and DRAM memory sizes aren’t scaling like the used to.

Wouldn’t it be nice if there were a new type of DRAM that could be easlly built closer or even layered on top of a CPU chip, with faster direct access from/to CPU cores. through inter chip electronics.

Oxide based 2T0C DRAM

DRAM was designed from the start with 1T1C so that it could hold a charge. With a charge in place it could be read out quickly and refreshed periodically without much of a problem.

The researcher found that at certain sizes (and with proper dopants) small transistors can also hold a (small) charge without needing any capacitor.

By optimizing the chemistry used to produce those transistors they were able to make 2T0C transistors hold memory values. And given the fabrication ease of these new transistors, they can easily be built on top of CPU cores, at a low enough temperature so as not to disturb the CPU core logic.

But, given these characteristics the new 2T0C DRAMB can also be built up in layers. Just like 3D NAND and unlike current DRAM technologies.

Today 3D NAND is being built at over 64 layers, with Flash NAND roadmap’s showing double or quadruple that number of layers on the horizon. Researchers presenting at IMEC were able to fabricate an 8 layer 2T0C DRAM on top of a microprocessor and provide direct, lightening fast access to it.

The other thing about the new DRAM technology is that it doesn’t need to be refreshed as often. Current DRAM must be refreshed every 64 msec. This new 2T0C technology has a much longer retention time and currently only needs to be refreshed every 400s and much longer retention times are technically feasible.

Some examples of processing needing more memory:

  • AI/ML and the memory wall -Deep learning models are getting so big that memory size is starting to become a limiting factor in AI model effectiveness. And this is just with DRAM today. Optane and other SCM can start to address some of this problem but ithe problem doesn’t go away, AI DL models are just getting more complex I recently read an article where Google trained a trillion parameter language model.
  • In memory databases – SAP HANA is just one example but they are other startups as well as traditional database providers that are starting to use huge amounts of memory to process data at lightening fast speeds. Data only seems to grow not shrink.

Yes Optane and other SCM today can solve some of thise problems. But having a 3D scaleable DRAM memory, that can be built right on chip core, with longer hold times and faster direct access can be a game changer.

It’s unclear whether we will see all DRAM move to the new 2T0C format, but if it can scale well in the Z direction has better access times, and longer retention, it’s unclear why this wouldn’t displace all current 1T1C DRAM over time. However, given the $Bs of R&D spend on new and current DRAM 1T1C fabrication technology, it’s going to be a tough and long battle.

Now if the new 2T0C DRAM could only move from 1 bit per cell to multiple bits per cell, like SLC to MLC NAND, the battle would heat up considerably.

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The rise of MinIO object storage

MinIO presented at SFD21 a couple of weeks back (see videos here). They had a great session, as always with Jonathan and AB leading the charge. We’ve had a couple of GreyBeardsOnStorage podcasts with AB as well (listen and see GreyBeards talk open source S3… and GreyBeards talk Data Persistence …). We first talked with MinIO last year at SFD 19 where AB made a great impression on the bloggers (see videos here)

Their customers run the gamut from startups to F500. AB said that ~58% of the F500 have MinIO installed and over 8% of the F500 have added capacity over the last year. AB said they have a big presence in Finance, e.g., the 10 largest banks run MinIO, also the auto and Space/Defense sectors have adopted their product.

One reason for the later two sectors (auto & space/defense) is the size of MinIO’s binary, 50MB. And my guess for why the rest of those customers have adopted MinIO is because it’s S3 API compatible, it’s open source, and it’s relatively inexpensive.

Object storage trends

Customers running in the cloud have a love-hate relationship with object storage, they love that it scales but hate what it costs. There are numerous on prem object storage alternatives from traditional and non-traditional storage vendors, but most are deployed on appliances.

With appliances, customers have to order, wait for delivery, rack-configure-set up and after maybe weeks to months finally they have object storage on prem. But with MinIO a purely software, open source solution, it can be tried by merely downloading a couple of (Docker) containers and deployed/activated in under an hour..

As mentioned above, MinIO is API compatible with AWS S3 which helps with adoption. Moreover, now that it’s an integral part of VMware (see their new Data Persistence Platform), it can be enabled in seconds on your standard enterprise VMware cluster with Tanzu.

The other trend is that the edge needs storage, and lots of it. The main drivers of massive edge storage requirement are TelCos deploying 5G and auto industry’s self-driving cars. But this is just a start, industrial IoT will be generating reams of sensor log data at the edge, it will need to be stored somewhere. And what better place to store all this data, but on object storage. Furthermore, all this is driving more adoption of object storage, with MinIO picking up the lion’s share of deployments.

In addition, MinIO recently ported their software to run on ARM. AB said this was to support the expanding hobbyist and developers community driving edge innovation.

And then there was Kubernetes. Everyone in the industry (with the possible exception of Google) is surprised by the adoption of K8S. Google essentially gifted ~$1Bs in R&D on how to scale apps to the world of IT, and now any startup, anywhere, can scale with as well as Google can. And scaling is the “killer app” for the SW industry.

But performance isn’t bad either

Jonathan made mention of MinIO performance (see MinIO 24 node disk and MinIo 32 node NVMe SSD reports) benchmarks. Their disk data shows avg read and write performance of 16.3GB/s and 9.4GB/s, respectively and their NVMe SSD average read and write performance of 183.2GB/s and 171.3GB/s, respectively. The disk numbers are very good for object storage, but the SSD numbers are spectacular.

It turns out that modern, cloud native apps don’t need quick access to data as much as high data throughput. Modern apps have moved to a processing data in memory rather than off of storage, which means they move (large) chunks of data to memory and crunch on it there, and then spit it back out to storage This type of operating mode seems to scale better (in the cloud at least) than having a high priced storage system servicing a blizzard of IO requests from everywhere.

Other vendors had offered SSD object storage before but it never took off. But nowadays, with NVMe SSDs, MinIO is seeing starting to see healthcare, finance, and any AI/ML workloads all deploying NVMe SSD object storage. Yes for large storage repositories, (object storage’s traditional strongpoint), ie, 5PB to 100PB, disk can’t be beat but where blistering high throughput, is needed, NVMe SSD object storage is the way to go.

Open source vs. open core

AB mentioned that MinIO business model is 100% open source vs. many other vendors that use open source but whose business model is open core. The distinction is that open core vendors use open source as base functionality and then build proprietary, charged for, software features/functions on top of this.

But open source vendors, like MinIO offer all their functionality under an open source license (Apache SM License V2.0, GNU AGPL v3 Open Source license and other FOSS licenses), but if you want to use it commercially, build products with it embedded inside, or have enterprise class support, one purchases a commercial license.

As presented at SFD21, but their website home page has updated numbers reflected below

The pure open source model has some natural advantages:

  1. It’s a great lead gen solution because anyone, worldwide, 7X24X365 can download the software and start using it, (see Docker Hub or MinIO’s download page
  2. It’s a great hiring pool. Anyone, who has contributed to the MinIO open source is potentially a great technical hire. MinIO stats says they have 685 contributors, 19 in just the last month for MinIO base code (see MinIO’s GitHub repo).
  3. It’s a great development organization. With ~20 commits a weekover the last year, there’s a lot going on to add functionality/fix bugs. But that’s the new world of software development. Given all this activity, release frequencies increase, ~4 releases a month ((see GitHub repo insights above).
  4. It’s a great testing pool with, ~480M Docker Pulls (using a Docker container to run a standard, already configured MinIO server, mc, console, etc.) and ~18K enterprises running their solution, that’s an awful lot of users. With open source a lot of eye’s or contributors make all problems visible, but what’s more typical, from my perspective, is the more users that deploy your product, the more bugs they find.

Indeed, with the VMware’s Data Persistence Platform, Tanzu customers can use MinIO’s object storage at the click of a button (or three).

Of course, open source has downsides too. Anyone can access packages directly (from GitHub repo and elsewhere) and use your software. And of course, they can clone, fork and modify your source code, to add any functionality they want to it. Historically, open source subscription licensing models don’t generate as much revenues as appliance purchases do. And finally, open source, because it’s created by geeks, is typically difficult to deploy, configure, and use.

But can they meet the requirements of an Enterprise world

Because most open source is difficult to use, the enterprise has generally shied away from it. But that’s where there’s been a lot of changes to MinIO.

MinIO always had a “mc” (minio [admin] client) that offered a number of administrative services via an API, programmatically controlled interface. but they have recently come out with a GUI offering, the minIO console, which has a similarly functionality to their mc APU. They demoed the console on their SFD21 sessions (see videos above).

Supporting 18K enterprise users, even if only 8% are using it a lot, can be a challenge, but supporting almost a half a billion docker pulls (even if only 1/4th of these is a complete minIO deployment) can be hell on earth. The surprising thing is that MinIO’s commercial license promises customers direct-to-engineer support.

At their SFD21 sessions, AB stated they were getting ~2.7 new (tickets) problems a day. I assume these are what’s just coming in from commercial licensed users and not the general public (using their open source licensed offerings). AB said their average resolution time for these tickets was under 15 minutes.

Enter SubNet, the MinIO Subscription Network and their secret (not open source?) weapon to scale enterprise class support. Their direct-to-engineer support model involves a much, more collaborative approach to solving customer problems then you typical enterprise support with level 1, 2 & 3 support engineers. They demoed SubNet briefly at SFD21, but it could deserve a much longer discussion/demostration.

What little we saw (at SFD21) was that it looked almost like slack-PM dialog between customer and engineer but with unlimited downloads and realtime interaction.

MinIO also supports a very active Slack discussion group with ~11K users. Here anyone can ask a question and it will get answered by anyone. MinIO’s Slack has 2 channels: (Ggeneral and GitHub for notifications). It seems like MinIO is using Slack as a crowdsourced level 1 support.

But in the long run, to continue to offer “direct-to-engineer” levels of support, may require adding a whole lot more engineers. But AB seems prepared to do just that.

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MinIO is an interesting open source S3 API compatible, object storage solution that seems to run just about anywhere, is freely deployable with enterprise class support available (at a price) and has high throughput performance. What’s not to like.

cOAlition S requires open access to funded research

I read a Science article this last week (A new mandate highlights costs and benefits of making all scientific articles free) about a group of funding organizations that have come together to mandate open access to all peer-reviewed research they fund called Plan S. The list of organizations in cOAlition S is impressive including national R&D funding agencies from UK, Ireland, Norway, and a number of other countries, charitable R&D funding agencies from WHO, Welcome Trust, Bill&Melinda Gates Foundation and more, and the group is also being funded by the EU. Plan S takes effect this year.

Essentially, all research funded by these organizations must be immediately published in open access forum, open access journals or be freely available in an open access section of a publishers website which means it could be free to be read by anyone worldwide with access to the web. Authors and institutions will retain copyright for the work and the work will be published under an open access license such as the CC BY (Creative Commons Attribution) license.

Why open access is important

At this blog, frequently we find ourselves writing about research which is only available on a paid subscription or on a pay per article basis. However, sometimes, if we search long enough, we find a duplicate of the article published in pre-print form in some preprint server or open access journal.

We have written about open access journals before (see our New Science combats Coronavirus post). Much of what we do on this blog would not be possible without open access journals like PLoS, BioRxiv, and PubMed.

Open access mandates are trending

Open access mandates have been around for a while now. And even the US Gov’t got into the act, mandating all research funded by the NIH be open access by 2008, with Dept of Agriculture and Energy following later (see wikipedia Open access mandates).

In addition, given the pandemic emergency, many research publishers like Nature and Elsevier made any and all information about the Coronavirus free access on their websites.

Impacts and R&D research publishing business model

Although research is funded by public organizations such as charities and government agencies, prior to open access mandates, most research was published in peer-reviewed journal magazines which charged a fee for access. For many research organizations, those fees were a cost of doing research. If you were an independent researcher or in an institution that couldn’t afford these fees, attempting to do cutting edge research was impossible without this access.

Yes in some cases, those journal repositories waved these fees for deserving institutions and organizations but this wasn’t the case for individual researchers. Or If you were truly diligent, you could request a copy of a paper from an author and wait.

Of course, journal publishers have real expenses they needed to cover, as well as make a reasonable profit. But due to business consolidation, there were fewer independent journals around and as a result, they charged bundled license fees for vast swathes of research articles. Such a wide bundle may or may not be of interest to an individual or an institution. That plus with consolidation, profits were becoming a more significant consideration.

So open access mandates, often included funding to cover fees for publishers to supply open access. Such fees varied widely. So open access mandates also began to require fees to be published and to be supplied a description how prices were calculated. By doing so, their hope was to make such costs more transparent

Impacts on authors of research articles

Somewhere there’s an aphorism for researchers that says “publish or perish“, which means you must publish research in order to become a recognized expert in your field. Recognition often the main driver behind better academic employment and more research funding.

However, it’s not just about volume of published papers, the quality of research also matters. And the more highly regarded publishing outlets have an advantage here, in that they are de facto gatekeepers to whats published in their journals. As such, where you publish can often lend credibility to any research.

Another thing changed over the last few decades, judging the quality of research has become more quantative. Nowadays, research quality is also dependent on the number of citations it receives. The more popular a publisher is, the more readers it has which increases the possibility for citations.

Thus, most researchers try to publish their best work in highly regarded journals. And of course, these journals have a high cost to provide open access.

Successful research institutions can afford to pay these prices but those further down the totem pole cannot.

Most mandates come with additional funding to support paying the cost to supply open access. But they also require publishing and justifying these. In the belief that in doing this so it will lend some transparency to these costs.

So the researcher is caught in the middle. Funding organizations want open access to research they fund. And publishers want to be paid a profit for that access.

History of research publication

Nature magazine first started publishing research in 1859, Science magazine first published in 1880, the Royal Society first published research in 1665. So publishing research has been going on for 350 years, and at least as a for profit business model, since the mid-1800s.

Research prior to being published in journals was only available in books. And more than likely, the author of the research had to pay to have a book published and the publisher made money only when those books were sold. And prior to that, scientific research was mostly only available in a course of study, also mostly paid for by the student.

So science has always had a cost to access. What open access mandates are doing is moving this cost to something added to the funding of research.

Now if open access can only solve the reproducibility crisis in science we could have us a real scientific revolution.

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