General articles on technical subjects.

PDFs of Monday 16 April

By exception, another PDF-Monday.

OpenCL vs. OpenMP: A Programmability Debate. The one moment OpenCL and the other mom ent OpenMP produces faster code. From the conclusion: “OpenMP is more productive, while OpenCL is portable for a larger class of devices. Performance-wise, we have found a large variety of ratios between the two solutions, depending on the application, dataset sizes, compilers, and architectures.”

Improving Performance of OpenCL on CPUs. Focusing on how to optimise OpenCL. From the abstract: “First, we present a static analysis and an accompanying optimization to exclude code regions from control-flow to data-flow conversion, which is the commonly used technique to leverage vector instruction sets. Second, we present a novel technique to implement barrier synchronization.”

Variants of Mersenne Twister Suitable for Graphic Processors. Source-code at http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/MTGP/

Accelerating the FFTD method using SSE and GPUs. “The Finite-Difference Time-Domain (FDTD) method is a computational technique for modelling the behaviour of electromagnetic waves in 3D space”. This is a project-plan, but describes the theories pretty well. Continue reading “PDFs of Monday 16 April”

5 types of loops you should avoid

In “Separation of compute, control and transfer” I talked about node-wise programming as a method we should embrace instead of trying to unroll the existing loops. In this article I get into loops and discuss a few types and how they can be run in a parallel form. Dependency is the big variable in each type: the lower the dependency on previous iterations, the better it can be parallelised. Another one is the known iteration-dimensions known before the loop is started.

The more you think about it, the more you find that a loop is not a loop.

Continue reading “5 types of loops you should avoid”

Supporting OpenCL on your own hardware

Say you have a device which is extremely good in numerical trigoniometrics (including integrals, transformations, etc to support mainly Fourier transforms) by using massive parallelism. You also have an optimised library which takes care of the transfer to the device and the handling of trigoniometric math.

Then you find out that the strength of your company is not the device alone, but also the powerful and easy-to-use library. You also find out that companies are willing to pay for the library, if it would work with other devices too. From your own helpdesk you hear that most questions are about extending the library with specialised functions. Giving this information, you define new customer groups for device-only and library-only – so just by adopting a standard you can increase revenue. Read below which steps you have to take to adopt OpenCL.

Continue reading “Supporting OpenCL on your own hardware”

Separation of Compute and Transfer from the rest of the code.

What if trees had the roots, trunk and crown were mixed up? Would it still have the advantage over other plants?

In the beginning of 2012 I spoke with Patrick Viry, former CEO of Ateji – now out-of-business. We shared ideas on GPGPU, OpenCL and programming in general. While talking about the strengths of his product, he came with a remark which I found important and interesting: separation of transfer. This triggered me to think further – those were the times when you could not read on modern computing, but had to define it yourself.

Separation of focus-areas are known to increase effectiveness, but are said to be for experts only. I disagree completely – the big languages just don’t have good support for defining the separations of concerns.

For example, the concepts of loops is well-known to all programmers, but OpenCL and CUDA have broken with that. Instead of using huge loops, those languages describe what has to be done at one location in the data and what the data is to be processed. From what I see, this new type of loop is getting abandoned in higher level languages, while it is a good design pattern.

I would like to discuss separation of compute and transfer from the rest of the code, to show that this will improve the quality of code. Continue reading “Separation of Compute and Transfer from the rest of the code.”

StreamHPC flirts with ARM

 With the launch of twitter-channel @OpenCLonARM we now officially show a strong interest in ARM for compute. And we are not the only ones, as the twitter already has 80 followers (60 in 1.5 day and 12 retweets of the welcome-message).

ARM has made tremendous progress in both technology and market-share. With ARM-64, companies like NVidia (and maybe AMD) in the field, X86 seems to be getting a real competitor. This could happen because since a few years computers are fast enough and are not being replaced by a faster one, but a smaller one (tablet, phone) or extra one. By the rules of the market, current technologies are replaced by the ones that give those other needs. ARM is fast (enough), flexible in design, very cheap, low-power and passively cooled. The biggest obstacle seems to be only getting a standard for a docking-station to connect your mobile, tablet or watch to keyboard, mouse and large screen.

OpenCL is perfect for ARM, as it gives the computation-power to the intensive computations not already covered by hardware-support. In the world of X86 this interests high performance and big data companies, where on ARM this interests also more. Without the need for OpenCL you can already watch HD video, with OpenCL you can encode the video with MP4. This year you will certainly hear more about new possibilities of OpenCL on ARM.

What do you think. Why does Intel not sell IP to ARM-companies as many technologies could be reused? Could Intel be the next ARM as an IP-seller, or will they stay the defender of X86 for many years to come?

streamhpc.com is not affiliated with ARM.

AccelerEyes ArrayFire

There is a lot going on at the path to GPGPU 2.0 – the libraries on top of OpenCL and/or CUDA. Among many solutions we see for example Microsoft with C++ AMP on top of DirectCompute, NVidia (and more) with OpenACC, and now AccelerEyes (most known for their Matlab-extension Jacket and libJacket) with ArrayFire.

I want you to show how easy programming GPUs can be when using such libraries – know that for using all features such as complex numbers, multi-GPU and linear algebra functions, you need to buy the full version. Prices start at $2500,- for a workstation/server with 2 GPUs.

It comes in two flavours: for OpenCL (C++) and for CUDA (C, C++, Fortran). The code for both is the same, so you can easily switch – though you still see references to cuda.h you can compile most examples from the CUDA-version using the OpenCL-version with little editing. Let’s look a little into what it can do.

Continue reading “AccelerEyes ArrayFire”

Theoretical transfer speeds visualised

There are two overviews I use during my training, and I would like to share with you. Normally I write them on a whiteboard, but it has advantages having it in a digital form.

Transfer speeds per bus

The below image gives an idea of theoretical transfer speeds, so you know how a fast network (1GB of data in 10 seconds) compares to GPU-memory (1GB of data in 0.01 seconds). It does not show all the ins and outs, but just give an idea how things compare. For instance it does not show that many cores on a GPU need to work together to get that maximum transfer rate. Also I have not used very precise benchmark-methods to come to these views.

We zoom into the slower bus-speeds. So all the good stuff is at the left and all buses to avoid are on the right.  What should be clear is that a read from or write to a SSD will make the software very slow if you use write-trough instead of write-back.

What is important to see that localisation of data makes a big difference. Take a look at the image and then try to follow with me. When using GPUs the following all can increase the speed on the same hardware: not using hard-disks in the computation-queue, avoiding transfers to and from the GPU and increasing the computations per byte of data. When an algorithm needs to do a lot of data-operations such as transposing a matrix, then it’s better to have a GPU that has high memory-access. When the number of operations is important, then clock-speed and cache-speed is most important.

Continue reading “Theoretical transfer speeds visualised”

Do your (X86) CPU and GPU support OpenCL?

Does your computer have OpenCL-capable hardware? Read on and find out if your computer is compatible…

If you want to know what other non-PC hardware (phones, tablets, FPGAs, DSPs, etc) is running OpenCL, see the OpenCL SDK page.

For people who only want to run OpenCL-software and have recent hardware, just read this paragraph. If you have recent drivers for your GPU, you can be sure OpenCL is already supported and you can run OpenCL-capable software. NVidia has support for OpenCL 1.1 since drivers 280.13, so if you need OpenCL 1.1, then make sure you have this version or later. If you want to use Intel-processors and you don’t have an AMD GPU installed, you need to download the runtime of Intel OpenCL.

If you want to know if your X86 device is supported, you’ll find answers in this article.

Often it is not clear how OpenCL works on CPUs. If you have a 8 core processor with double threading, then it mostly is understood that 16 pipelines of instructions are possible. OpenCL takes care of this threading, but also uses parallelism provided by SSE and AVX extension. I talked more about this here and here. Meaning that an 8-core processor with AVX can compute 8 times 32 bytes (8*8 floats or 8*4 doubles) in parallel. You could see it as parallelism of parallelism. SSE is designed with multimedia-operations in mind, but has enough to be used with OpenCL. The minimum requirement for OpenCL-on-a-CPU is SSE 4.2, though.

A question I see often is what to do if you have more devices. There is no OpenCL-package for all the available devices, so you then need to install drivers for each device. CPU-drivers are often included in the GPU-drivers.

Read on to find out exactly which processors are supported.

Continue reading “Do your (X86) CPU and GPU support OpenCL?”

Basic concepts: Function Qualifiers

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Optimisation of one’s thoughts is a complex problem: a lot of interacting processes can be defined, if you think of it.

In the OpenCL-code, you have run-time and compile-time of the C-code. It is very important to make this clear when you talk about compile-time of the kernel as this can be confusing. Compile-time of the kernel is at run-time of the software after the compute-devices have been queried. The OpenCL-compiler can make better optimised code when you give as much information as possible. One of the methods is using Function Qualifiers. A function qualifier is notated as a kernel-attribute:

__kernel __attribute__((qualifier(qualification)))  void foo ( …. ) { …. }

There are three qualifiers described in OpenCL 1.x. Let’s walk through them one by one. You can also read about them here in the official documentation, with more examples.

Continue reading “Basic concepts: Function Qualifiers”

Black-Scholes mixing on SandyBridge, Radeon and Geforce

Intel, AMD and NVidia have all written implementations of the Black-Scholes algorithm for their devices. Intel has described a kernels in their OpenCL optimisation-document (page 28 and further) with 3 random factors as input: S, K and T, and two configuration-constants R and V. NVidia is easy to compare to Intel’s, while AMD chose to write down the algorithm quite different.
So we have three different but comparable kernels in total. What will happen if we run these, all optimised for specific types of hardware, on the following devices?

  • Intel(R) Core(TM) i7-2600 CPU @3.4GHz, Mem @1333MHz
  • GeForce GTX 560 @810MHz, Mem @1000MHz
  • Radeon HD 6870 @930MHz, Mem @1030MHz

Three different architectures and three different drivers. To complete the comparison I also try to see if there is a difference when using Intel’s and AMD’s driver for CPUs. Continue reading “Black-Scholes mixing on SandyBridge, Radeon and Geforce”

OpenCL potentials: Watermarked media for content-protection

HTML5 has the future, now Flash and Silverlight are abandoning the market to make the way free for HTML5-video. There is one big problem and that is that it is hard to protect the content – before you know the movie is on the free market. DRM is only a temporary solution and many times ends in user-frustration who just want to see the movie wherever they want.

If you look at e-books, you see a much better way to make sure PDFs don’t get all over the web: personalizing. With images and videos this could be done too. The example here at the right has a very obvious, clearly visible watermark (source), but there are many methods which are not easy to see – and thus easier to miss by people who want to have needs to clean the file. It therefore has a clear advantage over DRM, where it is obvious what has to be removed. Watermarks give the buyers freedom of use. The only disadvantage is that personalised video’s ownership cannot be transferred.

Continue reading “OpenCL potentials: Watermarked media for content-protection”

Differences from OpenCL 1.1 to 1.2

This article will be of interest if you don’t want to read the whole new specifications [PDF] for OpenCL 1.2.

As always, feedback will be much appreciated.

After many meetings with the many members of the OpenCL task force, a lot of ideas sprouted. And every 17 or 18 months a new version comes out of OpenCL to give form to all these ideas. You can see totally new ideas coming up and already brought outside in another product by a member. You can also see ideas not appearing at all as other members voted against them. The last category is very interesting and hopefully we’ll see a lot of forum-discussion soon what should be in the next version, as it is missing now.

With the release of 1.2 there was also announced that (at least) two task forces will be erected. One of them will target integration in high-level programming languages, which tells me that phase 1 of creating the standard is complete and we can expect to go for OpenCL 2.0. I will discuss these phases in a follow-up and what you as a user, programmer or customer, can expect… and how you can act on it.

Another big announcement was that Altera is starting to support OpenCL for a FPGA-product. In another article I will let you know everything there is to know. For now, let’s concentrate on the actual differences in this version software-wise, and what you can do with it. I have added links to the 1.1 and 1.2 man-pages, so you can look it up.

Continue reading “Differences from OpenCL 1.1 to 1.2”

Basic Concepts: online kernel compiling

Typos are a programmers worst nightmare, as they are bad for concentration. The code in your head is not the same as the code on the screen and therefore doesn’t have much to do with the actual problem solving. Code highlighting in the IDE helps, but better is to use the actual OpenCL compiler without running your whole software: an Online OpenCL Compiler. In short is just an OpenCL-program with a variable kernel as input, and thus uses the compilers of Intel, AMD, NVidia or whatever you have installed to try to compile the source. I have found two solutions, which both have to be built from source – so a C-compiler is needed.

  • CLCC. It needs the boost-libraries, cmake and make to build. Works on Windows, OSX and Linux (needs possibly some fixes, see below).
  • OnlineCLC. Needs waf to build. Seems to be Linux-only.

Continue reading “Basic Concepts: online kernel compiling”

Kernels and the GPL. Are we safe and linking?

Disclaimer: I am not a lawyer and below is my humble opinion only. The post is for insights only, not for legal matters.

GPL was always a protection that somebody or some company does not run away with your code and makes the money with it. Or at least force that improvements get back into the community. For unprepared companies this was quite some stress when they were forced to give their software away. Now we have host-kernels-languages such as OpenCL, CUDA, DirectCompute, RenderScript don’t really link a kernel, but load it and launch it. As GPL is quite complicated if it comes to mixing with commercial code, I try to give a warning that GPL might not be prepared for this.

If your software is dual-licensed, you cannot assume the GPL is not chosen when eventually used in commercial software. Read below why not.

I hope we can have a discussion here, so we get to the bottom of this.

Continue reading “Kernels and the GPL. Are we safe and linking?”

Basic Concepts: OpenCL Convenience Methods for Vector Elements and Type Conversions

In the series Basic Concepts I try to give an alternative description to what is said everywhere else. This time my eye fell on alternative convenience methods in two cases which were introduced there to be nice to devs with i.e. C/C++ and/or graphics backgrounds. But I see it explained too often from the convenience functions and giving the “preferred” functions as a sort of bonus which works for the cases the old functions don’t get it done. Below is the other way around and I hope it gives better understanding. I assume you have read another definition, so you see it from another view not for the first time.

 

 

Continue reading “Basic Concepts: OpenCL Convenience Methods for Vector Elements and Type Conversions”

Installing both NVidia GTX and AMD Radeon on Linux for OpenCL

August 2012: article has been completely rewritten and updated. For driver-specific issues, please refer to this article.

Want to have both your GTX and Radeon working as OpenCL-devices under Linux? The bad news is that attempts to get Radeon as a compute device and the GTX as primary all failed. The good news is that the other way around works pretty easy (with some luck). You need to install both drivers and watch out that libglx.so isn’t overwritten by NVidia’s driver as we won’t use that GPU for graphics – this is also the reason why it is impossible to use the second GPU for OpenGL.

Continue reading “Installing both NVidia GTX and AMD Radeon on Linux for OpenCL”

OpenCL Potentials: Investment-industry

This is the second in the series “OpenCL potentials“. I chose this industry because it is the finest example where you are always late, even if you were first. So it always must be faster if you want to make the better analyses. Before I started StreamHPC I worked for an investment-company, and one of the things I did was reverse engineering a few megabytes of code with the primary purpose of updating the documentation. I then made a proof-of-concept to show the data-processing could be accelerated with a factor 250-300 using Java-tricks only and no GPGPU. That was the moment I started to understand that real-time data-computation was certainly possible. Also that IO is the next bottle-neck after computional power. Though I am more interested in other types of research, I do have my background and therefore try to give an overview for this sector and why it matters.

Continue reading “OpenCL Potentials: Investment-industry”

AMD OpenCL coding competition

The AMD OpenCL coding competition seems to be Windows 7 64bit only. So if you are on another version of Windows, OSX or (like me) on Linux, you are left behind. Of course StreamHPC supports software that just works anywhere (seriously, how hard is that nowadays?), so here are the instructions how to enter the competition when you work with Eclipse CDT. The reason why it only works with 64-bit Windows I don’t really get (but I understood it was a hint).

I focused on Linux, so it might not work with Windows XP or OSX rightaway. With little hacking, I’m sure you can change the instructions to work with i.e. Xcode or any other IDE which can import C++-projects with makefiles. Let me know if it works for you and what you changed.

Continue reading “AMD OpenCL coding competition”

The current state of WebCL

Years ago Microsoft was in court as it claimed Internet Explorer could not be removed from Windows without breaking the system, while competitors claimed it could. Why was this so important? Because (as it seems) the browser would get more important than the OS and internet as important as electricity in the office and at home. I was therefore very happy to see the introduction of WebGL, the browser-plugin for OpenGL, as this would push web-interfaces as the default for user-interfaces. WebCL is a browser-plugin to run OpenCL-kernels. Meaning that more powerful hardware-devices are available to JavaScript. This post is work-in-progress as I try to find more resources! Seen stuff like this? Let me know.

Continue reading “The current state of WebCL”

Dutch: Gratis kennisochtend over de nieuwe generatie processoren

Ergens opgevangen dat grafische kaarten tegenwoordig ingezet kunnen worden voor zware berekeningen? Tijdens een koffiegesprek gehoord over vector-processors als aanvulling op scalaire processors? Dan wordt het tijd dat u de grote veranderingen op processorgebied op een rijtje krijgt om uw organisatie beter op innovatief gebied te kunnen sturen.

Zie https://streamhpc.com/education/gratis-kennislunch/ voor een uur uitleg op lokatie.

Voor wie is deze kennis-ochtend?

Bedrijven voor wie snelheid belangrijk is en grote hoeveelheden data moeten verwerken. Bijvoorbeeld rekencentra, R&D-afdelingen, financiele instituten, ontwikkelaars van medische software, algoritme-ontwikkelaars en vision-bedrijven. Ook investeerder met hitech-bedrijven in hun portfolio kunnen gratis op de hoogte gebracht worden van de huidige ontwikkelingen.

U heeft geen technische achtergrond nodig, maar u zult zich niet vervelen indien u bits&bytes spreekt. Wij vragen uw achtergrond aan te geven, zodat we de juiste details in het programma kunnen toevoegen.

Wat is het programma?

In het eerste uur hoort u hoe de huidige processor-markt veranderd zijn ten opzichte van enkele jaren geleden – en welke nieuwe software-ontwikkelmethodes zijn geintroduceerd. Daarna krijgt u een overzicht van de nieuwe oplossingen die beschikbaar zijn en hoe dit zich verhouden tot de bestaande. Dit geeft u dan voldoende inzichten om te bepalen of het toepasbaar is binnen uw bedrijf. Het uur wordt afgesloten met wat StreamHPC voor u kan betekenen, maar ook wat u zelf kunt doen.

In het tweede uur bespreken we enkele use-cases en is er tijd voor vragen. De use-cases die worden besproken zijn afhankelijk van de achtergronden van de aanwezigen; denk aan bijvoorbeeld Monte Carlo, physics, enzym-werkingen, matrix-berekeningen en neurale netwerken.

Wanneer?

Indien er minimaal 10 aanmeldingen zijn, wordt er een datum geprikt.

Indien u binnen uw bedrijf direct interesse heeft, is het mogelijk dat StreamHPC bij u langs komt om deze presentatie te geven aangepast aan uw achtergrond. Neem daarvoor contact met ons op.

PDFs of Monday 19 September

Already the fourth PDF-Monday. It takes quite some time, so I might keep it to 10 in the future – but till then enjoy! Not sure which to read? Pick the first one (for the rest there is not order).

Edit: and the last one, follow me on twitter to see the  PDFs I’m reading. Reason is that hardly anyone clicked on the links to the PDFs.

I would like if you let others know in the comments which PDF you liked a lot.

Adding Physics to Animated Characters with Oriented Particles (Matthias Müller and Nuttapong Chentanez). Discusses how to accelerate movements of pieces of cloth attached to the bodies. Not time to read? There are nice pictures.

John F. Peddy’s analysis on the GPU market.

Hardware/Software Co-Design. Simple Solution to the Matrix Multiplication Problem using CUDA.

CUDA Based Algorithms for Simulating Cardiac Excitation Waves in a Rabbit Ventricle. Bioinformatics.

Real-time implementation of Bayesian models for multimodal perception using CUDA.

GPU performance prediction using parametrized models (Master-thesis by Andreas Resios)

A Parallel Ray Tracing Architecture Suitable for Application-Specific Hardware and GPGPU Implementations (Alexandre S. Nery, Nadia Nedjah, Felipe M.G. Franca, Lech Jozwiak)

Rapid Geocoding of Satellite SAR Images with Refined RPC Model. An ESA-presentation by Lu Zhang, Timo Balz and Mingsheng Liao.

A Parallel Algorithm for Flight Route Planning with CUDA (Master-thesis by Seçkîn Sanci). About the travelling salesman problem and much more.

Color-based High-Speed Recognition of Prints on Extruded Materials. Product-presentation on how to OCR printed text on cables.

Supplementary File of Sequence Homology Search using Fine-Grained Cycle Sharing of Idle GPUs (Fumihiko Ino, Yuma Munekawa, and Kenichi Hagihara). They sped up the BOINC-system (Folding@Home). Bit vague what they want to tell, but maybe you find it interesting.

Parallel Position Weight Matrices Algorithms (Mathieu Giraud, Jean-Stéphane Varré). Bioinformatics, DNA.

GPU-based High Performance Wave Propagation Simulation of Ischemia in Anatomically Detailed Ventricle (Lei Zhang, Changqing Gai, Kuanquan Wang, Weigang Lu, Wangmeng Zuo). Computation in medicine. Ischemia is a restriction in blood supply, generally due to factors in the blood vessels, with resultant damage or dysfunction of tissue

Per-Face Texture Mapping for Realtime Rendering. A Siggraph2011 presentation by Disney and NVidia.

Introduction to Parallel Computing. The CUDA 101 by Victor Eijkhout of University of Texas.

Optimization on the Power Efficiency of GPU and Multicore Processing Element for SIMD Computing. Presentation on what you find out when putting the volt-meter directly on the GPU.

NUDA: Programming Graphics Processors with Extensible Languages. Presentation on NUDA to write less code for GPGPU.

Qt FRAMEWORK: An introduction to a cross platform application and user interface framework. Presentation on the Qt-platform – which has great #OpenCL-support.

Data Assimilation on future computer architectures. The problems projected for 2020.

Current Status of Standards for Augmented Reality (Christine Perey1, Timo Engelke and Carl Reed). not much to do with OpenCL, but tells an interesting purpose for it.

Parallel Computations of Vortex Core Structures in Superconductors (Master-thesis by Niclas E. Wennerdal).

Program the SAME Here and Over There: Data Parallel Programming Models and Intel Many Integrated Core Architecture. Presentation on how to program the Intel MIC.

Large-Scale Chemical Informatics on GPUs (Imran S. Haque, Vijay S. Pande). Book-chapter on the design and optimization of GPU implementations of two popular chemical similarity techniques: Gaussian shape overlay (GSO) and LINGO.

WebGL, WebCL and Beyond! A presentation by Neil Trevett of NVidia/Khronos.

Biomanycores, open-source parallel code for many-core bioinformatics (Mathieu Giraud, Stéphane Janot, Jean-Frédéric Berthelot, Charles Delte, Laetitia Jourdan , Dominique Lavenier , Hélène Touzet, Jean-Stéphane Varré). A short description on the project http://www.biomanycores.org.