Dr Donald Kinghorn (HPC and Scientific Computing)

Docker and NVIDIA-docker on your workstation: Installation

Written on February 24, 2017 by Dr Donald Kinghorn

In this second post on Docker and Nvidia-Docker we will do an install and setup on an Ubuntu 16.04 workstation.


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Dr Donald Kinghorn (HPC and Scientific Computing)

Docker and NVIDIA-docker on your workstation: Motivation

Written on February 16, 2017 by Dr Donald Kinghorn

Docker containers together with the NVIDIA-docker can provide relief from dependency and configuration difficulties when setting up GPU accelerated machine learning environments on a workstation. In this post I will discuss motivation for considering this.


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Dr Donald Kinghorn (HPC and Scientific Computing)

NVIDIA Quadro GP100 Tesla P100 power on your desktop

Written on February 5, 2017 by Dr Donald Kinghorn

NVIDIA has released the Quadro GP100 bringing Tesla P100 Pascal performance to your desktop. This new card gives you the compute performance of the NVIDIA Tesla P100 together with Quadro display capability. That means full double precision floating point capability of the P100 and NVLINK for multiple cards.


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Dr. Donald Kinghorn (HPC and Scientific Computing)

PCIe X16 vs X8 for GPUs when running cuDNN and Caffe

Written on January 16, 2017 by Dr. Donald Kinghorn

Does PCIe X16 give better performance than X8 for training models with Caffe when using cuDNN? Yes, but not by much!



Dr Donald Kinghorn (HPC and Scientific Computing)

Kabylake vs Skylake for compute on Linux -- Linpack on Ubuntu 1610

Written on January 3, 2017 by Dr Donald Kinghorn

OK, Intel Core-i7 7th gen Kabylake is out. Of course the first thing I want to do is drop a Core i7 7700K in a new Z270 based motherboard, install Linux and run a Linpack benchmark. You know, GFLOP/s and all that. We installed Ubuntu 1610 with a recent release of Intel MKL and fired up a few Linpack job runs. Read on for the not-so dramatic results.


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Dr Donald Kinghorn (HPC and Scientific Computing)

NVIDIA DIGITS with Caffe - Performance on Pascal multi-GPU

Written on December 23, 2016 by Dr Donald Kinghorn

NVIDIA's Pascal GPU's have twice the computational performance of the last generation. A great use for this compute capability is for training deep neural networks. We have tested NVIDIA DIGITS 4 with Caffe on 1 to 4 Titan X and GTX 1070 cards. Training was for classification of a million image data set from ImageNet. Read on to see how it went.



Dr Donald Kinghorn (HPC and Scientific Computing)

Install Ubuntu 16.04 or 14.04 and CUDA 8 and 7.5 for NVIDIA Pascal GPU

Written on August 29, 2016 by Dr Donald Kinghorn

You got your new wonderful NVIDIA Pascal GPU ... maybe a GTX 1080, 1070, or Titan X(P) ... And, you want to setup a CUDA environment for some dev work or maybe try some "machine learning" code with your new card. What are you going to do? At the time of this writing CUDA 8 is still in RC and the deb and rpm packages have drivers that don't work with Pascal. I'll walk through the tricks you need to do a manual setup of CUDA 7.5 and 8.0 on top of Ubuntu 16.04 or 14.04 that will work with the new Pascal based GPU's



D (HPC and Scientific Computing)

NVIDIA Titan GPUs (3 generations) - CUDA 8 rc performance on Ubuntu 16.04

Written on August 12, 2016 by D

I have a Titan Black, Titan X (Maxwell) and a new Titan X (Pascal) in a system for a quick CUDA performance test. Install is on Ubuntu 16.04 with CUDA 8.0rc. We'll look at nbody from the CUDA samples code and NAMD Molecular Dynamics. It is stunning to see how much the CUDA performance has increased on these wonderful GPU's in just 3 years.



Dr Donald Kinghorn (HPC and Scientific Computing)

Intel Xeon E5 v4 Broadwell Buyers Guide (Parallel Performance)

Written on July 1, 2016 by Dr Donald Kinghorn

Intel's Xeon E5 v4 processors are available and there are lots of them! The changes from the v3 Haswell are mostly small clock changes and increases in core count. You can now get a E5-2699v4 with 22 cores. In a dual socket system that's 44 cores to work with. If the programs you want to run scale well with thread count then that could be a great processor for you. However, if your parallel scaling is not near linear then it may not be the best value. We have a dynamic chart of performance based on Amdahl's Law that may help you decide which processor is best for your uses.



Dr Donald Kinghorn (HPC and Scientific Computing)

NAMD Molecular Dynamics Performance on NVIDIA GTX 1080 and 1070 GPU

Written on June 23, 2016 by Dr Donald Kinghorn

The new NVIDIA GeForce GTX 1080 and GTX 1070 GPU's are out and I've received a lot of questions about NAMD performance. The short answer is -- performance is great! I've got some numbers to back that up below. We've got new Broadwell Xeon and Core-i7 CPU's thrown into the mix too. The new hardware refresh gives a nice step up in performance.



Dr Donald Kinghorn (HPC and Scientific Computing)

GTX 1080 CUDA performance on Linux (Ubuntu 16.04) preliminary results (nbody and NAMD)

Written on May 27, 2016 by Dr Donald Kinghorn

Just got a NVIDIA GTX 1080 for testing. I hacked up an install with Ubuntu 16.04 and CUDA 7.5 along with a beta display driver that works! First run after compiling the cuda samples nbody gave 5816 GFLOP/s! A GTX 980 on the same system does 2572 GFLOP/s. However, it's not all good news ...



Dr. Donald Kinghorn (HPC and Scientific Computing)

Intel Broadwell Xeon E5 2600v4 performance test

Written on May 18, 2016 by Dr. Donald Kinghorn

The Intel Xeon E5 2600 v4 Broadwell processors are finally available. My first Linpack testing with a E5-2687W v4 shows a greater than 35% performance increase over the v3 Haswell version! And, it's the same price as the v3 version! It's significantly better than expected.



Dr Donald Kinghorn (HPC and Scientific Computing)

Install Intel Python using conda from Anaconda Python

Written on May 13, 2016 by Dr Donald Kinghorn

You can try Intel Python from your Anaconda install using conda!



Dr Donald Kinghorn (HPC and Scientific Computing)

NVIDIA DIGITS Install

Written on March 28, 2016 by Dr Donald Kinghorn

If you are happy to use Ubuntu 14.04 LTS (Ubuntu-MATE in our case) then setting up a system with the NVIDIA DIGITS software stack is simple. I'll give you some guidance on getting everything working, from the Linux install to the DIGITS web interface.



William George (Customer Service)

Working around TDR in Windows for a better GPU computing experience

Written on March 17, 2016 by William George

A brief description of graphics driver Timeout Detection and Recovery, why it can be problematic for intensive GPU codes, and how to work around it so that Windows can be a viable GPU computing platform.


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Dr Donald Kinghorn (HPC and Scientific Computing)

NVIDIA CUDA with Ubuntu 16.04 beta on a laptop (if you just cannot wait)

Written on March 8, 2016 by Dr Donald Kinghorn

I was preparing a Puget Systems Traverse Skylake based laptop for GPU accelerated molecular dynamics demos at the upcoming ACS meeting and decided to see if I could get Ubuntu 16.04 beta working with NVIDIA CUDA 7.5. It worked!



Chris Stephens (Manager, Sales & Service)

The HPC Podcast #12 -- Intel Python (and Supercomputing 15!)

Written on February 11, 2016 by Chris Stephens

Don and I sit down after a holiday hiatus to talk about an interesting development. Intel has announced they are going to maintain a build of Python. Good news for a language that has been around for a long time. We also discuss our time at Supercomputing 2015 and FPGAs.


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Dr Donald Kinghorn (HPC and Scientific Computing)

Xeon E5v3 All Core Turbo and Amdahl's Law

Written on January 8, 2016 by Dr Donald Kinghorn

Intel E5 v3 processors will run at "All Core Turbo" under load if properly cooled. This "clock" measurement is a better predictor of theoretical performance than base clock. We present a table of CPU performance at "all-core-turbo" using different parallel scaling factors from Amdhal's Law. We have a dynamic graph that will show how much performance you lose when your parallel scaling is less than perfect. Just because your dual socket 16-core system shows all 32 cores at 100% doesn't mean your problem is running 32 times faster!


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Dr Donald Kinghorn (HPC and Scientific Computing)

What is Machine Learning

Written on January 6, 2016 by Dr Donald Kinghorn

Machine Learning is getting a lot of attention these days and with good reason. There are mountains of data to work with and computing resources to handle the problems are easily attainable. Even a single GPU accelerated workstation is capable of serious work.



Dr Donald Kinghorn (HPC and Scientific Computing)

Intel Python Preview

Written on December 23, 2015 by Dr Donald Kinghorn

Intel is working on an optimized Python! I did a quick test with the preview version and it looks good.


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Dr Donald Kinghorn (HPC and Scientific Computing)

Windows 10 with Xeon Phi

Written on November 13, 2015 by Dr Donald Kinghorn

Can you use an Intel Xeon Phi with Windows 10? Yes, you can. However, just because you can do something, doesn't mean that you should do it! I did a set up and a little testing mainly just to see if it would work -- it does!



Dr Donald Kinghorn (HPC and Scientific Computing)

Molecular Dynamics Performance on GPU Workstations -- NAMD

Written on October 27, 2015 by Dr Donald Kinghorn

Molecular Dynamics programs can achieve very good performance on modern GPU accelerated workstations giving job performance that was only achievable using CPU compute clusters only a few years ago. The group at UIUC working on NAMD were early pioneers of using GPU's for compute acceleration and NAMD has very good performance acceleration using NVIDIA CUDA. We show you how good that performance is on modern Nvidia GPU's



Dr. Donald Kinghorn (HPC and Scientific Computing)

Intel Skylake 6700K with Parallel Studio XE 2016 vs 2015 on Fedora 23 Much Better!

Written on September 13, 2015 by Dr. Donald Kinghorn

Intel Skylake Core-i7 CPU -- 256 GFLOP/s Linpack result with Intel Parallel Studio XE 2016 and MKL 11.3 vs 200 GFLOP/s using Intel Parallel Studio XE 2015 and MKL 11.2!



Dr. Donald Kinghorn (HPC and Scientific Computing)

Skylake-S i7 6700K and i5 6600K for compute? maybe?

Written on August 5, 2015 by Dr. Donald Kinghorn

I have done a little informal testing with the new i7 and i5 processor running the Linpack benchmark and a NAMD MD simulation. Mixed results!


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Chris Stephens (Manager, Sales & Service)

The HPC Podcast #11 -- Skylake Launches

Written on August 5, 2015 by Chris Stephens

In this episode of the HPC Podcast, Chris and Don discuss today's launch of the first Skylake chips from Intel.


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