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Read this article at https://www.pugetsystems.com/guides/820
Dr Donald Kinghorn (Scientific Computing Advisor)

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.


Read this article at https://www.pugetsystems.com/guides/815
Dr Donald Kinghorn (Scientific Computing Advisor)

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.


Read this article at https://www.pugetsystems.com/guides/803
Dr Donald Kinghorn (Scientific Computing Advisor)

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 ...


Read this article at https://www.pugetsystems.com/guides/801
Dr Donald Kinghorn (Scientific Computing Advisor)

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.


Read this article at https://www.pugetsystems.com/guides/775
Dr Donald Kinghorn (Scientific Computing Advisor)

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!


Read this article at https://www.pugetsystems.com/guides/733
Dr Donald Kinghorn (Scientific Computing Advisor)

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!


Read this article at https://www.pugetsystems.com/guides/719
Dr Donald Kinghorn (Scientific Computing Advisor)

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


Read this article at https://www.pugetsystems.com/guides/682
Dr Donald Kinghorn (Scientific Computing Advisor)

OpenACC for free! -- NVIDIA OpenACC Toolkit

Written on July 14, 2015 by Dr Donald Kinghorn

NVIDIA and PGI are offering "PGI Accelerator with OpenACC" free to academia (or 90 day trial for commercial users) under the banner "NVIDIA OpenACC Toolkit". It's about time!


Read this article at https://www.pugetsystems.com/guides/670
Dr Donald Kinghorn (Scientific Computing Advisor)

Xeon Phi 5110p and Free Intel Parallel Studio Cluster Edition

Written on June 22, 2015 by Dr Donald Kinghorn

Another amazing deal on Xeon Phi from Intel! This time you can get a 90% discount on a Phi 5110p and get the Intel Parallel Studio Cluster edition with a 1 year license for free.


Read this article at https://www.pugetsystems.com/guides/654
Dr Donald Kinghorn (Scientific Computing Advisor)

Install NVIDIA CUDA on Fedora 22 with gcc 5.1

Written on May 19, 2015 by Dr Donald Kinghorn

Fedora 22 is full of new goodness like kernel 4.0 and gcc 5.1 and yes, you can install and run CUDA on it! It's not officially supported but I did manage to get it working!


Read this article at https://www.pugetsystems.com/guides/579
Dr Donald Kinghorn (Scientific Computing Advisor)

POV-ray on Quad Xeon and Opteron

Written on July 14, 2014 by Dr Donald Kinghorn

POV-ray is an open source ray tracing package with a long history. It has been a favorite system performance testing package since it's inception because of the heavy load it places on the CPU. It has had an SMP parallel implementation since the mid 2000's and is often used as a multi-core CPU parallel performance benchmark on both Linux and Windows. So lets try it on our Quad socket many-core systems!


Read this article at https://www.pugetsystems.com/guides/577
Dr Donald Kinghorn (Scientific Computing Advisor)

Install CUDA and PGI Accelerator with OpenACC

Written on June 27, 2014 by Dr Donald Kinghorn

I'm going to walk you through a basic install and configuration for a development system to do CUDA and OpenACC GPU programming. This is not a detailed howto but if you have some linux admin skills it will be a reasonable guide to get you started. We'll do a basic NVIDIA GPU programming setup including CentOS 6.5, CUDA development environment and a PGI compiler setup with OpenACC. The most interesting part may be the OpenACC setup. OpenACC is a relatively new option for GPU programming and allows for a directive (pragma) based coding model.


Read this article at https://www.pugetsystems.com/guides/576
Dr Donald Kinghorn (Scientific Computing Advisor)

Quad Xeon vs Opteron, Zemax OpticStudio

Written on June 18, 2014 by Dr Donald Kinghorn

We take a look at Quad Xeon and Quad Opteron performance and parallel scaling with Zemax OpticStudio including an analysis using Amdahl's Law. Based on this analysis we then make performance predictions for other processors.


Read this article at https://www.pugetsystems.com/guides/570
Dr Donald Kinghorn (Scientific Computing Advisor)

NVIDIA GPU Starter DevKit with OpenACC

Written on June 2, 2014 by Dr Donald Kinghorn

NVIDIA Tesla K20 plus PGI Accelerator compilers with OpenACC in a package deal with a system. Yes, it's official. If you've wanted to do some development work with OpenACC on Tesla, this is a nice way to get started with a heavily discounted K20 and PGI compiler package pre loaded on a Peak Mini.