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Read this article at https://www.pugetsystems.com/guides/1832
Dr Donald Kinghorn (Scientific Computing Advisor )

Does Enabling WSL2 Affect Performance of Windows 10 Applications

Written on July 17, 2020 by Dr Donald Kinghorn

WSL2 offers improved performance over version 1 by providing more direct access to the host hardware drivers. Recent "Insider Dev Channel" builds of Win10 even allows access to the Windows NVIDIA display driver for GPU computing applications for WSL2 Linux applications! The performance improvements with WSL2 are largely because this version is running as a privileged virtual machine on to of MS Hyper-V. This means that at least low level support for the Hyper-V virtualization layer needs to be enabled to use it. In particular, the Windows feature "VirtualMachinePlatform" must be enabled for WSL2. We tested to see if there was any negative application performance impact.


Read this article at https://www.pugetsystems.com/guides/1828
Dr Donald Kinghorn (Scientific Computing Advisor )

Note: How To Install JupyterLab Extensions (Globally for a JupyterHub Server)

Written on July 15, 2020 by Dr Donald Kinghorn

The current JupyterHub version 2.5.1 does not allow user installed extension for JupyterLab when it is being served from JupyterHub. This should be remedied in version 3. However, even when this is "fixed" it is still useful to be able to install extensions globally for all users on a multi-user system. This note will show you how.


Read this article at https://www.pugetsystems.com/guides/1811
Dr Donald Kinghorn (Scientific Computing Advisor )

Note: How To Copy and Rename a Microsoft WSL Linux Distribution

Written on June 19, 2020 by Dr Donald Kinghorn

WSL on Windows 10 does not (currently) provide a direct way to copy a Linux distribution that was installed from the "Microsoft Store". The following guide will show you a way to make a working copy of an installed distribution with a new name.


Read this article at https://www.pugetsystems.com/guides/1749
Dr Donald Kinghorn (Scientific Computing Advisor )

Note: Self-Signed SSL Certificate for (local) JupyterHub

Written on May 7, 2020 by Dr Donald Kinghorn

In this note I'll go through creating self-signed SSL certificates and adding them to a JupyterHub configuration running on a LAN or VPN. This will allow encrypted access to the server using https in a browser.


Read this article at https://www.pugetsystems.com/guides/1729
Dr Donald Kinghorn (Scientific Computing Advisor )

Note: JupyterHub with JupyterLab Install using Conda

Written on April 17, 2020 by Dr Donald Kinghorn

This is a quick note about setting up a JupyterHub server and JupyterLab using conda with Anaconda Python.


Read this article at https://www.pugetsystems.com/guides/1717
Dr Donald Kinghorn (Scientific Computing Advisor )

HPC Parallel Performance for 3rd gen Threadripper, Xeon 3265W and EPYC 7742 (HPL HPCG Numpy NAMD)

Written on April 9, 2020 by Dr Donald Kinghorn

On March 19, 2020 I did a webinar titled, "AMD Threadripper 3rd Gen HPC Parallel Performance and Scaling ++(Xeon 3265W and EPYC 7742)" The "++(Xeon 3265W and EPYC 7742)" part of that title was added after we had scheduled the webinar. It made the presentation a lot more interesting than the original Threadripper only title! This is a follow up post with the charts and plots of testing results presented in that webinar.


Read this article at https://www.pugetsystems.com/guides/1692
Dr Donald Kinghorn (Scientific Computing Advisor )

Threadripper 3990x vs 3970x Performance and Scaling (HPL, Numpy, NAMD plus GPUs)

Written on March 6, 2020 by Dr Donald Kinghorn

Is 32-cores enough? I had some testing time again on an AMD Threadripper 32-core 3970x and thought it would be interesting to compare that to the 64-core 3990x. In this post I take a comparative look at parallel performance and scaling for HPL Linpack, Python numpy and the NAMD molecular dynamics program.


Read this article at https://www.pugetsystems.com/guides/1680
Dr Donald Kinghorn (Scientific Computing Advisor )

Threadripper 3990x 64-core Parallel Scaling

Written on February 25, 2020 by Dr Donald Kinghorn

64 cores is a lot of cores! How well will parallel applications scale on that many cores? The answer, of course, is, it depends on the application. In this post I look at Amdhal's Law parallel scaling for HPL Linpack, Python numpy and the NAMD molecular dynamics program.


Read this article at https://www.pugetsystems.com/guides/1673
Dr Donald Kinghorn (Scientific Computing Advisor )

Note: How To Install JupyterHub on a Local Server

Written on February 19, 2020 by Dr Donald Kinghorn

This note describes installing and configuring JupyterHub and JupyterLab on a "bare-metal" server.


Read this article at https://www.pugetsystems.com/guides/1666
Dr Donald Kinghorn (Scientific Computing Advisor )

AMD Threadripper 3990x 64-core Linpack and NAMD Performance (Linux)

Written on February 7, 2020 by Dr Donald Kinghorn

64 cores! The latest AMD Threadripper is out, the 3990x 64-core. I've spent the last couple of days running benchmarks and have some results showing raw numerical compute performance using my standard CPU testing applications HPL Linpack and the molecular dynamics program NAMD. The 3990x is a great processor with exceptional performance. Especially for NAMD! (There were some difficulties and disappointments during the testing and I report those here too.)


Read this article at https://www.pugetsystems.com/guides/1654
Dr Donald Kinghorn (Scientific Computing Advisor )

Note: Auto-Install Ubuntu with Custom Preseed ISO

Written on January 30, 2020 by Dr Donald Kinghorn

This note describes creating an ISO image for a fully automatic, customized Ubuntu 18.04 server install.


Read this article at https://www.pugetsystems.com/guides/1653
Dr Donald Kinghorn (Scientific Computing Advisor )

Note: Setup Git for PowerShell on Windows 10

Written on January 24, 2020 by Dr Donald Kinghorn

How to setup PowerShell nicely for using git with command completion and color highlighted shell prompt git status/action notifications.


Read this article at https://www.pugetsystems.com/guides/1646
Dr Donald Kinghorn (Scientific Computing Advisor )

Notes on "Notes" (new blog post format)

Written on December 31, 2019 by Dr Donald Kinghorn

Starting 2020 off with an addition to my writing, "micro blogging" via GitHub Gists


Read this article at https://www.pugetsystems.com/guides/1641
Dr Donald Kinghorn (Scientific Computing Advisor )

NVIDIA (Computing Hardware) Company of the Decade!

Written on December 13, 2019 by Dr Donald Kinghorn

It's the end of the 2010's and start of 2020's. Time to reflect ...


Read this article at https://www.pugetsystems.com/guides/1638
Dr Donald Kinghorn (Scientific Computing Advisor )

SC19 A look at the high end of HPC

Written on December 10, 2019 by Dr Donald Kinghorn

The Super Computing conference annual US counterpart is always a great meeting. It's a chance to see the trend and get sentiment for the highest performance end of computing. I have written up a few observations and provided a few interesting links for SC19.


Read this article at https://www.pugetsystems.com/guides/1637
Dr Donald Kinghorn (Scientific Computing Advisor )

How To Use MKL with AMD Ryzen and Threadripper CPU's (Effectively) for Python Numpy (And Other Applications)

Written on November 27, 2019 by Dr Donald Kinghorn

In this post I'm going to show you a simple way to significantly speedup Python numpy compute performance on AMD CPU's when using Anaconda Python.


Read this article at https://www.pugetsystems.com/guides/1631
Dr Donald Kinghorn (Scientific Computing Advisor )

AMD Threadripper 3970x Compute Performance Linpack and NAMD

Written on November 25, 2019 by Dr Donald Kinghorn

AMD Threadripper 3970x 32-core! ...The, third new AMD processor I've had the pleasure of trying recently. I'm running it through the same double precision floating point performance tests as the recently tested Ryzen processors, Linpack and NAMD.


Read this article at https://www.pugetsystems.com/guides/1617
Dr Donald Kinghorn (Scientific Computing Advisor )

AMD Ryzen 3950x Compute Performance Linpack and NAMD

Written on November 14, 2019 by Dr Donald Kinghorn

The, much anticipated, AMD Ryzen 3950x 16-core processor is out! As always the first thing I wanted know was the double precision floating point performance. My two favorite applications for a "first look" at a new CPU are Linpack and NAMD.


Read this article at https://www.pugetsystems.com/guides/1568
Dr Donald Kinghorn (Scientific Computing Advisor )

Workstation Setup for Docker with the New NVIDIA Container Toolkit (nvidia-docker2 is deprecated)

Written on September 13, 2019 by Dr Donald Kinghorn

It's time for a "Docker with NVIDIA GPU support" update. This post will guide you through a useful Workstation setup (including User-name-spaces and performance tuning) with the new versions of Docker and the NVIDIA GPU container toolkit.


Read this article at https://www.pugetsystems.com/guides/1560
Dr Donald Kinghorn (Scientific Computing Advisor )

AMD Ryzen 3900X vs Intel Xeon 2175W Python numpy - MKL vs OpenBLAS

Written on August 20, 2019 by Dr Donald Kinghorn

In this post I've done more testing with Ryzen 3900X looking at the effect of BLAS libraries on a simple but computationally demanding problem with Python numpy. The results may surprise you! I start with a little bit of history of Intel vs AMD performance to give you what may be a new perspective on the issue.


Read this article at https://www.pugetsystems.com/guides/1551
Dr Donald Kinghorn (Scientific Computing Advisor )

2 x RTX2070 Super with NVLINK TensorFlow Performance Comparison

Written on August 14, 2019 by Dr Donald Kinghorn

This is a short post showing a performance comparison with the RTX2070 Super and several GPU configurations from recent testing. The comparison is with TensorFlow running a ResNet-50 and Big-LSTM benchmark.


Read this article at https://www.pugetsystems.com/guides/1540
Dr Donald Kinghorn (Scientific Computing Advisor )

AMD 3900X (Brief) Compute Performance Linpack and NAMD

Written on July 26, 2019 by Dr Donald Kinghorn

I was able to spend a little time with an AMD Ryzen 3900X. Of course the first thing I wanted know was the double precision floating point performance. My two favorite applications for a "first look" at a new processor are Linpack and NAMD. The Ryzen 3900X is a pretty impressive processor!


Read this article at https://www.pugetsystems.com/guides/1527
Dr Donald Kinghorn (Scientific Computing Advisor )

NVIDIA Docker2 with OpenGL and X Display Output

Written on July 11, 2019 by Dr Donald Kinghorn

Docker is a great Workstation tool. It is mostly used for command-line application or servers but, ... What if you want to run an application in a container, AND, use an X Window GUI with it? What if you are doing development work with CUDA and are including OpenGL graphic visualization along with it? You CAN do that!


Read this article at https://www.pugetsystems.com/guides/1520
Dr Donald Kinghorn (Scientific Computing Advisor )

Install TensorFlow 2 beta1 (GPU) on Windows 10 and Linux with Anaconda Python (no CUDA install needed)

Written on June 26, 2019 by Dr Donald Kinghorn

TensorFlow 2.0.0-beta1 is available now and ready for testing. What if you want to try it but don't want to mess with doing an NVIDIA CUDA install on your system. The official TensorFlow install documentations has you do that, but it's really not necessary.


Read this article at https://www.pugetsystems.com/guides/1477
Dr Donald Kinghorn (Scientific Computing Advisor )

How To Run Remote Jupyter Notebooks with SSH on Windows 10

Written on June 11, 2019 by Dr Donald Kinghorn

Being able to run Jupyter Notebooks on remote systems adds tremendously to the versatility of your workflow. In this post I will show a simple way to do this by taking advantage of some nifty features of secure shell (ssh). What I'll do is mostly OS independent but I am putting an emphasis on Windows 10 since many people are not familiar with tools like ssh on that OS.