Note: Adding Anaconda PowerShell to Windows Terminal
Written on October 1, 2020 by Dr Donald KinghornWhen you install Miniconda3 or Anaconda3 on Windows it adds a PowerShell shortcut that has the necessary environment setup and initialization for conda. It's listed in the Windows menu as "Anaconda Powershell Prompt (Anaconda3)". However, this opens a separate/detached PowerShell instance and it would be nice to have this as an optional shell from Windows Terminal! In this post we will add that functionality as a new shell option in Windows Terminal.
RTX3090 TensorFlow, NAMD and HPCG Performance on Linux (Preliminary)
Written on September 24, 2020 by Dr Donald KinghornThe second new NVIDIA RTX30 series card, the GeForce RTX3090 has been released. The RTX3090 is loaded with 24GB of memory making it a good replacement for the RTX Titan... at significantly less cost! The performance for Machine Learning and Molecular Dynamics on the RTX3090 is quite good, as expected.
RTX3080 TensorFlow and NAMD Performance on Linux (Preliminary)
Written on September 17, 2020 by Dr Donald KinghornThe much anticipated NVIDIA GeForce RTX3080 has been released. How good is it with TensorFlow for machine learning? How about molecular dynamics with NAMD? I've got some preliminary numbers for you!
Does Enabling WSL2 Affect Performance of Windows 10 Applications
Written on July 17, 2020 by Dr Donald KinghornWSL2 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.
Note: How To Install JupyterLab Extensions (Globally for a JupyterHub Server)
Written on July 15, 2020 by Dr Donald KinghornThe 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.
Note: How To Copy and Rename a Microsoft WSL Linux Distribution
Written on June 19, 2020 by Dr Donald KinghornWSL 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.
Note: Self-Signed SSL Certificate for (local) JupyterHub
Written on May 7, 2020 by Dr Donald KinghornIn 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.
Note: JupyterHub with JupyterLab Install using Conda
Written on April 17, 2020 by Dr Donald KinghornThis is a quick note about setting up a JupyterHub server and JupyterLab using conda with Anaconda Python.
HPC Parallel Performance for 3rd gen Threadripper, Xeon 3265W and EPYC 7742 (HPL HPCG Numpy NAMD)
Written on April 9, 2020 by Dr Donald KinghornOn 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.
Threadripper 3990x vs 3970x Performance and Scaling (HPL, Numpy, NAMD plus GPUs)
Written on March 6, 2020 by Dr Donald KinghornIs 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.
Threadripper 3990x 64-core Parallel Scaling
Written on February 25, 2020 by Dr Donald Kinghorn64 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.
Note: How To Install JupyterHub on a Local Server
Written on February 19, 2020 by Dr Donald KinghornThis note describes installing and configuring JupyterHub and JupyterLab on a "bare-metal" server.
AMD Threadripper 3990x 64-core Linpack and NAMD Performance (Linux)
Written on February 7, 2020 by Dr Donald Kinghorn64 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.)
Note: Auto-Install Ubuntu with Custom Preseed ISO
Written on January 30, 2020 by Dr Donald KinghornThis note describes creating an ISO image for a fully automatic, customized Ubuntu 18.04 server install.
Note: Setup Git for PowerShell on Windows 10
Written on January 24, 2020 by Dr Donald KinghornHow to setup PowerShell nicely for using git with command completion and color highlighted shell prompt git status/action notifications.
Notes on "Notes" (new blog post format)
Written on December 31, 2019 by Dr Donald KinghornStarting 2020 off with an addition to my writing, "micro blogging" via GitHub Gists
NVIDIA (Computing Hardware) Company of the Decade!
Written on December 13, 2019 by Dr Donald KinghornIt's the end of the 2010's and start of 2020's. Time to reflect ...
SC19 A look at the high end of HPC
Written on December 10, 2019 by Dr Donald KinghornThe 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.
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 KinghornIn 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.
AMD Threadripper 3970x Compute Performance Linpack and NAMD
Written on November 25, 2019 by Dr Donald KinghornAMD 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.
AMD Ryzen 3950x Compute Performance Linpack and NAMD
Written on November 14, 2019 by Dr Donald KinghornThe, 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.
Workstation Setup for Docker with the New NVIDIA Container Toolkit (nvidia-docker2 is deprecated)
Written on September 13, 2019 by Dr Donald KinghornIt'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.
AMD Ryzen 3900X vs Intel Xeon 2175W Python numpy - MKL vs OpenBLAS
Written on August 20, 2019 by Dr Donald KinghornIn 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.
2 x RTX2070 Super with NVLINK TensorFlow Performance Comparison
Written on August 14, 2019 by Dr Donald KinghornThis 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.
AMD 3900X (Brief) Compute Performance Linpack and NAMD
Written on July 26, 2019 by Dr Donald KinghornI 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!