Molecular Dynamics Benchmarks GPU Roundup GROMACS NAMD2 NAMD 3alpha on 12 GPUs
Written on May 9, 2022 by Dr Donald KinghornWe have a new collection of GPU accelerated Molecular Dynamics benchmark packages put together for GROMACS, NAMD 2, and NAMD 3-alpha10. (The benchmark packages will be available to the public soon.) In this post we present results for, - 3 applications: GROMACS, NAND 2 and NAMD 3alpha10, - 8 MD simulations, - 12 different NVIDIA GPUs, - 96 total results.
Intel Ice Lake Xeon-W vs AMD TR Pro Compute Performance (HPL, HPCG, NAMD, Numpy)
Written on July 29, 2021 by Dr Donald KinghornThe single socket version of Intel third generation Xeon SP is out, the Ice Lake Xeon W 33xx. This is a much better platform with faster large capacity 8 channel memory and PCIe v4 with plenty of lanes. The new Intel platform is very much like the AMD Threadripper Pro (single socket version of EPYC Rome) so this is the obvious comparison to make. Read on to see how the numerical computing testing went!
NVIDIA 3080Ti Compute Performance ML/AI HPC
Written on June 18, 2021 by Dr Donald KinghornFor computing tasks like Machine Learning and some Scientific computing the RTX3080TI is an alternative to the RTX3090 when the 12GB of GDDR6X is sufficient. (Compared to the 24GB available of the RTX3090). 12GB is in line with former NVIDIA GPUs that were "work horses" for ML/AI like the wonderful 2080Ti.
Outstanding Performance of NVIDIA A100 PCIe on HPL, HPL-AI, HPCG Benchmarks
Written on May 21, 2021 by Dr Donald KinghornThe NVIDIA A100 (Compute) GPU is an extraordinary computing device. It's not just for ML/AI types of workloads. General scientific computing tasks requiring high performance numerical linear algebra run exceptionally well on the A100.
Intel Rocket Lake Compute Performance Results HPL HPCG NAMD and Numpy
Written on March 31, 2021 by Dr Donald KinghornThe new Intel Rocket Lake CPUs have been officially released. There were numerous posts and reviews before the official release date of March 30 2021, but I haven't seen anything about the numerical compute performance. I've had access to a Core-i9 11900KF 8-core CPU and have compared it with (my own) AMD 5800X system.
AMD Threadripper Pro 3995x HPL HPCG NAMD Performance Testing (Preliminary)
Written on March 5, 2021 by Dr Donald KinghornThreadripper Pro! AMD has released the long awaited Threadripper Pro CPUs. I was able to spend a (long) day (and night) running compute performance testing on the flagship 64-core TR Pro 3995WX. In this post I've got some HPC workload benchmark results from putting this excellent CPU through its compute paces.
Intel oneAPI AI Analytics Toolkit -- Introduction and Install with conda
Written on February 17, 2021 by Dr Donald KinghornI recently wrote a post introducing Intel oneAPI that included a simple installation guide of the Base Toolkit. In that post I promised a follow-up about the the oneAPI AI Analytics Toolkit. This is it! I'll describe what it is and give recommendations for doing an install setup of the AI toolkits using conda with Anaconda Python.
Intel oneAPI Developer Tools -- Introduction and Install
Written on February 3, 2021 by Dr Donald KinghornIntel oneAPI is a massive collection of very high quality developer tools, and, it's free to use! In this post I'll give you a little background on what oneAPI is and my recommendations for doing an install setup to get started exploring the collection of tool-kits.
How To Install TensorFlow 1.15 for NVIDIA RTX30 GPUs (without docker or CUDA install)
Written on December 9, 2020 by Dr Donald KinghornIn this post I will show you how to install NVIDIA's build of TensorFlow 1.15 into an Anaconda Python conda environment. This is the same TensorFlow 1.15 that you would have in the NGC docker container, but no docker install required and no local system CUDA install needed either.
Quad RTX3090 GPU Power Limiting with Systemd and Nvidia-smi
Written on November 24, 2020 by Dr Donald KinghornThis is a follow up post to "Quad RTX3090 GPU Wattage Limited "MaxQ" TensorFlow Performance". This post will show you a way to have GPU power limits set automatically at boot by using a simple script and a systemd service Unit file.
Quad RTX3090 GPU Wattage Limited "MaxQ" TensorFlow Performance
Written on November 13, 2020 by Dr Donald KinghornCan you run 4 RTX3090's in a system under heavy compute load? Yes, by using nvidia-smi I was able to reduce the power limit on 4 GPUs from 350W to 280W and achieve over 95% of maximum performance. The total power load "at the wall" was reasonable for a single power supply and a modest US residential 110V, 15A power line.
RTX3070 (and RTX3090 refresh) TensorFlow and NAMD Performance on Linux (Preliminary)
Written on October 29, 2020 by Dr Donald KinghornThe GeForce RTX3070 has been released. The RTX3070 is loaded with 8GB of memory making it less suited for compute task than the 3080 and 3090 GPUs. we have some preliminary results for TensorFlow, NAMD and HPCG.
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!
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.
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.)
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.
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.