Benchmarking gromacs – 2 quick questions

With gromacs there are all these things you have to do when benchmarking, it's a little bit of a mess. One question that I always wondered about was – well – how long do you have to run to get a reliable performance number, in ns/day? 1e0 MD step is certainly too short but 1e7 steps seems like unnecessarily excessive.

Second question was, could one get away with measuring benchmarking speed of just a box of water? Currently people use system like DHPR or APOA1 (protein in water) to asses but those are arbitrary.  A box of water has dramatically simpler topology than a protein but maybe it doesn't matter?

One thing that this asses is absolute performance of gromacs: the ns/day below are low but that's because an old workstation is used, without GPU acceleration.


The answer are pretty simple: 1e4–1e5 steps are required to 'converge' the performance estimate, for my test system. Also,  a water box of very similar dimensions (and # of particles) but without the protein runs a little faster than. The effect is not huge, 20-30% so it could easily be used as a meaningful benchmark but maybe I'm missing something.

The simplicity of the water box benchmark (where the size of the box can be varied) is pretty cool. In my mind, it totally offsets the intellectually infertile discussion about "oh which protein big or small to choose to show that my favorite code is better".

Comments

Post a Comment

Popular posts from this blog

React.js – edit and delete comments in CommentBox

It appears customary for high-intelligence, high-skills groups of engineers to "roll their own" whenever they have a chance to. Counter-intuitively to most managerial/MBA types out there, re-inventing the wheel can give you... a better wheel. Success is not guaranteed though – but these people may leave sooner rather than later if you don't let them... Having looked at number of JS frameworks (ember, backbone, angular) there was no clear winner. They were all a mess, at least to me. So I approached React.js with no hopes – how much better could it possible be? It turns out, a lot! This post will be an extension of the official React.js tutorial . The tutorial stops at the stage where you can add comments to a dynamic lists, that will grow as you add comments. This falls short of the functionality displayed on facebook: once you add a comment you can edit or delete it, so that's what're going to do. Full disclosure, I only started using React this weekendo so m...
Read more

Example slurm cluster on your laptop (multiple VMs via vagrant)

To anybody who's considering a switch to modern queuing systems, like slurm, this will be an useful guide. Rather than doing a roll out on production nodes, we'll try things out in vagrant. This text assumes you have vagrant installed on your local machine (it's very easy). The ultimate aim will be to setup 2 servers (worker nodes) and one master/controller, and run a simple job on them. There are multiple great guides out there: most of them are out of date, and won't work without some tweaking on Ubuntu 16.04 Xenial. The entirety of the code is hosted at https://github.com/jandom/gromacs-slurm-openmpi-vagrant The README.md file will show you how to set it up, with checks on every step. References https://mussolblog.wordpress.com/2013/07/17/setting-up-a-testing-slurm-cluster/ https://github.com/gabrieleiannetti/slurm_cluster_wiki/wiki/Installing-a-Slurm-Cluster http://philipwfowler.me/2016/04/14/how-to-setup-a-gramble/ https://github.com/dakl/slurm-clus...
Read more

Wrapping openbabel in python - using cython

The previous post showed a contrived example of how one could access the openbabel functionality in python using the boost libraries. There is alternative to boost to wrap around c/c++ code, it's called cython. Here is an example openbabel wrapper, exposing some very simple functionality. Just before diving in, you should know that there already exists a wrapper around openbabel in python (it is called pybel). What I'm showing here doesn't even come close to pybel in terms of usefulness, the idea here is to show a demo of how easy wrapping things in python is. #! /usr/bin/python from ez_setup import use_setuptools use_setuptools() from setuptools import setup, Extension, find_packages from Cython.Distutils import build_ext import sys, os import glob import subprocess as sub def get_include(name="openbabel"): p = sub.Popen('locate %s' % name ,stdout=sub.PIPE,stderr=sub.PIPE, shell=True) output, errors = p.communicate() ...
Read more