collect examples of systems where users tried to do something that performed badly
This task aims to collect examples of inputs that users thought were reasonable, but whose performance was unexpectedly poor. These may be useful targets for performance optimization (or better documentation/warnings), or benchmark sets. I suspect there are other examples in Redmine (perhaps even from Chris Neale) which I can cross-reference here when I can find them.
#1 Updated by Roland Schulz about 4 years ago
For now you mean manual right? I think it would be worth considering whether we want to add automatic data collection. Of course usage tracking has a bad reputation and we would need to make sure we do it with well understood opt-in. But I think both for funding as well as for the goals laid out in your task description it could be very valuable.
#3 Updated by Szilárd Páll about 4 years ago
A separate tool that when manually invoked can collects data (log, input files) and submit it to us could work (something like some Linux distros' bug reporting tool). There would only need to be a simple collection server on the other end. I guess sorting things out might end up being the most tedious work.
#4 Updated by Chris Neale about 4 years ago
in gromacs5.1.2 (with or without GPU) and 2016-beta1 (with GPU not tested)
More information can be found here:
tarball includes all files needed to run the testing and includes the output from a short run with 128 separate pull restraints. In this case, I get 8.6 ns/day vs. 55.1 ns/day without using any pull groups (whereas adding a single pull restraint only slows the sampling down to 51.3 ns/day)
#5 Updated by Chris Neale almost 4 years ago
Large free energy decoupling groups slow down gromacs enormously. Even groups of modest size compared with the system size really slow things down too much to be useful for things like REST. Files to test this can be found in issue 742 ( https://redmine.gromacs.org/issues/742 ) named as RESTandREMDtprs.tgz . The plumed/gromacs solution for REST works well, so it is unclear that the REST use-case is strong enough to support modifications of gromacs, but I am cross-posting for completeness since I think this thread is a fantastic idea.