Two weeks? we have been running Docker in production for over one year and have thousands of separate instances. No big issues os far. All that is said is true, it's just a matter of weighting pro's and con's.
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I would be really curious to see how you are actually managing these thousands of separate instances? Do you have some kind of a management GUI to do this? Are you managing them through command line? If so are you running into issues where managing these take up most of your time and adding more complexity into your environment? I honestly want to see a good example of how you manage your docker containers where you have thousands of containers instead of say 10.