I can see a few things that might need working out.
At work, the first system to download and start running the new client first gets stopped, send all the tiny number of folds back, and then the directory is copied to C:\Folding2. I then stop the other machines, and copy this to their drive, kill c:\folding and rename this to c:\folding.
(If I ever start running large numbers of systems again, I know I can try and get the proxy server to work - but for 2-3 machines I have on for the whole protein - that equal the 10 I was running, I'll refrain from trying to figure out what was wrong with the proxy server setup.)
When I get new systems to test out - (Brand new Dells or slightly older 256Meg+ machines) I'll copy this same directory on new systems and run it overnight (or 3 weeks, if they take forever to pick it up).
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So it would be nice if the program doesn't get hard coded for the machine it was installed on.
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At least one member of my team is using a computer at his wive's work that isn't connected to the internet. Once a week, he'll stop by to get the filelist & .bz2 files, (delete and reinstall the program) take them home, copy them into a blank folding directory - and run the copy of DF in that directory to upload the folds.
Others have mentioned using "sneakernet" approaches on a weekly basis.
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Will there be a way to upload sneakernetted folds, and over a longer period than 2 days for those machines not connected to the internet? (or will we have to start bringing them back seed information to get them to start up again after the first "generation 50" sequence is finished?)