The trouble with having two copies is that it is all too easy to start one copy twice, and that results in an instant nuke of your work in progress. You have to create two different folders with a copy of the console folder in each, and then remember (a) to type "-local" every time you start one, and (b) to check carefully which of your multiple copies is already running before you start an instance.
Windows, alas, does not seem to have the basic facility to specify if an executable (or shortcut to an executable) should create a fresh instance the second time it is invoked, or simply bring the already-running process to the foreground. (OS/2 has had this ability forever, I assume that Linux does it too - it would seem a pretty basic and sensible facility to have as part of the OS shell.)
In any case, the only way I know of to get around this is to use batch files.
Anyone who is interested can download this:
http://www.redhill.net.au/sf/foldit.zip
To use it, take an empty floppy disk. Copy the current version of the folding@home console client onto it, making sure that you rename it to "fold.exe". Unzip the contents of the zip file onto the disk too (in the root folder).
Then, every time you want to set up a new machine, simply insert the floppy disk and type "install".
Install.bat will:
1: Create a folder on your hard drive called "fold"
2: Copy the empty file "empty.dat" into it. This will serve as our "busy flag" so that we can't accidently run two copies of the same executable at the same time and thus nuke our work in progress.
3:Create the subfolders "1" and "2".
4: Copy fold.exe (the console client) into each of those subfolders, renaming it to "fold1.exe" and "fold2.exe".
5: Copy fold1.bat and fold2.bat into c:\fold
Now, simply drag a pair of shortcuts to those batch files onto your desktop (or to whatever other place is convenient).
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Disclaimer:
I've been using this method, more or less, for ages now, but didn't have my original batch files handy here at the office. So these are rewritten from memory. They look allright to my quick, rough eye, but I may have made a typo somewhere in them. I'll post again if I discover any errors.