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This is probably due to the NTFS backing of Cygwin on windows more than anything. NTFS stores all tiny little files inside the MFT which is write blocked. So every time you write a pissy little file out (compiling and VCS stuff does this lots!) it has to lock the MFT, extend and then write the file, then unlock it. This causes MFT contention which reduces the effective IOPS to the disk to virtually nothing even if the thing is fast. In fact mechanical disks can suck less because the kernel has time to order the writes while it's waiting for the disk to go round!
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Thanks, I didn't go into NTFS that far, but one can always notice Windoze slowing down to a crawling turtle's speed when copying a large set of rather small files, no matter if one uses that Exploder thing or cmdline (e.g. xcopy or robocopy).
BTW, the old machine from work flies like hell with this compile job if natively booted into debian
(don't tell our IT dept, but I think that'll be my workaround, using the new windoze box just as the frontend for Outlock and Orifice)