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Is there any Vmware or 3rd party tool to compress and store large vmdk files?

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The first thing you'll want to do is shrink the virtual disk itself to get rid of unused space. You can then use a compression utility like 7-zip to get them even smaller.

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Old post but I'll answer it in case anyone else has the same question. You want to do this to archive unused VMDKs? I don't think there's much benefit to shrinking the VMDK first. Just do a cleanup within the OS (delete unnecessary and temp files, etc). Then use a zip program to compress the VMDK and optionally break it down to smaller chunks. I had to do this to transfer a VMDK to a consultant. I used a quad-core VM with 8 GB RAM using 7-Zip with the ultra compression level and split it into 4480 MB (DVD) size chunks. I got 8 GB per hour at 28% compression ratio. Your mileage will vary.

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