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I currently have a 3 hard drive set up. One disk is 250GB and contains the Ubuntu OS while the other two are each 1TB and intended to store all the actual data (this is a lab server). It's worth mentioning that I've configured the two 1TB drives in RAID 1 using mdadm. Now that I'm trying to dump all the old server's data onto the new machine it's sending it to the smaller drive. Is there any way to make it so that this data from the external gets redirected to the RAID disks?

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    More worth mentioning would be how/where you mounted the resulting RAID volume, and how exactly you are "trying to dump all the old server's data" – steeldriver Jun 29 '17 at 23:01
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mount the new raid array to the folder where the data is downloaded to.

first copy any data there to the new drives; data left in the folder will be unseen when the drive is mounted to it, thus should be empty.

mount /dev/md0 /where/the/folder/is

will mount it

edit /etc/fstab for auto-mount at boot: add/change line to read

UUID=<id of raid> /where/the/folder/is ext4 default 0 0

you can get the UUID of the raid array by using sudo blkid

this effectively replaces the folder with the drive and all files written to that folder will go the the drive.

NOTE:change device name, file system type, and mount path as is appropriate

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