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My powerful Linux desktop (12 core, 32GB RAM, SSD, fast processor, ubuntu 13.10) slows down to a crawl when I rsync from my internal drive to an attached USB3 NTFS drive. Typing any command, like "df" or "ls", takes 5-10 seconds to respond. The slow feel reminds me of a heavily swapping computer, but the "free" command says swap size is zero, with 29GB of RAM free (buffers). "uptime" shows a load average of about 4.0, and "top" shows that the top processes are the rsync commands. I also see kswapd0 in the top few processes, but no swap space is being used and there's tons of free RAM.

The slowdown occurs even when I run rsync at a "nice" level of 19. The slowdown also lasts for about 1-2 minutes after I kill the rsync.

The slowdown doesn't happen with my other ext4 USB3 disk.

The actual transfer rate to the USB disk is fine: it is not slow. I'm asking about the heavy impact on the usability of the system during the rsync. Anybody know why this happens and how to prevent it?

Some disk info on the USB disk:

$ sudo hdparm -acdgkmurABCMNQW /dev/sdi1

/dev/sdi1:
 multcount     =  0 (off)
 readonly      =  0 (off)
 readahead     = 256 (on)
 geometry      = 364799/255/63, sectors = 5860507648, start = 16384
 drive state is:  active/idle
 look-ahead    =  1 (on)
 write-caching =  1 (on)
 APM_level      = 128
 acoustic      = not supported
 max sectors   = 5860533168/5860533168, HPA is disabled

I omitted these errors from the above output, presumably from unsupported features:

 HDIO_GET_32BIT failed: Invalid argument
 HDIO_GET_UNMASKINTR failed: Invalid argument
 HDIO_GET_DMA failed: Invalid argument
 /sys/block/sdi/sdi1/device/queue_depth: No such file or directory
 HDIO_GET_KEEPSETTINGS failed: Invalid argument
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Answering my own question: the answer is "user error." The whole USB/NTFS thing was a red herring!

My rsync command was supposed to back up my internal drive to an external USB drive, like this:

$ rsync -avx / /media/backupdrive

After a recent OS upgrade, however, Ubuntu changed the auto-mounted destination to /media/username/backupdrive, inserting my username into the path. So, my script was not actually hitting the USB drive, but writing to /media locally on my boot drive.

In other words, my boot drive (an SSD) was being hammered by rsync and filling up to 100%. This caused the system slowness.

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