How to interpret and fix a Input/output error in Linux?

The rsync error

 read errors mapping ....: Input/output error (5)

indicates the impossibility of rsync to read or write a file. The most likely causes of this error are disk defects, either in the SRC or in the TGT directory. Other possibilities however include insufficient permissions, file lock by anti-virus programs, and maybe other causes.

The first step toward a diagnosis is to try to copy the files manually. This may work if, for instance, the source of the error was a disk defect in the TGT directory; by repeating the operation at a later time, you will write into a different section of the disk, and the problem may have evaporated.

Alternatively, you may discover that you cannot access the file in the SRC directory. In this case I suggest that you employ any of the disk checking utilities available to your distro.

Insufficient privileges, anti-virus, are easier to diagnose.

Lastly, if you have a bad sector on your SRC directory, you may exclude that from future runs of rsync by means of

rsync -av --exclude='/home/my_name/directory_with_corrupt_files/*'

I had a similar issue, I had a with fuse-mounted device via USB, which would frequently disconnect, causing IO errors. My backup could never finish because the IO errors would start mid-way into the rsync, and despite running rsync repeatedly, at some point the sync would not progress beyond updating existing files.

My solution was to use

--ignore-existing 

option. This way I could run the sync in a loop until seeing a 0 exit status.

Of course, in this case I didn't care about updates to existing files.

I have 2 external drives I keep in sync, using rsync. I perform this task regularly on either of two machines, and frequently switch from one to the other for the sake of convenience. I have 4 machines running Debian 9, and use these drives on each of them.

This morning I used the following:

rsync -ahv --delete drive-x drive-y 

and was surprised to have a few hundred reported failures.

mostly: rsync: readlink_stat... failed: Input/output error (5)
also: rsync: rsync: recv_generator: mkdir ... failed: Read-only file system (30)

In the process to find out what happened, I remounted the drives twice, rebooted, ran rsync without --delete and basically my normal tries to fix something that has reliably worked for a long time. Even thought about installing rsync again. Before I would do that I decided to rsync the 2 drives on the other machine, which I run offline. rsync worked just the way it should.

Having read the material posted here, I installed clamav, updated the signatures, and scanned my home directory. I use this regularly on a different machine. I found 1 and only 1 PUA, and I deleted it. I always delete PUA's. I then remounted the two drives with this machine, and added different test files and folders to each drive.

I ran rsync -ahv --delete drive_x drive_y and everything worked fine.