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I'm not sure if this forum is most appropriate to ask.

However, I'm transferring large batch of files from a external HD via scp, between a raspberry pi and my desktop

Looking back, many of the files contained an input/output error upon transfer, and now the original and copied files are corrupted

Some of the files had been transferred previously and copied over fine. Comparing the files with md5, there appear to be differences

Can anyone help narrow down the issue, as well as potential repair solutions to the file if at all possible?

Please let me know if I can provide more information.

  • Did not the input/output error upon transfer tell you what was wrong? – joan Nov 30 '18 at 16:23
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    now the original and copied files are corrupted Why are the original files corrupted? If you sent the files both ways they would not be originals anymore, but copies of copies... So what I find puzzling is why the originals were overwritten with copies. – Dirk Nov 30 '18 at 17:53
  • Execute the command journalctl --boot --unit=ssh.service and look if you see some error messages belonging to corrupted data transfer. – Ingo Nov 30 '18 at 22:56
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Sounded like you have a problem with your network.

On my Rpi0 running with Kali Linux, I installed a package called par2 (PAR 2.0 compatible file verification and repair tool). From its man page, it can create PAR2 recovery files for as few as 1 or as many as 32768 files. So, perhaps you can use this tool to generate .par2 files to transfer through your network and use par2 utility to extract and/or rebuild if the transfer gives some errors.

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I'm transferring large batch of files from a external HD

Plug that HDD into your desktop (or any other computer you have) and copy the files via USB. It's much more reliable than a network connection, and it may have a more reliable USB functionality than your RPi, especially regarding power distribution.

I would also check the drive for filesystem errors and bad sectors. That's the only explanation I have for original files getting corrupted.

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