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I was running a multi-threaded program that makes huge amount of I/O operations, Basically reading/writing Millions of files. I had some problems/bugs and I used to halt the program to fix something and then run again.

Now the problem is after sometime everything went extremely slow, What are the possible reasons for the unexpected slowness? Could it be bad sectors? or problems with the filesystem?

I tried to copy the data to an external drive and the approximated time was 350 Hours!! with a speed of (4 kB/sec).

File System : Ext4
Platform : Ubuntu 13.04

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There are tools to verify if there are bad sectors, use those tools, and report back to us. – Ramhound Mar 27 '14 at 13:57
Don't try to access too many files at the same time. If you do, you wind up spending most of your time waiting for the disk head to move from file to file. Your data access pattern may be pathological, and that will hurt performance. – David Schwartz Mar 28 '14 at 17:13

First you have to identify the cause of the problem by yourself. This may happen dues to several reasons: hardware or software.

I do the following checks:

  • check the data cable(SATA mostly) and replace it with another when and test.
  • move the data cable to another port on your mother board(move from SATA0 to SATA1 for example or whatever) and test.
  • check the SMART data for your harddisk. There is a software called disks in Ubuntu 13.04 just open the dash and search for. This will show you the smart data and if there is a logical bad sectors.
  • If there is a logical bad sector you can correct them. check my answer here
  • If you still have the problem you probably have a physical bad sector which is a bad thing and you must not rely anymore on this disk and it's better to show it to some data recovery professional to help you extracting your data if its important.
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