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My computer is suffering of slow-downs and I'm not surprised (it's around 6 years old). Here's what I've verified:

  1. They are not very frequent (only a couple of times a day).
  2. When they happen a single application will hang for 10-60 seconds, while the rest don't hang but also get slow.
  3. Even as it is happening, the CPU usage stays low.
  4. It happens to applications (such as text editor, firefox, skype).
  5. It never happens to some applications (such as games) which I use for hours under heavy CPU load.

Also of note:

  1. The Graphics card and PSU are new (around a year).
  2. Though I have a decent amount of software installed right now, this was happening even right after I reinstalled Windows.
  3. This HDD has been through many partinioning schemes, and a few heavy operations (such as moving around 200GB of data).

Because of the above, I am already 70% sure the problem is with the hard drive. Before I replace it, however, I want to rule out other less likely possibilities (such as RAM, software, or PSU).

I don't have the money to replace the entire box right now, but I can easily replace one of the components.

I've read several questions (such as this one) which give general guidance on troubleshooting an unknown issue, that is not what I'm looking for here.

My main question is:
What tests or benchmarks can I run to verify I have a problematic hard drive?
I don't need to solve this problem, I am content with just making sure it's the hard drive.

I could borrow a newer hard drive from a friend and see if it gets better. A positive result would rule out all other components, but it wouldn't rule out a software issue (since this new hard drive won't have any of the software I use daily).

Running on Windows/Linux.

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As it stands this question is MUCH too vague. What specifically have to tried already, and where are you getting stuck? There's no way for us to tell you how to be 100% confident in your diagnosis. If you want to test a replacement drive, get a hard drive and duplicate your drive onto it. You can find out how to do that searching here on SU. Or take it to someone who can do it for you (like a computer shop). –  techie007 Jun 29 '12 at 23:34
    
If you are just looking for a list of HDD Diagnostics software, please clarify that by editing your question, and include a list of which ones you've tried already, and why the many related questions on SU were of no help. –  techie007 Jun 29 '12 at 23:39
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Regarding your last paragraph: if diagnostics don't report any problems with the hard drive but you want to confirm that the new drive exhibits the same issue, you can clone your drive's contents onto a new one--in which case, you will have the same software on both drives. –  rob Jun 29 '12 at 23:45
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@techie007 The answers to those questions you linked to don't seem to be very comprehensive... :\ –  Deltik Jun 30 '12 at 0:30
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@techie007 I tried clarifying what you asked for in my edit. I hadn't tried any tools before asking this question, I didn't even know any, and SU is usually my first stop when tackling something I don't know :). I did search around first, but I hadn't found any of those questions because I was restricting the search to the [troubleshoot] and [hard-drive] tags (which seemed to me like the bare minimum). –  Bruce Connor Jun 30 '12 at 1:35
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3 Answers

up vote 10 down vote accepted

Checking the S.M.A.R.T. attributes is a useful at-a-glance first step to identifying hard drive issues.

Accessing S.M.A.R.T. Attributes

You can view S.M.A.R.T. attributes on Windows using third-party tools such as PassMark DiskCheckup™.

On Mac OS X, you can use Disk Utility, though it isn't very verbose. The other tools I found were paid products, and I didn't investigate them.

On Linux, the command smartctl -a /dev/hda (from the package smartmontools) gives S.M.A.R.T. information about a hard drive, where /dev/hda is replaced with the device in question. palimpsest is a graphical utility that can give some more advice about the condition of your hard drive.

[Palimpsest shows a bad HDD.]

Understanding S.M.A.R.T. Attributes

Here are some attributes that are relevant and worth noting. A larger list can be found here.

A non-zero Read Error Rate (ID 1) indicates a problem with either the disk surface or the read/write heads.

The Throughput Performance (ID 2) is the average efficiency of the disk. If the value drops below the threshold, something may be wrong with the disk.

A high Spin-Up Time (ID 3) (recorded in milliseconds) may indicate that the hard drive is having trouble spinning up.

An increasing Reallocated Sectors Count (ID 5) means that areas on the hard drive are failing in integrity, and data had to be moved. This causes performance decreases when sectors are being remapped, but it may be more serious in that the hard drive is about to fail.

A low Seek Time Performance (ID 8) is a sign of a mechanical issue with the magnetic heads.

The Spin Retry Count (ID 10) goes up when a spin-up fails. If this happens, input/output operations are queued until the hard drive can spin normally, which causes slowdowns. More importantly, though, if the hard drive has to retry spinning up, it's a sign of imminent failure.

A non-zero Reported Uncorrectable Errors (ID 187) count means that that number of sectors could not be corrected by hardware error correction. Here's a sign of old age.

The Current Pending Sector Count (ID 197) is the number of sectors waiting to be remapped. This indicates old age of the hard drive.

Source: palimpsest

HDD Benchmarks

[Palimpsest HDD Read Test]

If there's a certain location in the hard drive that is getting poor performance (maybe where a shared library is stored), hard drive read benchmarks can help confirm this. Above is a screenshot of a palimpsest benchmark on a hard drive.

On Windows, you can use tools like HD Tune to do hard drive benchmarks.

On Mac OS X, you can use tools like Blackmagic Disk Speed Test to do hard drive benchmarks.

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To add to this answer: reallocated sectors will cause slowdowns whenever you try to access the address that was remapped. The more reallocated sectors, the more likely it is that you'll notice the slowdown as the hard drive seeks to a different part of the disk surface to read from the remapped address. –  rob Jun 29 '12 at 23:42
    
A non-zero Raw Read Error Rate does not necessarily indicate a problem with the drive, see my explanation on superuser.com/questions/393257/…. –  Gurken Papst Jun 29 '12 at 23:55
    
The Spin Up Time is reported as a raw value of 5458, and the Power On Time is 13477. Is that a problem? 5 seconds sounds like a lot. –  Bruce Connor Jun 30 '12 at 0:41
    
5.448 seconds for Spin-Up Time? That may seem like a long time, but it could be in the ballpark of normal. Source: Western Digital Scorpio ML40 Optimized Spinup Feature. 561.5-ish days for Power-On Hours? To me, it doesn't mean much because I leave my SATA devices powered on almost 24/7. –  Deltik Jun 30 '12 at 0:47
    
Pretty thorough. Usually, I just run chkdsk, though. Either it solves the issue, or I get a new harddrive. If it doesn't solve the issue, the drive is typically 5-10 years old, anyway. I figure, these things break. –  Wolfpack'08 Jun 30 '12 at 1:47
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Check your drives S.M.A.R.T. status with a tool like GSmartControl. If there are serious problems like defective sectors, these are probably visible in the data. You can also launch a self-test to find out about new errors, that haven't been logged yet.

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Another way you can test within Windows is to run the Command Prompt (Run as Administrator in Vista or Windows 7). From there, type CHKDSK C: /f /r and press Enter. This will scan the file system, and the free space for errors

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... and might cause data loss on a drive that is seriously damaged, as writing to damaged sectors will eat up the reserved reallocation sectors and then finally lead to write errors. So don't do this if you are unsure about the disk's health or have valuable data on it and no backup available. S.M.A.R.T. data or diagnostic tests however are read only and should not hurt. If there are problems reported, data should be backed up immediately. –  Gurken Papst Jul 1 '12 at 15:57
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