System freezes regularly

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My operating system/applications periodically freeze, typically for about 15 seconds (sometimes longer). Then it unfreezes and continues working as usual.

It is not a conflict between running applications. It happens, even if I have an unusual single application running, or if I have a bunch running.

How do I clean the operating system so that mis-set bits (or something) will be cleared? I am running OSX 10.9.5

Thanks for any suggestions.
 
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A couple of questions:

1. What exact Mac model do you have?

2. Have you ever done any disk cleanup/maintenance/repairs? There are excellent tools available (both free and commercial) that can help you with that. And you can do some on your own.

3. Most importantly, are you making backups to an external device? And (hopefully) if you are, what software are you using for that?
 
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1) MacBook Pro (Early 2011, I belive). OSX10.9.5
2) The local Apple Store just had me go thru a procedure where I restarted the computer while holding down command-R and then running Disk Utility
3) I do regular backups to an external drive using Time Machine.

I am just starting to look for system maintenance software - CleanMyMac 3 popped up, but I'm not finished looking.

Thanks for any suggestions you can make.
 
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OK, thanks for that.

Now, as far as system maintenance software, stay away from CleanMyMac (MacKeeper also)! It will do more harm than good. One excellent, free product that has been around for a long time (and has had numerous, excellent reviews) is the venerable Onyx. You can get it from here:

http://www.titanium.free.fr/onyx.html

Note that there are specific versions for each specific Mac OS. So, in your case, you would need version 2.8.8. One of its useful features is Repairing Permissions.

Additionally, while Disk Utility is OK, you should consider investing in a more robust disk maintenance program An excellent one (I have been using it, along with Onyx, for a number of years) is TechTool Pro. This link describes it:

https://www.micromat.com/products/techtool-pro

By the way, what did Disk Utility tell you about the health of the internal drive on your machine?
 
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Thanks for the suggestions, honestone. I'll try them.

I don't remember specifically about the internal drive. There were some problems that were repaired, but eventually it said everything was OK.
 
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OK, sounds fine. However, if the internal drive is the original one that came with the machine, it could be going bad. In your case, that drive would be about 6 years old, which is "old" for standard HDDs (SSDs last longer). TechTool Pro is actually better than Disk Utility for performing more extensive (software-related) repairs.
 
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Is the TechToolPro software likely to detect hardware failures? Are there other things I should do to check on this?

Thanks.
 
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Yes, TechTool Pro can detect hardware failures. It actually goes through at least 4 more additional tasks than Disk Utility that are very useful. Also, it has a built-in SMART (Self-Monitoring, Analysis and Reporting Technology) utility to help with checking the health of disks. This link describes that technology better:

https://en.wikipedia.org/wiki/S.M.A.R.T.

There are separate products for SMART checking, but given that TechTool Pro also does other useful tasks, it would be more cost efficient to use it.

As for other things to do, you could start with Onyx and use it to 1) Repair Permissions, and 2) do some disk cleanup. Onyx does have limited disk maintenance/"repair" tasks, but nowhere near as extensive as TechTool Pro does.

The other thing you can do is to perform as much disk cleanup as you can on your own. Get rid of old versions of software, permanently delete EMails, etc. For permanently deleting EMails, I am only aware of how to do that with Outlook 2016, which is my EMail client. Don't know how to do that with Apple's Mail program, Thunderbird, etc.
 
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Thanks, honestone. I really appreciate your help. Hopefully this will clear up whatever it is that is causing my problems.

Tres
 
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I have a couple of more suggestions, along with some guidance on how you should proceed. But, I have to do a couple of things before I post them. I'll be back soon.
 
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OK, I'm back. It is, of course, unknown at this time whether or not you need to do a complete Erase, Format, OS 10.9.5 installation, and "if feasible", a restore from your most recent Time Machine backup. But, as some preliminary steps, I would recommend you do the following:

1. Do as much "self" disk cleanup as possible.

2. Download, install, and run Onyx. Use it to Repair Permissions, and do various disk cleanup chores.

3. Download, install, and run the excellent free Anti-Malware program Malwarebytes. You can get it from here:

https://www.malwarebytes.com/mac/

That is a very good program, and myself (and others here) have used it. But, it is not a "complete" virus checking program. So:

4. Download and run the excellent virus detection program ClamXav. You can get it form here:

https://www.clamxav.com/

You can run it in demo mode for 30 days. Let it do the various "upgrades" first (you'll be prompted about that). I used to use it when it was free, and yesterday I downloaded it, installed it, and ran it on both of my Macs. It did find a couple of "obscure" files, and I got rid of them.

5. In an "isolated" manner (ie, booting to the (hidden) Recovery HD partition), use Disk Utility to do First Aid on your drive.

6. If you don't have it, go to the App Store and download the file for OS 10.9.5 (I assume you want to remain with that OS). When that download completes, there will be a file inside your Applications folder entitled "Install Mac OS Mavericks". Make a copy of it in another location on your internal drive.

Doing those first 5 steps will insure, as best as possible at this point, your machine is as "clean as possible". If you see improvement in its performance, good. If not, then a purchase of TechTool Pro would be the next step. We can "cross that bridge" when you are ready for that purchase, as there are some more steps to go through.
 
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One other item I forgot to mention is that when you use the Repair Permissions feature of Onyx, you'll most likely need to run it a few times, as it does not "catch" all the permissions to be repaired on the first pass.
 
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