Whole system regularly hangs for about 10-20 seconds

[baryon]

Ever since upgrading to El Capitan, I have had this issue happen regularly, about once or twice a day. I'd be using Safari and all of a sudden every app freezes, like with a beachball, except there isn't always necessary a beachball (I think).

During the hang, I can still switch spaces using gestures, maybe even get into Mission Control, move the mouse, but the keyboard won't respond and clicking doesn't respond so no getting into Activity Monitor. Then after about 15 seconds suddenly everything works, and everything I've typed or clicked on suddenly gets typed and clicked in rapid succession.

Late 2013 15-inch Retina MacBook Pro
Happens both on OS X 10.11.0 and 10.11.1
Never happened on previous version of OS X on this Mac

Here's a console log from around the last time it happened:

25/10/15 10:30:15,759 am com.apple.xpc.launchd[1]: (com.apple.WebKit.Networking.9A1EDC77-7679-499C-8245-2F26EC5DCD48[4263]) Service exited with abnormal code: 1
25/10/15 10:30:18,435 am Safari[3738]: KeychainGetICDPStatus: keychain: -25300
25/10/15 10:30:18,435 am Safari[3738]: KeychainGetICDPStatus: status: off
25/10/15 10:30:32,815 am Safari[3738]: KeychainGetICDPStatus: keychain: -25300
25/10/15 10:30:32,815 am Safari[3738]: KeychainGetICDPStatus: status: off
25/10/15 10:30:37,430 am nbagent[861]: XPC Activity invoked with state=2
25/10/15 10:30:41,057 am diagnostics_agent[371]: AutoSubmitPreference is 1
25/10/15 10:30:48,254 am Safari[3738]: KeychainGetICDPStatus: keychain: -25300
25/10/15 10:30:48,255 am Safari[3738]: KeychainGetICDPStatus: status: off
25/10/15 10:30:50,039 am SubmitDiagInfo[379]: Submitted problem report file:///Library/Logs/DiagnosticReports/awdd_2015-10-25-084840-1_Users-rMBP.awd
25/10/15 10:30:50,406 am SubmitDiagInfo[379]: Submitted problem report file:///Library/Logs/DiagnosticReports/awdd_2015-10-25-084840_Users-rMBP.awd
25/10/15 10:30:52,552 am SubmitDiagInfo[379]: SubmitDiagInfo sucessfully uploaded 157 diagnostic messages
25/10/15 10:30:52,581 am SubmitDiagInfo[379]: Submitted problem report file:///Users/User/Library/Logs/DiagnosticReports/Safari_2015-10-24-163720_Users-rMBP.crash
25/10/15 10:30:52,582 am SubmitDiagInfo[379]: Submitted problem report file:///Users/User/Library/Logs/DiagnosticReports/Safari_2015-10-24-200832_Users-rMBP.crash
25/10/15 10:31:15,383 am Safari[3738]: KeychainGetICDPStatus: keychain: -25300
25/10/15 10:31:15,383 am Safari[3738]: KeychainGetICDPStatus: status: off
25/10/15 10:31:26,000 am kernel[0]: IOHIDSystem: postEvent LLEventQueue overflow.
25/10/15 10:31:27,891 am locationd[81]: NETWORK: requery, 0, 0, 0, 0, 4, items, fQueryRetries, 0, fLastRetryTimestamp, 467452172.7
25/10/15 10:31:28,892 am Spotlight[343]: XPC connection was invalidated
25/10/15 10:31:28,909 am Spotlight[343]: XPC connection was invalidated
25/10/15 10:31:29,816 am Spotlight[343]: XPC connection was invalidated
25/10/15 10:31:29,848 am Spotlight[343]: XPC connection was invalidated
25/10/15 10:31:29,925 am Spotlight[343]: XPC connection was invalidated
25/10/15 10:31:29,994 am Spotlight[343]: XPC connection was invalidated
25/10/15 10:31:30,070 am Spotlight[343]: XPC connection was invalidated
25/10/15 10:31:30,232 am com.apple.xpc.launchd[1]: (com.apple.quicklook[4277]) Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.quicklook
25/10/15 10:31:30,252 am Spotlight[343]: XPC connection was invalidated
25/10/15 10:31:30,412 am QuickLookSatellite[4278]: CGSConnectionByID: 0 is not a valid connection ID.
25/10/15 10:31:30,412 am QuickLookSatellite[4278]: Invalid Connection ID 0
25/10/15 10:31:30,424 am QuickLookSatellite[4278]: CGSConnectionByID: 0 is not a valid connection ID.
25/10/15 10:31:30,424 am QuickLookSatellite[4278]: CGSConnectionByID: 0 is not a valid connection ID.
25/10/15 10:31:30,424 am QuickLookSatellite[4278]: CGSConnectionByID: 0 is not a valid connection ID.
25/10/15 10:31:30,691 am lsd[237]: LaunchServices: Could not store lsd-identifiers file at /private/var/db/lsd/com.apple.lsdschemes.plist
25/10/15 10:31:30,763 am Console[4279]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable

Here's another time it happened, the freeze happened in Safari again during the animation when I closed a tab and it was "sliding" over:

26/10/15 4:49:14,437 pm com.apple.cts[232]: com.apple.AddressBook.ScheduledSync: scheduler_evaluate_activity told me to run this job; however, but the start time isn't for 500 seconds.  Ignoring.
26/10/15 4:50:14,395 pm watchdogd[341]: [watchdog_daemon] @(_wd_daemon_service_thread) - service (com.apple.WindowServer) reported as unresponsive
26/10/15 4:50:19,953 pm spindump[3307]: Saved userspace_watchdog_timeout.spin report for WindowServer version ??? (???) to /Library/Logs/DiagnosticReports/WindowServer_2015-10-26-165019_Users-rMBP.userspace_watchdog_timeout.spin
26/10/15 4:50:19,974 pm watchdogd[341]: [watchdog_daemon] @(__wd_service_report_unresponsive_block_invoke) - spindump gathered for (com.apple.WindowServer) at (/Library/Logs/DiagnosticReports/WindowServer_2015-10-26-165019_Users-rMBP.userspace_watchdog_timeout.spin)
26/10/15 4:50:33,169 pm WindowServer[167]: _CGXRemoveWindowFromWindowMovementGroup: window 0x75d is not attached to window 0x75e
26/10/15 4:50:35,568 pm Spotlight[343]: XPC connection was invalidated
26/10/15 4:50:35,588 pm Spotlight[343]: XPC connection was invalidated
26/10/15 4:50:35,597 pm Spotlight[343]: XPC connection was invalidated
26/10/15 4:50:35,599 pm Spotlight[343]: XPC connection was invalidated
26/10/15 4:50:35,599 pm Spotlight[343]: XPC connection was invalidated
26/10/15 4:50:35,599 pm Spotlight[343]: XPC connection was invalidated
26/10/15 4:50:35,676 pm Spotlight[343]: XPC connection was invalidated
26/10/15 4:50:36,050 pm locationd[81]: NETWORK: requery, 0, 0, 0, 0, 8, items, fQueryRetries, 0, fLastRetryTimestamp, 467558927.5
26/10/15 4:50:36,315 pm com.apple.xpc.launchd[1]: (com.apple.quicklook[5382]) Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.quicklook
26/10/15 4:50:36,610 pm Console[5383]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable

Third hang:

28/10/15 10:26:34,988 pm Safari[3738]: KeychainGetICDPStatus: keychain: -25300
28/10/15 10:26:34,988 pm Safari[3738]: KeychainGetICDPStatus: status: off
28/10/15 10:27:52,000 pm kernel[0]: IOHIDSystem: postEvent LLEventQueue overflow.
28/10/15 10:27:54,500 pm locationd[81]: NETWORK: requery, 0, 0, 0, 0, 8, items, fQueryRetries, 0, fLastRetryTimestamp, 467753167.1
28/10/15 10:27:55,676 pm Spotlight[343]: XPC connection was invalidated
28/10/15 10:27:55,696 pm Spotlight[343]: XPC connection was invalidated
28/10/15 10:27:55,703 pm Spotlight[343]: XPC connection was invalidated
28/10/15 10:27:55,705 pm Spotlight[343]: XPC connection was invalidated
28/10/15 10:27:55,706 pm Spotlight[343]: XPC connection was invalidated
28/10/15 10:27:55,817 pm Spotlight[343]: XPC connection was invalidated
28/10/15 10:27:56,161 pm Console[7307]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable

31/10/15 6:19:33,324 pm Safari[3738]: KeychainGetICDPStatus: keychain: -25300
31/10/15 6:19:33,324 pm Safari[3738]: KeychainGetICDPStatus: status: off
31/10/15 6:20:00,397 pm Safari[3738]: KeychainGetICDPStatus: keychain: -25300
31/10/15 6:20:00,397 pm Safari[3738]: KeychainGetICDPStatus: status: off
31/10/15 6:20:00,855 pm Safari[3738]: KeychainGetICDPStatus: keychain: -25300
31/10/15 6:20:00,855 pm Safari[3738]: KeychainGetICDPStatus: status: off
31/10/15 6:20:03,177 pm locationd[81]: NETWORK: requery, 0, 0, 0, 0, 7, items, fQueryRetries, 0, fLastRetryTimestamp, 467996374.9
31/10/15 6:20:03,214 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:03,234 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:03,235 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:03,236 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:03,236 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:06,579 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:06,600 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:06,609 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:06,612 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:06,612 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:06,613 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:06,613 pm Spotlight[343]: XPC connection was invalidated
31/10/15 6:20:06,857 pm Console[9703]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable

02/11/15 9:22:04,732 pm watchdogd[341]: [watchdog_daemon] @(_wd_daemon_service_thread) - service (com.apple.WindowServer) reported as unresponsive
02/11/15 9:22:07,246 pm spindump[3307]: Saved userspace_watchdog_timeout.spin report for WindowServer version ??? (???) to /Library/Logs/DiagnosticReports/WindowServer_2015-11-02-212207_Users-rMBP.userspace_watchdog_timeout.spin
02/11/15 9:22:07,249 pm watchdogd[341]: [watchdog_daemon] @(__wd_service_report_unresponsive_block_invoke) - spindump gathered for (com.apple.WindowServer) at (/Library/Logs/DiagnosticReports/WindowServer_2015-11-02-212207_Users-rMBP.userspace_watchdog_timeout.spin)
02/11/15 9:22:15,235 pm WindowServer[167]: send_datagram_available_ping: pid 3738 failed to act on a ping it dequeued before timing out.
02/11/15 9:22:15,417 pm Safari[3738]: KeychainGetICDPStatus: keychain: -25300
02/11/15 9:22:15,417 pm Safari[3738]: KeychainGetICDPStatus: status: off
02/11/15 9:22:18,362 pm locationd[81]: NETWORK: requery, 0, 0, 0, 0, 10, items, fQueryRetries, 0, fLastRetryTimestamp, 468183979.7
02/11/15 9:22:18,960 pm Console[12991]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable
02/11/15 9:22:19,087 pm Spotlight[343]: XPC connection was invalidated
02/11/15 9:22:19,160 pm Spotlight[343]: XPC connection was invalidated
02/11/15 9:22:19,181 pm Spotlight[343]: XPC connection was invalidated
02/11/15 9:22:19,192 pm Spotlight[343]: XPC connection was invalidated
02/11/15 9:22:19,195 pm Spotlight[343]: XPC connection was invalidated

06/11/15 3:19:25,601 pm com.apple.usbmuxd[78]: _SendAttachNotification Device 60:fa:cd:41:d2:36@fe80::62fa:cdff:fe41:d236._apple-mobdev2._tcp.local. has already appeared on interface 4. Suppressing duplicate attach notification.
06/11/15 3:19:46,006 pm iTunes[14059]: Entered:_AMMuxedDeviceDisconnected, mux-device:543
06/11/15 3:19:46,006 pm iTunes[14059]: Entered:__thr_AMMuxedDeviceDisconnected, mux-device:543
06/11/15 3:19:46,006 pm iTunes[14059]: tid:1113f - Mux ID not found in mapping dictionary
06/11/15 3:19:46,006 pm iTunes[14059]: tid:1113f - Can't handle disconnect with invalid ecid
06/11/15 3:19:51,442 pm com.apple.usbmuxd[78]: LOCKDOWN_V2_BONJOUR_SERVICE_NAME is _apple-mobdev2._tcp,905407e1
06/11/15 3:19:56,000 pm syslogd[44]: ASL Sender Statistics
06/11/15 3:20:02,502 pm locationd[81]: NETWORK: requery, 0, 0, 0, 0, 9, items, fQueryRetries, 0, fLastRetryTimestamp, 468492523.2
06/11/15 3:20:02,792 pm Console[15913]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable
06/11/15 3:20:03,728 pm Spotlight[343]: XPC connection was invalidated
06/11/15 3:20:03,748 pm Spotlight[343]: XPC connection was invalidated
06/11/15 3:20:03,756 pm Spotlight[343]: XPC connection was invalidated
06/11/15 3:20:03,758 pm Spotlight[343]: XPC connection was invalidated
06/11/15 3:20:03,758 pm Spotlight[343]: XPC connection was invalidated
06/11/15 3:20:03,758 pm Spotlight[343]: XPC connection was invalidated
06/11/15 3:20:03,759 pm Spotlight[343]: XPC connection was invalidated

07/11/15 3:38:05,251 pm com.apple.WebKit.WebContent[16556]: [15:38:05.251] <<<< Boss >>>> figPlaybackBossPrerollCompleted: unexpected preroll-complete notification
07/11/15 3:38:29,113 pm com.apple.usbmuxd[78]: _SendAttachNotification Device 60:fa:cd:41:d2:36@fe80::62fa:cdff:fe41:d236._apple-mobdev2._tcp.local. has already appeared on interface 4. Suppressing duplicate attach notification.
07/11/15 3:38:39,607 pm iTunes[14059]: Entered:_AMMuxedDeviceDisconnected, mux-device:582
07/11/15 3:38:39,607 pm iTunes[14059]: Entered:__thr_AMMuxedDeviceDisconnected, mux-device:582
07/11/15 3:38:39,607 pm iTunes[14059]: tid:1e05f - Mux ID not found in mapping dictionary
07/11/15 3:38:39,607 pm iTunes[14059]: tid:1e05f - Can't handle disconnect with invalid ecid
07/11/15 3:38:57,049 pm watchdogd[341]: [watchdog_daemon] @(_wd_daemon_service_thread) - service (com.apple.WindowServer) reported as unresponsive
07/11/15 3:39:00,058 pm spindump[3307]: Saved userspace_watchdog_timeout.spin report for WindowServer version ??? (???) to /Library/Logs/DiagnosticReports/WindowServer_2015-11-07-153900_Users-rMBP.userspace_watchdog_timeout.spin
07/11/15 3:39:00,061 pm watchdogd[341]: [watchdog_daemon] @(__wd_service_report_unresponsive_block_invoke) - spindump gathered for (com.apple.WindowServer) at (/Library/Logs/DiagnosticReports/WindowServer_2015-11-07-153900_Users-rMBP.userspace_watchdog_timeout.spin)
07/11/15 3:39:08,848 pm Spotlight[343]: XPC connection was invalidated
07/11/15 3:39:08,870 pm Spotlight[343]: XPC connection was invalidated
07/11/15 3:39:08,877 pm Spotlight[343]: XPC connection was invalidated
07/11/15 3:39:08,879 pm Spotlight[343]: XPC connection was invalidated
07/11/15 3:39:08,880 pm Spotlight[343]: XPC connection was invalidated
07/11/15 3:39:08,918 pm Spotlight[343]: XPC connection was invalidated
07/11/15 3:39:09,052 pm Spotlight[343]: XPC connection was invalidated
07/11/15 3:39:09,259 pm locationd[81]: NETWORK: requery, 0, 0, 0, 0, 9, items, fQueryRetries, 0, fLastRetryTimestamp, 468579818.4
07/11/15 3:39:09,408 pm Console[16563]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable

Looks like this is common between the logs:

08/11/15 2:08:18,606 pm watchdogd[341]: [watchdog_daemon] @(_wd_daemon_service_thread) - service (com.apple.WindowServer) reported as unresponsive
08/11/15 2:08:21,006 pm spindump[3307]: Saved userspace_watchdog_timeout.spin report for WindowServer version ??? (???) to /Library/Logs/DiagnosticReports/WindowServer_2015-11-08-140821_Users-rMBP.userspace_watchdog_timeout.spin
08/11/15 2:08:21,008 pm watchdogd[341]: [watchdog_daemon] @(__wd_service_report_unresponsive_block_invoke) - spindump gathered for (com.apple.WindowServer) at (/Library/Logs/DiagnosticReports/WindowServer_2015-11-08-140821_Users-rMBP.userspace_watchdog_timeout.spin)
08/11/15 2:08:31,391 pm WindowServer[167]: Surface testing disallowed updates for 10 sequential attempts...
08/11/15 2:08:31,400 pm WindowServer[167]: Surface test allowed updates after 11 attempts (44 ms)
08/11/15 2:08:35,743 pm locationd[81]: NETWORK: requery, 0, 0, 0, 0, 7, items, fQueryRetries, 0, fLastRetryTimestamp, 468665838.1
08/11/15 2:08:36,639 pm Spotlight[343]: XPC connection was invalidated
08/11/15 2:08:36,660 pm Spotlight[343]: XPC connection was invalidated
08/11/15 2:08:36,668 pm Spotlight[343]: XPC connection was invalidated
08/11/15 2:08:36,670 pm Spotlight[343]: XPC connection was invalidated
08/11/15 2:08:37,247 pm com.apple.xpc.launchd[1]: (com.apple.quicklook[17210]) Endpoint has been activated through legacy launch(3) APIs. Please switch to XPC or bootstrap_check_in(): com.apple.quicklook
08/11/15 2:08:37,364 pm Console[17211]: Failed to connect (_consoleX) outlet from (NSApplication) to (ConsoleX): missing setter or instance variable

Spotlight[343]: XPC connection was invalidated

Maybe it has nothing to do with Safari, it's just that I spend most of my time there so whenever it happens, I'm always using Safari.

Looks like others are having this issue too: https://discussions.apple.com/thread/7255321

 

[Steve121178]

Out of interest, did you just upgrade to El Cap, or do it properly via a clean install?

 

[baryon]

Out of interest, did you just upgrade to El Cap, or do it properly via a clean install?

I did and upgrade - it came with Mavericks, I upgraded to Yosemite and then to El Capitan. Can't be arsed to do a clean install every single year.

 

[Steve121178]

Practically everyone I have come across that has had issues have been those who upgraded. I don't recall seeing anyone who clean installed having issues.

Obviously the upgrade route works for most people but I'd personally rather spend a few hours doing a clean install than upgrade and run the risk of issues. It's also nice to start with a clean slate & not have crap carried forward from previous installs.

 

[chevalier433]

Practically everyone I have come across that has had issues have been those who upgraded. I don't recall seeing anyone who clean installed having issues.

Obviously the upgrade route works for most people but I'd personally rather spend a few hours doing a clean install than upgrade and run the risk of issues. It's also nice to start with a clean slate & not have crap carried forward from previous installs.

Clean install mania is a myth it's useful when you already have problems.

 

[Weaselboy]

Is there anything suspicious in this console log?

There are a couple crash reports there showing Safari crashing. Try making a new (temp) admin account and logout of your account and into the temp account then test for a while and see if it happens in that account.

If it does not happen in the test account, that tells us it is something specific to your account, like perhaps a bad Safari extension. It the temp account fixes it, try running the app Etrecheck. That will create an anonymized report showing everything running on your system. Post the report here for us to look at and try to help you.

 

[baryon]

There are a couple crash reports there showing Safari crashing. Try making a new (temp) admin account and logout of your account and into the temp account then test for a while and see if it happens in that account.

If it does not happen in the test account, that tells us it is something specific to your account, like perhaps a bad Safari extension. It the temp account fixes it, try running the app Etrecheck. That will create an anonymized report showing everything running on your system. Post the report here for us to look at and try to help you.

Thanks! I'll try to investigate that then.

 

[ctg7w6]

There is no reason we should have to clean install. That is shabby design work.

And, by the way, I've heard of plenty people saying they did do a clean install and are still seeing all of these issues with El Capitan.

At this point I honestly don't know if Windows 10 is better enough to switch. I use both... Windows 10 has many day to day problems with programs becoming slow, unresponsive, etc. But the OS works like a charm. OS X's operating system is basically broken for me. Third party apps work great still, except Office still kind of sucks. Guess I will still stick with OS X because of the programs I use, but I wish the features of the OS would work for me like they do in Windows.

After all, it is a little fishy that my bluetooth Beats headphones work perfectly on Windows 10, but I get terrible choppy sound on OS X (same computer, btw.). Little bit ridiculous.

 

[dogslobber]

Clean install mania is a myth it's useful when you already have problems.

A more useful metric after upgrade is whether the problem behavior occurs with a newly created account. I agree that clean install is a big hammer. I've not clean installed since Tiger.

 

[baryon]

Update: Looks like every time this happens, I get "Spotlight[343]: XPC connection was invalidated" a bunch of times in the console (see original post).

What does this mean? I can't find enough info about it. Could this be more related to Spotlight than to Safari?

 

[Weaselboy]

Update: Looks like every time this happens, I get "Spotlight[343]: XPC connection was invalidated" a bunch of times in the console (see original post).

What does this mean? I can't find enough info about it. Could this be more related to Spotlight than to Safari?

Did you try making a new test account and seeing if the issue occurs there like I suggested?

 

[dogslobber]

Update: Looks like every time this happens, I get "Spotlight[343]: XPC connection was invalidated" a bunch of times in the console (see original post).

What does this mean? I can't find enough info about it. Could this be more related to Spotlight than to Safari?

This might help also:

https://support.apple.com/en-us/HT201716

 

[baryon]

Did you try making a new test account and seeing if the issue occurs there like I suggested?

So far I have not been able to use that account for long enough for this to pop up - I'd have to use it for two days straight to have a chance, but I need my regular account to do most of my work because it has all my stuff.

 

[Weaselboy]

So far I have not been able to use that account for long enough for this to pop up - I'd have to use it for two days straight to have a chance, but I need my regular account to do most of my work because it has all my stuff.

What I was getting at with that test method is if it does not happen in the new account, that tells us it is something you have installed in your existing account. Try running the app Etrecheck in the old account. That will create a list of all launch and startup items and maybe give us a clue what it causing this. You can post the anonymized report here for us to take a look.

It would be worth your time to test some more on the test account as that will prove where the issue is.

 

[bobright]

I came into this forum trying to decide if I should upgrade from Yosemite or not , everything running stable. Should I just hold off? Hearing about a lot of problems with Capitan.

 

[pickaxe]

OP the bug you're having is something I've experienced regularly as well for the past several months. I've reported it, Apple is aware of it (and closed it as duplicate) but it's still there. I'm starting to think Apple's OS X department is just a bunch of script kiddies at this point.

 

[baryon]

I deleted the Spotlight index and let it rebuild, but it didn't solve the issue at all. The Console hints at a Spotlight issue, but my experience hints at a Safari issue, so I'm clueless. I've updated the original post with a bunch more Console logs, if anyone understands them, it would be great if you could fish out any useful clues for me...

What I was getting at with that test method is if it does not happen in the new account, that tells us it is something you have installed in your existing account. Try running the app Etrecheck in the old account. That will create a list of all launch and startup items and maybe give us a clue what it causing this. You can post the anonymized report here for us to take a look.

It would be worth your time to test some more on the test account as that will prove where the issue is.

Thanks! I made the report with EtreCheck, here it is:

Spoiler: EtreCheck Report (click to show)

EtreCheck version: 2.6.3 (223)

Report generated 08/11/15 2:14 pm

Runtime 1:22

Download EtreCheck from http://etresoft.com/etrecheck



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Hardware Information: (What does this mean?)

MacBook Pro (Retina, 15-inch, Late 2013)

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MacBook Pro - model: MacBookPro11,3

1 2.3 GHz Intel Core i7 CPU: 4-core

16 GB RAM Not upgradeable

BANK 0/DIMM0

8 GB DDR3 1600 MHz ok

BANK 1/DIMM0

8 GB DDR3 1600 MHz ok

Bluetooth: Good - Handoff/Airdrop2 supported

Wireless: en0: 802.11 a/b/g/n/ac

Battery: Health = Normal - Cycle count = 239 - SN = D863386Y441F9CP85



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Kernel Extensions: (What does this mean?)

/Library/Extensions

[not loaded] com.wacom.kext.ftdi (1 - SDK 10.9) [Click for support]



/System/Library/Extensions

[not loaded] com.wacom.kext.wacomtablet (6.3.10 - SDK 10.9) [Click for support]



Launch Agents: (What does this mean?)

[loaded] com.oracle.java.Java-Updater.plist [Click for support]

[running] com.wacom.wacomtablet.plist [Click for support]



Launch Daemons: (What does this mean?)

[loaded] com.oracle.java.Helper-Tool.plist [Click for support]

[loaded] com.oracle.java.JavaUpdateHelper.plist [Click for support]



User Launch Agents: (What does this mean?)

[loaded] com.valvesoftware.steamclean.plist [Click for support]



User Login Items: (What does this mean?)

iTunesHelper Application (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)

Dropbox Application (/Applications/Dropbox.app)



Other Apps: (What does this mean?)

[loaded] com.adobe.AdobeCreativeCloud

[loaded] com.adobe.SwitchBoard

[running] com.adobe.accmac.69792

[loaded] com.adobe.fpsaud

[running] com.apple.xpc.launchd.oneshot.0x10000001.Goofy

[running] com.apple.xpc.launchd.oneshot.0x1000006f.EtreCheck

[running] com.getdropbox.dropbox.55712

[loaded] com.github.GitHub.GHInstallCLI

[loaded] com.google.keystone.user.agent

[loaded] com.teamviewer.Helper

[running] com.valvesoftware.steam.ipctool

[running] com.wacom.TabletDriver.19232

[running] com.wacom.WacomTouchDriver.95712



Internet Plug-ins: (What does this mean?)

AdobeAAMDetect: Version: 3.0.0.0 - SDK 10.9 [Click for support]

FlashPlayer-10.6: Version: 19.0.0.226 - SDK 10.6 [Click for support]

QuickTime Plugin: Version: 7.7.3

Flash Player: Version: 19.0.0.226 - SDK 10.6 [Click for support]

Default Browser: Version: 601 - SDK 10.11

Unity Web Player: Version: UnityPlayer version 4.6.0f3 - SDK 10.6 [Click for support]

WacomTabletPlugin: Version: WacomTabletPlugin 2.1.0.6 - SDK 10.9 [Click for support]

JavaAppletPlugin: Version: Java 8 Update 45 Check version



Safari Extensions: (What does this mean?)

AdBlock

SafariKeywordSearch



3rd Party Preference Panes: (What does this mean?)

Flash Player [Click for support]

Java [Click for support]

WacomTablet [Click for support]



Time Machine: (What does this mean?)

Skip System Files: NO

Mobile backups: ON

Auto backup: YES

Volumes being backed up:

Macintosh HD: Disk size: 499.06 GB Disk used: 306.49 GB

Destinations:

Mac Backup [Local]

Total size: 800.00 GB

Total number of backups: 18

Oldest backup: 10/05/15 10:23 am

Last backup: 27/10/15 4:29 pm

Size of backup disk: Too small

Backup size 800.00 GB < (Disk used 306.49 GB X 3)



Top Processes by CPU: (What does this mean?)

4% WindowServer

3% com.apple.WebKit.WebContent(5)

2% Safari

2% fontd

1% hidd



Top Processes by Memory: (What does this mean?)

2.16 GB Safari

1.44 GB kernel_task

1.07 GB com.apple.WebKit.WebContent(5)

459 MB softwareupdated

360 MB iTunes



Virtual Memory Information: (What does this mean?)

3.05 GB Free RAM

13.00 GB Used RAM (2.43 GB Cached)

1.02 GB Swap Used



Diagnostics Information: (What does this mean?)

Nov 5, 2015, 05:22:17 PM ~/Library/Logs/DiagnosticReports/fontd_2015-11-05-172217_[redacted].crash

Nov 5, 2015, 03:34:20 PM /Library/Logs/DiagnosticReports/Adobe Bridge CC_2015-11-05-153420_[redacted].cpu_resource.diag [Click for details]

I have tried using a new account but so far I have to keep switching back to the old one as that's where I have all my everything basically. But so far the new account doesn't have issues, but I haven't used it for long enough for them to show up (I'd have to spend two or three whole days on there to be sure).

Reading that report I just realized I haven't rebooted in 16 days - wow I tend to forget these days. I guess that should be the first thing to do!

I came into this forum trying to decide if I should upgrade from Yosemite or not , everything running stable. Should I just hold off? Hearing about a lot of problems with Capitan.

I would say just stay with Yosemite for now, if it works fine for you. It's very rare to find a version of OS X that doesn't have issues that affect you, so stick with it while you can. Or at least wait until OS X 10.11.4. I strongly believe in "if it ain't broke, don't fix it" nowadays. Why upgrade when all you get is a new feature or two, with the possibility of literally any kind of problem to which there is no guaranteed fix? Even if you do upgrade, have a solid backup. But even then, should you want to go back, you'll have to do that soon as any files you make on the new system won't be restored from backup unless you manually screw around with them, which means you might miss some or forget some and lose them forever.

OP the bug you're having is something I've experienced regularly as well for the past several months. I've reported it, Apple is aware of it (and closed it as duplicate) but it's still there. I'm starting to think Apple's OS X department is just a bunch of script kiddies at this point.

Can you check if you're also seeing "Spotlight[343]: XPC connection was invalidated" in your Console at the time of the hang? Or any similarities between your Console and mine (see my original post)?
Also, how often does it happen to you, and does it happen in various apps, or just Safari?

 

[Weaselboy]

Looking at the Etrecheck report, the very first thing I would do is get rid of the Safari extension SafariKeywordSearch. From the Github site, that extension has not been updated in over two tears and may no longer be compatible with Safari under El Capitan.

If that does not fix it I would get rid of all the Steam launch agents and startup items you have. My next suspect would be the Wacom drivers.

 

[baryon]

Looking at the Etrecheck report, the very first thing I would do is get rid of the Safari extension SafariKeywordSearch. From the Github site, that extension has not been updated in over two tears and may no longer be compatible with Safari under El Capitan.

If that does not fix it I would get rid of all the Steam launch agents and startup items you have. My next suspect would be the Wacom drivers.

Thanks! I've now uninstalled SafariKeywordSearch (it will be missed though ), though a hang just happened while I was using Photoshop and Safari wasn't open. so I'm almost certain there is no relationship to Safari at all (just that I use it a lot).

If it's the Wacom stuff then I'm out of luck because I need that no matter what... I'll try to see if there's an update for them.

 

[Weaselboy]

Thanks! I've now uninstalled SafariKeywordSearch (it will be missed though ), though a hang just happened while I was using Photoshop and Safari wasn't open. so I'm almost certain there is no relationship to Safari at all (just that I use it a lot).

If it's the Wacom stuff then I'm out of luck because I need that no matter what... I'll try to see if there's an update for them.

You might try removing that stuff anyway just to prove what the issue is. Then at least you know where to focus your efforts. I seem recall seeing other posts here about Wacom drivers causing trouble with El Capitan.

 

[baryon]

The problem was solved by updating to 10.11.2.

Anything I would have done to fix this would have just been a futile attempt and a waste of time.

Note to most people with similar problems: instead of spending weeks troubleshooting your machine, deleting apps you depend on, deleting files you need, reinstalling software you need, migrating files that are already in their correct location, trying things that seem unrelated but since everything affects everything it could be related, etc, go outside and enjoy the sun. There are people working for Apple who are paid to do this. Wait until the next OS X update, maybe it fixes it. It probably will. If it doesn't, you've lived 3 months with the issue by then, might as well ignore it. I'm tired of troubleshooting computers. If it works, great, if it doesn't, too bad.

 

[Ebenezum]

The problem was solved by updating to 10.11.2.

Anything I would have done to fix this would have just been a futile attempt and a waste of time.

Note to most people with similar problems: instead of spending weeks troubleshooting your machine, deleting apps you depend on, deleting files you need, reinstalling software you need, migrating files that are already in their correct location, trying things that seem unrelated but since everything affects everything it could be related, etc, go outside and enjoy the sun. There are people working for Apple who are paid to do this. Wait until the next OS X update, maybe it fixes it. It probably will. If it doesn't, you've lived 3 months with the issue by then, might as well ignore it. I'm tired of troubleshooting computers. If it works, great, if it doesn't, too bad.

I'm glad the problem is solved.

However I would suggest waiting until .5 if you are using Mac for work because the odds of encountering problems are much less likely compared to installing new OS shortly after release.

 

[baryon]

I'm glad the problem is solved.

However I would suggest waiting until .5 if you are using Mac for work because the odds of encountering problems are much less likely compared to installing new OS shortly after release.

Yep I'm definitely doing that next time...