Blinking dot under finder in dock, mostly locked up

[glindauer]

So Yosemite has been occasionally locking up on my iMac. This started after the last update. The disk check found no problems. I have a bugreport (Bug ID 19678398) at https://bugreport.apple.com.

The latest is that I now have a 1 hertz blinking dot under finder. I have a solid dot under the X11 icon (I previously had opened it) and I am able to open an X11 terminal window.

Are there any diagnostics I should run from the shell to try to figure out what is going on?

I'd ask the bugreport guys, but (1) my laptop has snow leopard and apparently the bugreport website only supports lion on up, and (2) it takes them forever to respond, so I suspect I will have rebooted my iMac by the time they get back to me.

Thanks,
Greg

 

[glindauer]

Now it says "Device not configured"

Well, trying to troubleshoot from terminal may not work after all. From bash, ls shows no files in /usr/bin!

But, if I type /usr/bin/sudo, it says
bash: /usr/bin/sudo: Device not configured.

Same if I type /usr/bin/less or any other file that should be in /usr/bin.
If I type simply "less" at the command line, it tells me
less: command not found

If I type /usr/bin/bash (or /usr/bin/dummy for that matter), it correctly tells me "No such file or directory"

I'd love to hear any ideas.

Greg

 

[Taz Mangus]

Well, trying to troubleshoot from terminal may not work after all. From bash, ls shows no files in /usr/bin!

But, if I type /usr/bin/sudo, it says
bash: /usr/bin/sudo: Device not configured.

Same if I type /usr/bin/less or any other file that should be in /usr/bin.
If I type simply "less" at the command line, it tells me
less: command not found

If I type /usr/bin/bash (or /usr/bin/dummy for that matter), it correctly tells me "No such file or directory"

I'd love to hear any ideas.

Greg

Have you tried doing a repair permissions? If you really have lost /usr/bin then you will need to do a reinstall.

 

[glindauer]

/usr/bin reappeared after hard boot

As usual, trying to "soft boot" through the apple menu resulted in the SBOD indefinitely. I went ahead and hard booted. When the system came up, it was fine. /usr/bin now shows everything as anticipated, with no explanation for what happened.

/var/log/system.log shows these items around the time I hard booted:

Feb 26 19:00:14 iMac.local emond[6743]: SetUpLogs: opening /Library/Logs/EventMonitor/EventMonitor.error.log
Feb 26 19:00:14 iMac com.apple.xpc.launchd[1] (com.apple.emond): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Feb 26 19:00:24 iMac.local emond[6745]: SetUpLogs: uid = 0 gid = 0
Feb 26 19:00:24 iMac.local emond[6745]: SetUpLogs: opening /Library/Logs/EventMonitor/EventMonitor.error.log
Feb 26 19:00:24 iMac com.apple.xpc.launchd[1] (com.apple.emond): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Feb 26 19:00:33 iMac.local configd[25]: [0x7f97a1f50cd0] [m]DNS query timeout (query time = 35.135028), [46TE]
Feb 26 19:00:34 iMac.local emond[6746]: SetUpLogs: uid = 0 gid = 0
Feb 26 19:00:34 iMac.local emond[6746]: SetUpLogs: opening /Library/Logs/EventMonitor/EventMonitor.error.log
Feb 26 19:00:34 iMac com.apple.xpc.launchd[1] (com.apple.emond): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
Feb 26 19:00:37 iMac kernel[0]: PM response took 1008 ms (26, powerd)
Feb 27 17:24:09 localhost bootlog[0]: BOOT_TIME 1425075849 0
Feb 27 17:24:29 localhost syslogd[16]: Configuration Notice
.
.
.

As in the prior times the system has appeared to be locked up upon waking from sleep, the log stopped showing things prior to the wakeup (on 2-27-2015) which led to the lockup. Terminal was up and running from before 1100 (am) on 2-27-15 but nothing new logged until I hard booted the system.

I'm going to run disk utility (again)-- if it's the disk, maybe it's deteriorated enough to now finally show an error.

 

[glindauer]

Verify Disk found no problems

Verifying volume “iMac Internal Hybrid Drive”Verifying file system.Using live mode.Performing live verification.Checking Journaled HFS Plus volume.Checking extents overflow file.Checking multi-linked files.Checking catalog hierarchy.Checking extended attributes file.File system check exit code is 0.

Verify on the drive itself says
Verifying partition map for “ST500LM000-1EJ162 Media”Checking prerequisitesChecking the partition listChecking for an EFI system partitionChecking the EFI system partition’s sizeChecking the EFI system partition’s file systemChecking all HFS data partition loader spacesChecking booter partitionsChecking booter partition disk0s3Verifying file system.Checking Journaled HFS Plus volume.Checking extents overflow file.Checking catalog file.Checking multi-linked files.Checking catalog hierarchy.Checking extended attributes file.Checking volume bitmap.Checking volume information.The volume Recovery HD appears to be OK.File system check exit code is 0.Checking Core Storage Physical Volume partitionsThe partition map appears to be OK

Information on the 500GB drive says:
Name : ST500LM000-1EJ162 Media
Type : Disk

Partition Map Scheme : GUID Partition Table
Disk Identifier : disk0
Media Name : ST500LM000-1EJ162 Media
Media Type : Generic
Connection Bus : SATA
Device Tree : IODeviceTree:/PCI0@0/SATA@1F,2/PRT0@0/PMP@0
Writable : Yes
Ejectable : No
Location : Internal
Total Capacity : 500.11 GB (500,107,862,016 Bytes)
Disk Number : 0
Partition Number : 0
S.M.A.R.T. Status : Verified
Raw Error Rate : 0000031A6330
Spinup Time : 000000000000
Start/Stop Count : 000000000F88
Retired Sectors Count : 000000000000
Seek Error Rate : 000000076C77
Power-On Hours : 000000000325
Spinup Retries : 000000000000
Power Cycles : 0000000019A7
Emergency Retract Count : 0000000001FE
Load/Unload Cycles : 00000000D294
HDD Temperature : 000F00000019
Pending-Sparing Count : 000000000000
Uncorrectable Sector Count : 000000000000
UltraDMA CRC Errors : 000000000000
FFS Trigger Count : 000000000000

I also repaired permissions. The results are is in the attached files.