? in login box, can't type password can type p/w in safe mode

[Stubby]

Had a problem with this Mac Pro (2009) for a while, sometimes when i open an app from the dock it opens the applications
folder not the app it's self, this tells me it's weird time, all sorts of other things don't happen, web pages don't open & mouse clicks don't respond. I have up to now performed the IT joke turn it off & on this seemed to cure the problem for a while.

Things have now got a lot worse as stated above, in single user i could not log in, so i started in safe mode and disabled
security log in, so i can now get in but can't type anything in web browser or password in permission to make changes box.
There is nothing wrong with keyboards (one WIFI one wired) as i can type in safe mode, i was advised this could be a
corrupt settings preferance file this has been deleted without any difference.

This problem started while running OSX 10.10 i thought going to 10.11 would cure it, WRONG.
This was a proper refurbished Mac Pro 3.46gh 6 core Intel, 64 gig ram, 1tb Apple SSD 4 x 2gb drives one configered as
time machine. When this latest problem reared it's ugly head i did try a time machine restore from previous day, again
no joy!

The machine is now unusable any help will be most appreciated!

 

[honestone]

It sounds like you could have disk directory issues. Have you ever done any disk cleanup/maintenance/repairs?

Also, did you just upgrade from OS 10.10 to OS 10.11 "in place", that is, by basically having OS 10.11 "overwrite" OS 10.10? Also, are you using the latest version of El Capitan, OS 10.11.6?

What you could try is to boot your back to the (hidden) Recovery HD partition, and use Disk Utility to verify and repair your disk/disks. This link explains how to boot to that partition, and what its capabilities are:

https://support.apple.com/en-us/HT201314

I wonder if your Time machine backup/backups is/are "corrupt"?

Also, you might want to consider getting a more robust disk cleanup/maintenance/repair program, like either TechTool Pro or Disk Warrior. Also, Onyx is another excellent, free disk cleanup program. You can get it from here:

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

Note, though, that there is a version for each Mac OS. Not sure which one you need to get, as you have been running both OS 10.10 and OS 10.11. One thing that Onyx will help with is Repairing Permissions.

 

[Stubby]

Hello honestone i failed to mention i have run first aid in disk utility and also done all the checks in Onyx, both say disk is ok, El Capitan was done as an erase install (fresh) and is up to date 10.11.6
time machine is also backed up externally in case of total machine failure (although i can just pull the drive on the Pro)
I ran permissions repair in Onyx as on OSX you no longer have access to permissions repair in disk utility i am also using the latest version of Onyx.
Just seems such a large problem and everything i know how to do checks out.

 

[honestone]

Hello honestone i failed to mention i have run first aid in disk utility and also done all the checks in Onyx, both say disk is ok, El Capitan was done as an erase install (fresh) and is up to date 10.11.6
time machine is also backed up externally in case of total machine failure (although i can just pull the drive on the Pro)
I ran permissions repair in Onyx as on OSX you no longer have access to permissions repair in disk utility i am also using the latest version of Onyx.
Just seems such a large problem and everything i know how to do checks out.

Thanks for the update.

Sounds like you have been pro-active with disk cleanup/maintenance/repairs, and as you so correctly observe, Onyx repairs permissions, which was dropped in Disk Utility with El Capitan. And, an erase/install of El Capitan (and I assume a subsequent use of Migration Assistant to "migrate"/copy needed stuff from your Time Machine backup was also done) was/is prudent too.

Just to confirm, did you run First Aid from the (hidden) Recovery HD partition? Given the type of backups you have been making, that would be the only way to have those tasks performed in an "isolated" manner. Myself I use SuperDuper! for my backups, running it after using Onyx and TechTool Pro.

I wish I had something else to offer for suggestions. I'm not even sure if a more robust disk maintenance program like TechTool Pro or Disk Warrior would help. Do you have any idea how old the drives (I believe the one inside your MacPro is an SSD)? That could be a reach, as SSDs rarely go bad, especially after little usage (in terms to time).

Just to add one more thing: I see where you stated you have an Apple 1 TB SSD inside the machine. Another individual on one of these forums had an issue with a "lightly" used Apple SSD inside his machine. Strange, as Apple tends to use SSDs manufactured by Samsung, and such SSDs are (supposedly) the best. I have two "pure" Samsung SSDs, and the one that came inside my 13" mid-2013" MacBook Air, and they perform flawlessly.

I guess the last (and ugly) possibility is that the logic/motherboard has issues that also could be beyond repair.

 

[Stubby]

Yes that's correct i did use migration assistant with time machine, after doing much reading i decided this was the safest route to take.
I didn't run the first aid from the hidden backup, i am going to do that now, although it did check out with Onyx.
All the drives are two years old my main OSX disk is 1tb Apple ssd being an Apple drive it supports 'trimming' (i think) should help
with longevity, the other drives are disk drives.
I do take your point about the isolated test in the hidden partition, thanks for your input i will post the outcome.
The Mac Pro i have is the old 5.1 tower type not the newer rubbish bin type.

 

[honestone]

OK, that sounds good. Just in case, this link explains how to boot to that partition, and what it can do:

https://support.apple.com/en-us/HT201314

Also, are you using one of the "standard" HDDs for your backups?

 

[Stubby]

Thanks for that i have done it before but ages ago. Yes i use one internal non ssd and one external non ssd
for a second back up. I am using my old Macbook Pro that i repaired the mother board on when it died, not
to shabby with electronics just wish i was a bit better with the software side!

 

[Stubby]

Carried that out and disk checks out ok. Seems very odd that i can't type anything, i have an app called 'Deeper' part of the Onyx family i think
might try that in safe mode as i can type in that enviroment, the other clue i may pursue is the '?' in the password box, Apple tent to use ? when the
system can't find something eg a hard drive.

 

[honestone]

That "?" designation is (somewhat) typically used for, as you say, when the "boot" hard drive (SSD, in your case, from what I understand)) can't be "located".

Also, Deeper does not really contain any cleanup functions. Titanium software has another program called Maintenance, but it seems its functions already are performed by Onyx.

It just seems there are two possibilities:

1. The Volume disk directory seems to be somewhat "hosed". Both TechTool Pro and Disk Warrior can rebuild that directory. Disk Utility "supposedly" does it also, but I trust TechTool Pro much more. And TechTool Pro can perform a number of other useful functions.

2. There is an issue with the logic/mother board.

It's too bad this is not March, as my wife and I plan on visiting our oldest son at that time, who lives in London. The London "piece" will be in parts, as in between, we will visit the Canary Islands for about 8 to 10 days or so.

In any event, I guess there is one more thing you can try, and this might help in determining if there is a much deeper issue with the SSD. If you have enough room on your HDD that is connected externally to your machine, you could first partition it, leaving the Time machine part "as is" (although the size will be smaller), and having the other partition be somewhat larger than the total space you are using on the Apple SSD for the "boot" process. You can then use SuperDuper! to make a bootable backup/clone of the Apple SSD onto that "new", empty partition. Note that I said bootable. Once that backup is done, you can try and boot your Mac from that partition. If it works fine, and you can do things normally, then there is a definite, deeper issue with the Volume structure of the Apple SSD.

This link describes SuperDuper!:

http://www.shirt-pocket.com/SuperDuper/SuperDuperDescription.html

It is available in "demo" mode, and works just fine, although it runs slower in demo mode. I have been using it for a number of years, prefer it WAY over Time Machine, and it works extremely well. Recovery is much, much easier with it than with a Time Machine backup. In actuality, given that it is bootable, it's just about the same as having another machine!

 

[Stubby]

I realise deeper was not the way to go having now looked at it (never opened before) That's a great idea re patitioning the disk i have used SuperDuper in the past in trial mode and have just downloaded it again
i also have Carbon Copy Clone (full version) that does similar and can produce a bootable disk. I have plenty of free space on disk only 20gb used.

I don't suspect the mother board in all of this as i would have thought it would have exhibited the same or similar issues in safe mode were that the case, although having said that
i did reset the SMC and V ram, those straws are there to be clutched at i guess!

I think i may wipe the hard drive completely and clone and install my Mac Book Pro as i know this to be in good order, this drive doesn't contain all the apps i have on the Mac Pro so i can then
add my files bit by bit to see if they have an adverse affect also i may try and isolate my virtual machine, Parallels running Windows 8 first
just in case any nasties have got in the back door although i have Explorer disabled and any Windows programs are dowloaded via Firefox on the Mac side of things.

Thanks for the thought re visit in March to the UK, i think if it takes me that long to sort out the tower will be someone's iconic glass table top support and i will be in an asylum!

 

[honestone]

You had never mentioned the existence of the Windows partition on the 1 TB SSD, and that possibly could make trouble shooting more complex. But, if you first Erase and Format the 1 TB SSD, with just the 1 Mac partition, do a clean, "virgin" installation of El Capitan (OS 10.11.6; you'll need the file "Install OSX El Capitan, and (hopefully) it is the latest one from the App Store), and then from your backup/clone of the MacBook Pro, use Migration Assistant to "migrate"/copy the stuff from the MacBook Pro, that should work. Then, as you said, you can add the additional apps that you have on the Mac Pro one by one and see what occurs. Even if all that goes well, the next step would be dealing with the Windows stuff. Hopefully none of that is problematic!

I would think that Carbon Copy Cloner would be enough, but SuperDuper! is good also. One difference, though, is that SuperDuper! does not backup the (hidden) Recovery HD partition, whereas Carbon Copy Cloner does. For me, though, that is not an issue, as 1) it gets created again when one does a clean installation of the Mac OS, 2) I have a much better disk maintenance program in TechTool Pro that is superior to Disk Utility for trouble shooting, and 3) there are a couple of other ways of re-creating that partition. Recently, though, whenever I needed to do a complete recovery for an "issue", I would boot from my most recent SuperDuper! backup, run disk utility from there to Erase and Format my internal drive (SSD, in both cases), do a clean, "virgin" installation of the applicable OS (now that is OS 10.12.2 for me), and then use Migration Assistant to "migrate"/copy stuff from that SuperDuper! backup onto the internal SSD containing the "virgin" OS. That has worked well for me, including the creation of that (hidden) Recovery HD partition.

 

[Stubby]

I use Windows 8 so rarely i'd almost fogot it was on there, thanks for all the advice i'm not going to get a chance to anything till Sunday as work has gone mad and i am having
to do stupid hours!
The Mac Book Prro has never had a Windows partition so that takes one possible problem out the equation although i have had a copy of Parallels on my main machine since
version three without issue. I used some Windows cad programs but with the advent of Fusion 360 in 'the cloud' i now no longer need a copy of Windows and will not be
replacing that partition.
I am going to use SuperDuper for backups in future it seems a good safe way of managing the drive. I need to see if OSX 10.11.6 is still available as i don't want to go
to the new OS yet as i have an expensive Photoshop suit that i feel sure Apple will not support soon (Apple and Adobe seem to have fallen out of bed it seems)
also Apple seem to try and make going in to reverse in terms of OS next to impossible i'm sure that is the reason why you no longer get a recovery disk with a machine.

 

[honestone]

OS 10.11.6 should still be available from the App store. Just click on the "Purchased" tab to see all the stuff you have downloaded from the App Store.

 

[Stubby]

Ok so the Mac Pro is sorted, had lots of issues & Carbon Copy Clone has earnt it's keep! at one point it was telling me it only had 32gb of ram instead of the 64gb that is installed.
I only found the problem because there were some important folders on the desktop (about ten) one being a nearly finished web site that i've been building for my business and
associated folders jpg's of works done & logo's that i've built, anyway important folders that need to be worked on so i copied them to a flash drive and put them on the Mac Book Pro,
after a wile i opened Sublime text and here we go again the apps folder opened instead of the app, i went to the browser sure enough new tabs opening but nothing loading! that
AH-HA moment, took the folders back off and after some messing about all ok. I then went into Mac Pro in safe mode deleted folders changed boot disk to a copy of Mac Book Pro
then deleted the flash drive and cloned the Mac Book Pro to it, got my missing 32gb ram back 979mbs write & 890mbs read. I did cheat and not do the fresh install only because i
use a mobile internet 'dongle' as i live on a boat with no land line and was low on data allowance (needs must)

The only issue now is how to sort out which of the folders is the problem, i would very much welcome any advise programs / method to isolate and investigate these folders i
really don't want to do trial and error but at the same time a lot of work has gone into these folders and need to save what i can!