pingpong9

Q: messed up computer (10.9.4) after migration to SSD - permissions or java problem?

thanks in advance for reading!  I have a doozy:  I moved my hdd to my optibay and installed a new SSD into my main hdd bay (mbp late 2011)

transferred data from hdd to ssd using superduper

so the ssd is now a clone of the old hdd (and in the same place as the old hdd) and the ssd is the startup

BUT

seems permissions are wonky?

not sure what it is.  possibly java is a problem -- maybe via permissions?

 

here's the symptoms:

browsers/finder work great (faster with ssd)

but MANY apps just wont load or are wonky.

bluestacks won't load-- wont even get to the "loading" animation...  (have re-installed numerous times)

metasearch on vuze won't work -- I see it for 7 seconds and then it vanishes.

other apps wont load -- the problem seems to be java related maybe?  I'm not clear.

 

steps I've taken to resolve:

(all did nothin)

re-installed every app that wasn't working (ug!  endless!  appcleaner etc!  hard to say how far they were uninstalled but seemed pretty thorough)

 

re-installed OSX 10.9.4

 

repaired permissions in a few ways on ssd

 

even "Reset Home Folder permissions and ACLs"  via rebooting with cmnd+r

 

downgraded to java 6 (did nothin) then back up to java 7 (nothin)

erased all the java caches etc I could find

 

now I'm not really sure WHAT is going on here -- but my suspicion is that there's something funny about the superduper migration and permissions  (everything was working when I upgraded to 10.9 a month ago)

I noticed: when I open a lot of folders, like utilities etc, they're read-only.  huh?  I don't think that was true, before.

to fix this I made the possible mistake of GetInfo/giving read-write privileges to everyone and "applied to enclosed items"

maybe that was dumb?

either way, after rebooting and repairing permissions, it seems the read-only structure of much of the new ssd is back

(I'm logged in as my main account as always -- is this not root? I'm never clear on root stuff...) (with mavericks, before the migration, I was able to run all these apps fine.  but none of these odd "read-only" icons were showing up in my folders)

so maybe bad permissions -- or bad java -- is the reason apps won't connect to the internet?  sometimes they crash when running animations.

 

ANY help would be so appreciated!  already wasted many full days on this!  ack! 

Posted on Jul 3, 2014 8:11 PM

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Q: messed up computer (10.9.4) after migration to SSD - permissions or java problem?

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  • by Loner T,

    Loner T Loner T Jul 4, 2014 2:11 PM in response to pingpong9
    Level 7 (23,613 points)
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    Jul 4, 2014 2:11 PM in response to pingpong9

    Can you unmount the HDD from Finder/DU and retest your sample application(s)? The problem with cloning is that paths in applications and links can cause strange behavior if they reference across volumes.

  • by pingpong9,

    pingpong9 pingpong9 Jul 4, 2014 5:10 PM in response to Loner T
    Level 1 (0 points)
    Jul 4, 2014 5:10 PM in response to Loner T

    super smart, Loner T!  it didn’t fix stuff but it's interesting what happened:

    after dismounting my HDD and loading apps from my SSD...

    bluestacks (one of the unloading apps) suddenly showed it's "loading..." animation.  progress!  that's partly why I was thinking I had a java problem (not knowing much about java...)

    but then it still didn’t load or work. 

     

    I then uninstalled all the messed up apps, kept the HDD un-mounted, then re-installed the apps and...  no change 

     

    same with the other apps.  no progress.

    but yes, I can see it could be about pathways and stuff, especially because I have not yet deleted my library+ apps from the HDD

  • by Loner T,

    Loner T Loner T Jul 4, 2014 5:32 PM in response to pingpong9
    Level 7 (23,613 points)
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    Jul 4, 2014 5:32 PM in response to pingpong9

    Would you care to post the output of diskutil list and diskutil cs list form your setup? Remove any personal information as you see fit.

     

    There are caches and plists, which usually can be problematic, based on the assumptions made by application designers.

     

    If you want to dig deeper, Under Applications -> Uitlities -> Activity Monitor, if you click on the CPU tab and look at the processes, you can select a specific process or Application and click on the 'i'(nfo/nspect) button. One of the tabs in the resulting window is the 'Open Files and Ports' tab, you can try to look at a specific application that does not work and see what is in this list when it gets started.

     

    You may also want to look for any "verbose" or "debug" options that may be available for the misbehaving applications or logs, that may provide an insight. Here is an example of the screen referenced.

     

    OpenFilesAndPorts.png

  • by pingpong9,

    pingpong9 pingpong9 Jul 5, 2014 1:38 PM in response to Loner T
    Level 1 (0 points)
    Jul 5, 2014 1:38 PM in response to Loner T

    okay!  will get on that.

     

    was wondering if it might have to do with HOW I backed up everything, so here's a rundown of my process:

    used superduper to make a full clone of the internal mbp2011 HGST HDD onto an external LACIE firewire HDD. 

    Still connecting the LACIE by firewire, restarted the computer/ booted from the external LACIE (via firewire) and checked that everything worked.  It did -- tho admittedly, I did not run EVERY application -- just ran osx + firefox and saw that all my data files were where I'd thought they'd be.  ran ms word, too, I think.

     

    Then: moved HDD into optibay.

    (Then: endless process of having to "downclock" the speed of the HDD to run in the optibay (ugggg) -- had to re-install the optibay etc + then take it back out-- rough.)

    then: put the new SSD into the main-hdd-bay.

    then used superduper to copy the HDD onto the SSD

    used a superduper script that said: "DONT INCLUDE the movies data/or itunes folders" -- planning to keep those on the hdd.

    and voila.  had a supposedly perfect clone of the HDD (minus movie/itunes files) on the SSD, which then booted fine and seems normal except for the weird read/write issues and the odd application behavior.

     

    could using the superduper script that omitted copying the itunes/movie files have done something bad??  seems very unlikely to me.  (I've used the same script many times before -- it's part of superduper's process.)

     

    it seems unlikely that the script is at fault, as well, because now BOTH the HDD and the SSD have odd "read/write" rules.  (maybe because they were moved and that makes stuff go nuts??)

    I fixed the HDD odd authentication-requests (requiring password to simply move movie files etc) by opening getinfo+ checking the box "ignore ownership on this volume".  done.  no more odd authentication requests.  but that was on the HDD -- there seems to be no such box for the SSD/startup volume.

     

    (again, the folders that have required authentication / read-only (which never happened before) are now all on the SSD, and they are:

    ssd main volume folder ...users ....system ...library ...utilities  (not applications)

     

     

    none of the messed up applications require re-activation.  all are freeware.  and: oddly: reinstalling them has not helped!  so bizarre!

    and I worked pretty hard on REALLY uninstalling (using appcleaner etc)

    intriguingly, when I UNmount the HDD, and booted apps from the SSD, some apps allowed a bit of animation to their loading screens (which they DIDNT at first when they were failing to load -- hence my fear that this might relate to java) but then still ... the apps did not load/work      (so this means...?  some messed up pathways related to the HDD being mounted?)

     

    trying to load these applications from the HDD/in the optibay   also fails.

    and oddly: trying to load these applications from booting from the LACIE external HDD also fails!  huh.  (still a pathways thing?)

    I have an old backup from a week ago (on another external HDD) and that works fine... loads all the apps when you boot from it...

     

    also: repaired permissions and ran DiskWarrior on both -- no effect

    (would doing a "scavenge" rebuild of the desktop via diskwarrior help?)

     

     

    lastly, if it’s possible that the format for the two disks was different in some way:  both file systems for the HDD and the SSD are Mac OS Extended (Journaled) -- on the HDD and the cloned SSD

    but this raises an interesting point -- when I upgraded to Mavericks from SnowLep, I had to "turn on journaling," which maybe could've gone wonky?  not sure.

    I "converted"  my hdd to "journaled" and then used mavericks with no problems on the hdd for a month.

    then, with the moving these drives around and such, that's when the difficulty began.

     

    okay: off to activity monitor! 

  • by pingpong9,

    pingpong9 pingpong9 Jul 5, 2014 1:48 PM in response to Loner T
    Level 1 (0 points)
    Jul 5, 2014 1:48 PM in response to Loner T

    okay!  here's what you mentioned, Loner T.

    no clue what this all means, but I was interested to see the private/var anomalies in the middle and end-- maybe those mean something?  clueless.

     

    not sure how to access "verbose" or debug options.

     

    LOADED: BLUESTACKS app

     

     

     

    /

    /Applications/BlueStacks.app/Contents/MacOS/uHD-Frontend

    /System/Library/ColorSync/Profiles/Generic RGB Profile.icc

    /System/Library/ColorSync/Profiles/sRGB Profile.icc

    /System/Library/ColorSync/Profiles/Generic Gray Profile.icc

    /System/Library/ColorSync/Profiles/Generic Gray Gamma 2.2 Profile.icc

    /System/Library/Caches/com.apple.IntlDataCache.le.kbdx

    /System/Library/PrivateFrameworks/CommerceKit.framework/Versions/A/Frameworks/Co mmerceCore.framework/Versions/A/CommerceCore

    /System/Library/PrivateFrameworks/GPUSupport.framework/Versions/A/Libraries/libG PUSupport.dylib

    /usr/share/icu/icudt51l.dat

    /System/Library/PrivateFrameworks/FamilyControls.framework/Versions/A/FamilyCont rols

    /Applications/BlueStacks.app/Contents/Resources/BackButton.png

    /Applications/BlueStacks.app/Contents/Resources/MenuButton.png

    /Applications/BlueStacks.app/Contents/Resources/HomeButton.png

    /Applications/BlueStacks.app/Contents/Resources/SettingsButton.png

    /Applications/BlueStacks.app/Contents/Resources/FullScreenButton.png

    /Applications/BlueStacks.app/Contents/Resources/LoadingText.png

    /Applications/BlueStacks.app/Contents/Resources/LoadingBranding.png

    /Applications/BlueStacks.app/Contents/Resources/Cursor_0_Primary.png

    /Applications/BlueStacks.app/Contents/Resources/Cursor_0_Secondary.png

    /Applications/BlueStacks.app/Contents/Resources/Cursor_1_Primary.png

    /Applications/BlueStacks.app/Contents/Resources/Cursor_1_Secondary.png

    /Applications/BlueStacks.app/Contents/Resources/Cursor_2_Primary.png

    /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.fram ework/Versions/A/Resources/Extras2.rsrc

    /Applications/BlueStacks.app/Contents/Resources/Logo.png

    /Applications/BlueStacks.app/Contents/Resources/LoadingProgress.gif

    /Applications/BlueStacks.app/Contents/Resources/Cursor_2_Secondary.png

    /Applications/BlueStacks.app/Contents/Resources/Cursor_3_Primary.png

    /Applications/BlueStacks.app/Contents/Resources/Cursor_3_Secondary.png

    /private/var/folders/pk/cqp8pydd5qb9llzv89ghykr80000gn/C/com.apple.LaunchService s-044501.csstore

    /System/Library/Fonts/Helvetica.dfont

    /System/Library/Keyboard Layouts/AppleKeyboardLayouts.bundle/Contents/Resources/AppleKeyboardLayouts-L.d at

    /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/Resources/SArtFile .bin

    /System/Library/Fonts/LucidaGrande.ttc

    /System/Library/PrivateFrameworks/CoreUI.framework/Versions/A/Resources/ArtFile. bin

    /Applications/BlueStacks.app/Contents/Resources/LoadingBackground.png

    /System/Library/Extensions/AppleIntelHD3000GraphicsGLDriver.bundle/Contents/MacO S/AppleIntelHD3000GraphicsGLDriver

    /System/Library/Extensions/AMDRadeonX3000GLDriver.bundle/Contents/MacOS/AMDRadeo nX3000GLDriver

    /usr/lib/dyld

    /private/var/db/dyld/dyld_shared_cache_i386

    /tmp/bst-pga-server

    /dev/null

    /dev/null

    count=2, state=0x2

    /System/Library/Frameworks/Carbon.framework/Versions/A/Frameworks/HIToolbox.fram ework/Versions/A/Resources/Extras2.rsrc

    /Users/pfunk/Library/Logs/BlueStacks App Player/FrontendApp.log

    ->0x67384bbcb0e9c4b9

    *:54951

    localhost:ndmp

    localhost:ndmp

  • by Loner T,

    Loner T Loner T Jul 5, 2014 2:18 PM in response to pingpong9
    Level 7 (23,613 points)
    Safari
    Jul 5, 2014 2:18 PM in response to pingpong9

    1. Do you still have the LaCIE intact from which you can test your applications? Please unmount both SSD and HDD first and boot from LaCIE.

    2. If you can post the output of diskutil list and diskutil cs list, it would be helpful. I have seen cases under Mavericks, where installing a SSD and an existing HDD ended up creating a Fusion drive. If you have done a lot of poking with the HDD to make it work (speed adjustments), and the journaling recovery had issues on this resulting Fusion drive, it can lead to file system corruption. Hence my request to see what the OS considers these HDD/SSD disk combination to be.

    3. Your Bluestack file list does not show anything out of ordinary.

    4. Cloners can sometimes (accidentally or intentionally) ignore ACLs, which are hard to debug and address (as mentioned). If ACLs are copied and not restored in the original order, it can cause issues. ACLs are almost like a sieve, and if the order is broken, your applications may not execute, or some file it needs may not be readable when you start the application. Bad things happen. This can be a very involved discussion best left for a different thread.

  • by pingpong9,

    pingpong9 pingpong9 Jul 5, 2014 4:11 PM in response to Loner T
    Level 1 (0 points)
    Jul 5, 2014 4:11 PM in response to Loner T

    diskutil list

     

    /dev/disk0

       #:                       TYPE NAME                    SIZE       IDENTIFIER

       0:      GUID_partition_scheme                        *500.1 GB   disk0

       1:                        EFI EFI                     209.7 MB   disk0s1

       2:                  Apple_HFS SSD 500gb               499.2 GB   disk0s2

       3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3

    /dev/disk1

       #:                       TYPE NAME                    SIZE       IDENTIFIER

       0:      GUID_partition_scheme                        *1.0 TB     disk1

       1:                        EFI EFI                     209.7 MB   disk1s1

       2:                  Apple_HFS HDD 1tb                 999.3 GB   disk1s2

       3:                 Apple_Boot Recovery HD             650.0 MB   disk1s3

     

     

    diskutil cs list

     

    No CoreStorage logical volume groups found

  • by pingpong9,

    pingpong9 pingpong9 Jul 5, 2014 4:16 PM in response to Loner T
    Level 1 (0 points)
    Jul 5, 2014 4:16 PM in response to Loner T

    regarding the Lacie backup -- I can boot from it fine, but then it DOES have some problems with *some* of the same applications.  so odd. 

    I did NOT "repair permissions" on the lacie, yet.  I haven't done any fiddling with the lacie.  and yet, unlike the HDD it cloned, it does have some problems with some applications...  however, not all.  odd.

    the backup from a few days before, on another external Seagate, has NO problems booting or running apps.

  • by Loner T,

    Loner T Loner T Jul 5, 2014 4:45 PM in response to pingpong9
    Level 7 (23,613 points)
    Safari
    Jul 5, 2014 4:45 PM in response to pingpong9

    I suggest that the LaCIE be kept intact for future debugging/analysis of SuperDuper issues. You can, if you have the time and inclination, note down which applications have issues and which do not to further aid in such analysis, but that depends on how much you want to invest in this.

     

    It is good that you do not have Fusion drive.

     

    I personally prefer TM, rather than third-party backup/restore tools.

     

    Typically applications get started using scripts which may have additional command-line options, or may have a Preferences menu which allows logging. Pick the worst-offending applications that you have and see if this exists for that specific application or not.

     

    Were there any Apple OSX software updates applied between the Seagate and LaCIE backups to your machine?

  • by pingpong9,

    pingpong9 pingpong9 Jul 5, 2014 4:59 PM in response to Loner T
    Level 1 (0 points)
    Jul 5, 2014 4:59 PM in response to Loner T

    sorry -- yes -- shudda been more clear:  the lacie is 10.9.3  mavericks

    the seagate is 10.6.8 !

    so the one that works *fine* is the snow leopard version. (10.6.8 routed stuff differently?)

    but this is not a version I can go back to at this point — I can’t lose all the work I’ve done.

     

    amusingly: since all the fiddling with the SSD, the SSD is now 10.9.4 -- because when I did a clean install of the OS, it got the new update from the interwebs...

     

    so:  seagate 10.6.8 -- works /too old

    lacie 10.9.3 -- somehow worked fine when originally cloned, but now has some trouble with a few apps

    internal SSD 10.9.3 at first -- messed up.  then turned to 10.9.4 -- still messed up / odd read-write permissions all over. 

         (the original HDD, now in optibay, also had odd read/write stuff till I told it to "ignore ownership" -- that's not somehting I can do with the SSD?)

  • by Loner T,

    Loner T Loner T Jul 5, 2014 5:16 PM in response to pingpong9
    Level 7 (23,613 points)
    Safari
    Jul 5, 2014 5:16 PM in response to pingpong9

    Can I suggest that you boot from the Seagate and note the Application architecture that is used for each application that is not currently working and verify that Mavericks actually supports it? Between Snow Leopard (10.6.8) and Mavericks (10.9.4), quite a few applications changed architectures and support for hardware types (mainly PPC vs Intel, etc.)?

     

    I think your issue is very likely related to such differences. I assume the Seagate is still running 10.6.8 and everything works as designed.

  • by pingpong9,

    pingpong9 pingpong9 Jul 5, 2014 5:28 PM in response to Loner T
    Level 1 (0 points)
    Jul 5, 2014 5:28 PM in response to Loner T

    good thought, loner T, but insanely, everything worked perfect on 10.9.3 on the original HDD, so mavericks isn't to blame... 


    it IS odd that the Lacie backup of this perfectly working 10.9.3 HDD -- now that is having problems.  noooo idea why.  seems related to something pathway related or corruption or permissions?

     

    so yes, the seagate 10.6.8 definitely worked.  but the internal HDD 10.9.3 also worked perfect until I moved the drives around...

  • by pingpong9,

    pingpong9 pingpong9 Jul 5, 2014 5:37 PM in response to Loner T
    Level 1 (0 points)
    Jul 5, 2014 5:37 PM in response to Loner T

    does this stuff from the console help?

     

    7/5/14 5:51:37.994 PM uHD-Frontend[1800]: CGContextSetFillColorWithColor: invalid context 0x0. This is a serious error. This application, or a library it uses, is using an invalid context  and is thereby contributing to an overall degradation of system stability and reliability. This notice is a courtesy: please fix this problem. It will become a fatal error in an upcoming update.

     

    7/5/14 5:53:14.300 PM WindowServer[119]: disable_update_timeout: UI updates were forcibly disabled by application "BlueStacks App Player" for over 1.00 seconds. Server has re-enabled them.

     

     

    7/5/14 5:53:16.094 PM WindowServer[119]: common_reenable_update: UI updates were finally reenabled by application "BlueStacks App Player" after 2.79 seconds (server forcibly re-enabled them after 1.00 seconds)

  • by Loner T,

    Loner T Loner T Jul 5, 2014 6:49 PM in response to pingpong9
    Level 7 (23,613 points)
    Safari
    Jul 5, 2014 6:49 PM in response to pingpong9

    Looking at the BlueStacks App details, it is a virtualization layer (like a JVM or Vbox) which allows applications architected for one OS to run on another. Underlying OS updates will usually break such applications, unless the virtualization layer coordinates updates with the OS. There is no compatibility information that I can find except this

     

    http://support.bluestacks.com/hc/en-us/articles/202028178-Mac-OS-X-Installation- Requirements

     

    There is nothing on Mavericks or Yosemite. Hence YMMV. If it works correctly on SL (10.6.8), Mavericks (10.9.3) may bring one set of issues, 10.9.4 will just add to such issues.

     

    Finding issues in applications which are based on timers or events across OS versions gets even harder.

     

    To eliminate HW-specific issues, if you have another MAC which can run the Seagate backup and everything works fine, then HW can be eliminated. I have seen Adobe Flash Player version (14.0.0.x) break on specific HW, and the recommended solution was to go back to Adobe Flash Player 12.x.x.x.

     

    I would also suggest that applications should get prioritized in the order of criticality and need and specific issues should be analyzed otherwise this can take a long time to resolve.

     

    I do not think there is a Silver Bullet which will allow you to fix all your issues.

  • by pingpong9,

    pingpong9 pingpong9 Jul 6, 2014 5:19 PM in response to Loner T
    Level 1 (0 points)
    Jul 6, 2014 5:19 PM in response to Loner T

    you rock, Loner T -- thanks for explaining.

    I'm not sure exactly what to do at this point.

     

    re: the fact that many folders are read-only: is this something I can fix without doing some massive permissions overhaul?  I feel like maybe important application paths aren't being allowed because the files enclosed in these locked folders can't be accessed.

    (can I just use getinfo to give myUserName read/write access to these specific folders -- WITHOUT clicking "apply to enclosed items"?)

     

    or:

    I found this but it seems risky?  chmod 777 on the entire volume?

    terminal/Code:       sudo chmod 777 /Volumes/YOURHARDDRIVE

    Then press return and put in your password and let it run until you get another prompt. After it finished immediately reboot your Mac and this should help

     

    I would like to be able to do stuff on my computer (like before) without typing in an authorization all the time...

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