My hard drive is slower than ever - Late 2009 iMac - help requested

I was testing my hard disk via BlackMagic Disk Speed Test across the network (for copying files from my MacBook Pro to my Late 2009 iMac, and I was shocked at the write speeds.
Because of this, I went to the machine and ran local tests, both BlackMagic and xbench. Suddenly I was horrified when I saw the performance for write operations well below the speeds I'd observed in the past. Luckily, I had saved xbench files so I had the ability to compare old disk tests. In the summer of 2013 running 10.7.3, this same hard drive had an uncached write speed of 116 MB/s [4K blocks] and 94 MB/s [256K block]. Now, the drive running under 10.9.5 is performing very inconsistently, with top speeds around 80 MB/s and averages more like 50 MB/s.
I cannot think of any significant changes to tools or background applications installed since that time, so I ran EtreCheck -- the results of which I'm pasting below.
Any guidance as to what I should test would be greatly appreciated. Thanks for reading! --
Chris
Problem description:
Hard disk slowed to less than half the speed from Mac OS X 10.7.3, as I am now on 10.9.5 and the speed appears to be roughly 40M/s uncached write down from 119M/s previously. I am using the same drive, memory and most of the same applications.
The only large difference is the OS.
EtreCheck version: 2.1.8 (121)
Report generated March 8, 2015 at 3:30:34 PM CDT
Download EtreCheck from http://etresoft.com/etrecheck
Click the [Click for support] links for help with non-Apple products.
Click the [Click for details] links for more information about that line.
Hardware Information: ℹ️
    iMac (27-inch, Late 2009) (Technical Specifications)
    iMac - model: iMac10,1
    1 3.06 GHz Intel Core 2 Duo CPU: 2-core
    12 GB RAM Upgradeable
        BANK 0/DIMM0
            4 GB DDR3 1067 MHz ok
        BANK 1/DIMM0
            4 GB DDR3 1067 MHz ok
        BANK 0/DIMM1
            2 GB DDR3 1067 MHz ok
        BANK 1/DIMM1
            2 GB DDR3 1067 MHz ok
    Bluetooth: Old - Handoff/Airdrop2 not supported
    Wireless:  en1: 802.11 a/b/g/n
Video Information: ℹ️
    ATI Radeon HD 4670 - VRAM: 256 MB
        iMac 2560 x 1440
System Software: ℹ️
    OS X 10.9.5 (13F34) - Time since boot: 3 days 1:55:43
Disk Information: ℹ️
    Hitachi HDE721010SLA330 disk0 : (1 TB)
        EFI (disk0s1) <not mounted> : 210 MB
        myMac (disk0s2) / : 999.35 GB (204.80 GB free)
        Recovery HD (disk0s3) <not mounted>  [Recovery]: 650 MB
    HL-DT-ST DVDRW  GA11N 
USB Information: ℹ️
    Apple Inc. Built-in iSight
    Apple Internal Memory Card Reader 63.86 GB
        LYNX (disk1s1) /Volumes/LYNX : 63.85 GB (57.95 GB free)
    Apple Inc. BRCM2046 Hub
        Apple Inc. Bluetooth USB Host Controller
Firewire Information: ℹ️
    WD My Book 111D 800mbit - 800mbit max
        EFI (disk3s1) <not mounted> : 210 MB
        My Book 2TB (disk3s2) /Volumes/My Book 2TB : 2.00 TB (966.24 GB free)
Gatekeeper: ℹ️
    Mac App Store and identified developers
Kernel Extensions: ℹ️
        /Applications/ExpanDrive.app
    [not loaded]    com.expandrive.filesystems.strongfuse (2.5.6 - SDK 10.6) [Click for support]
        /Applications/NetShade.app
    [not loaded]    foo.tap (1.0) [Click for support]
    [not loaded]    foo.tun (1.0) [Click for support]
        /Applications/Parallels Access.app
    [loaded]    com.parallels.virtualsound (1.0 22641.906168 - SDK 10.6) [Click for support]
        /Applications/Parallels Desktop.app
    [not loaded]    com.parallels.kext.hidhook (9.0 24229.991745) [Click for support]
    [not loaded]    com.parallels.kext.hypervisor (9.0 24229.991745) [Click for support]
    [not loaded]    com.parallels.kext.netbridge (9.0 24229.991745) [Click for support]
    [not loaded]    com.parallels.kext.usbconnect (9.0 24229.991745) [Click for support]
    [not loaded]    com.parallels.kext.vnic (9.0 24229.991745) [Click for support]
        /System/Library/Extensions
    [loaded]    com.globaldelight.driver.BoomDevice (1.1 - SDK 10.9) [Click for support]
    [loaded]    com.globaldelight.driver.VoilaDevice (1.1 - SDK 10.1) [Click for support]
    [loaded]    org.dungeon.driver.SATSMARTDriver (1.1 - SDK 10.6) [Click for support]
Problem System Launch Agents: ℹ️
    [failed]    com.apple.AddressBook.SourceSync.plist [Click for details]
Launch Agents: ℹ️
    [running]    com.epson.eventmanager.agent.plist [Click for support]
    [loaded]    com.google.keystone.agent.plist [Click for support]
    [loaded]    com.oracle.java.Java-Updater.plist [Click for support]
    [running]    com.parallels.mobile.prl_deskctl_agent.launchagent.plist [Click for support]
    [running]    com.parallels.mobile.startgui.launchagent.plist [Click for support]
    [loaded]    org.macosforge.xquartz.startx.plist [Click for support]
Launch Daemons: ℹ️
    [loaded]    com.adobe.fpsaud.plist [Click for support]
    [loaded]    com.cocoatech.pathfinder.SMFHelper7.plist [Click for support]
    [running]    com.daz3d.content_management_service.plist [Click for support]
    [loaded]    com.ea.origin.ESHelper.plist [Click for support]
    [running]    com.freemacsoft.appcleanerd.plist [Click for support]
    [loaded]    com.github.GitHub.GHInstallCLI.plist [Click for support]
    [loaded]    com.google.keystone.daemon.plist [Click for support]
    [loaded]    com.marketcircle.billingspro.accessd.plist [Click for support]
    [loaded]    com.marketcircle.billingspro.backupd.plist [Click for support]
    [loaded]    com.marketcircle.billingspro.configd.plist [Click for support]
    [running]    com.marketcircle.billingspro.httpd.plist [Click for support]
    [running]    com.marketcircle.billingspro.portsd.plist [Click for support]
    [loaded]    com.oracle.java.Helper-Tool.plist [Click for support]
    [loaded]    com.oracle.java.JavaUpdateHelper.plist [Click for support]
    [running]    com.parallels.mobile.dispatcher.launchdaemon.plist [Click for support]
    [loaded]    com.parallels.mobile.kextloader.launchdaemon.plist [Click for support]
    [loaded]    com.raynersw.nshctldo.plist [Click for support]
    [running]    com.stclairsoft.AppTamerAgent.plist [Click for support]
    [loaded]    com.timesoftware.timemachineeditor.backup-auto.plist [Click for support]
    [loaded]    com.timesoftware.timemachineeditor.helper.plist [Click for support]
    [running]    com.zqueue.servetome-server.plist [Click for support]
    [loaded]    org.macosforge.xquartz.privileged_startx.plist [Click for support]
User Launch Agents: ℹ️
    [loaded]    com.valvesoftware.steamclean.plist [Click for support]
    [loaded]    de.metaquark.appfresh.plist [Click for support]
    [running]    ws.agile.1PasswordAgent.plist [Click for support]
User Login Items: ℹ️
    TotalSpaces2    Application  (/Applications/TotalSpaces2.app)
    Macs Fan Control    Application  (/Applications/Macs Fan Control.app)
    App Tamer    Application  (/Applications/App Tamer.app)
    Default Folder X Helper    Application  (/Library/PreferencePanes/Default Folder X.prefPane/Contents/Resources/Default Folder X Helper.app)
    Bartender    Application  (/Applications/Bartender.app)
    Dropbox    Application  (/Applications/Dropbox.app)
    AppCleaner Helper    Application  (/Applications/AppCleaner.app/Contents/Library/LoginItems/AppCleaner Helper.app)
    Box Sync    Application  (/Applications/Box Sync.app)
    Fantastical    Application  (/Applications/Fantastical.app)
    CopyLess    Application Hidden (/Applications/CopyLess.app)
Internet Plug-ins: ℹ️
    FlashPlayer-10.6: Version: 16.0.0.305 - SDK 10.6 [Click for support]
    QuickTime Plugin: Version: 7.7.3
    Flash Player: Version: 16.0.0.305 - SDK 10.6 [Click for support]
    Default Browser: Version: 537 - SDK 10.9
    SharePointBrowserPlugin: Version: 14.4.2 - SDK 10.6 [Click for support]
    AmazonMP3DownloaderPlugin101750: Version: AmazonMP3DownloaderPlugin 1.0.17 - SDK 10.4 [Click for support]
    Unity Web Player: Version: UnityPlayer version 4.3.5f1 - SDK 10.6 [Click for support]
    Silverlight: Version: 5.1.30317.0 - SDK 10.6 [Click for support]
    JavaAppletPlugin: Version: Java 8 Update 31 Check version
Safari Extensions: ℹ️
    AdBlock
    My eBay Manager
    1Password
    Quickscript
    DirectLinks
    Tabletoy
    ShowPass
    Ember
    Search Netflix from Wikipedia
    PopSearch
    Ultimate Status Bar
    The Camelizer - Amazon Price Tracker
    musicbox
    Duplicate Tab Button
    The Tracktor
    BackTrack
    Open in Internet Explorer
    Social Fixer
    QuickNuke
    InvisibleHand
3rd Party Preference Panes: ℹ️
    Default Folder X  [Click for support]
    FinderPop  [Click for support]
    Flash Player  [Click for support]
    Java  [Click for support]
    Perian  [Click for support]
    Printopia  [Click for support]
Time Machine: ℹ️
    Skip System Files: NO
    Mobile backups: OFF
    Auto backup: NO - Auto backup turned off
    Volumes being backed up:
        myMac: Disk size: 999.35 GB Disk used: 794.55 GB
    Destinations:
        My Book 2TB [Local]
        Total size: 2.00 TB
        Total number of backups: 108
        Oldest backup: 2013-08-09 19:35:21 +0000
        Last backup: 2015-03-08 18:41:10 +0000
        Size of backup disk: Too small
            Backup size 2.00 TB < (Disk used 794.55 GB X 3)
Top Processes by CPU: ℹ️
         5%    WindowServer
         2%    coreaudiod
         1%    Box Sync Monitor
         1%    ScreensharingAgent
         1%    Boom
Top Processes by Memory: ℹ️
    941 MB    Safari
    438 MB    mds_stores
    438 MB    iPhoto
    425 MB    Finder
    399 MB    com.apple.IconServicesAgent
Virtual Memory Information: ℹ️
    1.67 GB    Free RAM
    5.87 GB    Active RAM
    4.20 GB    Inactive RAM
    1.15 GB    Wired RAM
    3.83 GB    Page-ins
    0 B    Page-outs
Diagnostics Information: ℹ️
    Mar 7, 2015, 11:20:50 PM    /Users/[redacted]/Library/Logs/DiagnosticReports/AddressBookSourceSync_2015-03- 07-232050_[redacted].crash

Hi Eric -
I did a horrible job of explaining *when* the slow performance became noticeable. These changes did not happen when I installed Mavericks, I just don't have benchmarks *saved* to give the support community exact numbers after Mavericks was installed. The performance at that time was roughly the same, although you might recall that the old app xbench no longer worked to give a comparison because one or more of the sections of testing wouldn't work (memory, if I recall correctly, although I will run it when I am back at that machine and post here).
In any case, the only significant change since the slow down is the OS, but the decline in performance was noticed in the fall. It wasn't until I tried this network copying task the other day that I decided to run BlackMagic's test. This is when I realized I should go check the performance on the local machine. Having already run through many of the generic recommendations, I thought perhaps someone here who has a much deeper understanding of the storage abstraction layer would have guidance on specific preference files that might be corrupted since I can't find any tool to check them. I've noticed that many of the people seeking guidance are not very technical and the advice is similarly geared. I'm sure I could spend a little time this week finding comparable tools in Mac OS X to those I'd have used in the past on Windows (Sysinternals) to do real time debugging and process analysis.
So far I have found that there were a few processes running high, like the dashboard client, so I moved (deleted) the preference file and rebooted. This resulted in the gain to that 60 MB/sec write performance (up from the low of 40 MB/sec), but there must be other areas yet unexplored.
At this point I'm considering a fresh install, but I'd been told in previous exchanges when I first started developing on Macs (2008) that fresh installs were rarely the best solution on Macs.
Can you give me guidance on that? You probably know that in the Windows world it is often (depending on how you define often) necessary to format and reinstall the OS. As a long time systems architect developing everything from device drivers to enterprise solutions, I see that as a result of the attempts to maintain legacy support for so long and the convoluted resulting APIs and failure to make real fixes for fear of causing problems with older hardware and software. Would you suggest erasing and reinstalling?
@BobHarris - I know that's a problem and it's why I monitor the drive more than I do drives in other systems. My drive didn't qualify for replacement, but I think Apple doesn't always do a good job with the recalls. I was very fortunate that my old white MacBook qualified for quite a few replacement parts so it's a great browsing-the-web computer now, but at its age, it isn't capable of running most of the apps I need. I have considered selling the 27" iMac but when I last had it in for warranty repair, the DisplayPort was misaligned to the case, so I'm going to have to pay labor just to get it popped open to fix that (since the service center says they didn't cause the DP problem - although they must have!)... In any case, if I have to spend that money, I might as well use the drive doubler kit since I never use the optical drive in that box anyway. Mostly I love having it because of the gorgeous big screen. That being said, costs of repairs are silly when I can just buy another used MBP circa 2012 and get twice the processing power then use a CalDigit dock like the one I use with my existing MBP to use an inexpensive HD TV for the monitor.
Thanks for the replies folks - the input is awesome!
Chris

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        [not loaded]    com.adobe.ARM.[...].plist 3rd-Party support link
        [not loaded]    com.adobe.ARM.[...].plist 3rd-Party support link
        [not loaded]    com.crashplan.javacheck.plist 3rd-Party support link
        [not loaded]    com.facebook.videochat.[redacted].plist 3rd-Party support link
        [not loaded]    com.google.keystone.agent.plist 3rd-Party support link
        [not loaded]    jp.co.canon.Inkjet_Extended_Survey_Agent.plist 3rd-Party support link
        [not loaded]    uk.co.markallan.clamxav.freshclam.plist 3rd-Party support link
    User Login Items:
        iTunesHelper
        Adobe Bridge CS4
        CrashPlan menu bar
        ClamXavSentry
        AdobeResourceSynchronizer
        Canon IJ Network Scanner Selector2
    Internet Plug-ins:
        Default Browser: Version: 537 - SDK 10.9
        Flip4Mac WMV Plugin: Version: 2.3.8.1 3rd-Party support link
        Musicnotes: Version: 1.18.9 3rd-Party support link
        AdobePDFViewerNPAPI: Version: 11.0.03 - SDK 10.6 3rd-Party support link
        FlashPlayer-10.6: Version: 12.0.0.38 - SDK 10.6 3rd-Party support link
        Silverlight: Version: 4.0.51204.0 3rd-Party support link
        Flash Player: Version: 12.0.0.38 - SDK 10.6 Outdated! Update
        QuickTime Plugin: Version: 7.7.3
        iPhotoPhotocast: Version: 7.0
        SharePointBrowserPlugin: Version: 14.3.9 - SDK 10.6 3rd-Party support link
        AdobePDFViewer: Version: 11.0.03 - SDK 10.6 3rd-Party support link
        EPPEX Plugin: Version: 3.0.5.0 3rd-Party support link
        Scorch: Version: 6.1.0 3rd-Party support link
        JavaAppletPlugin: Version: 14.9.0 - SDK 10.7 Outdated! Update
    Audio Plug-ins:
        BluetoothAudioPlugIn: Version: 1.0 - SDK 10.9
        AirPlay: Version: 1.9 - SDK 10.9
        AppleAVBAudio: Version: 2.0.0 - SDK 10.9
        iSightAudio: Version: 7.7.3 - SDK 10.9
    User Internet Plug-ins:
        WebEx: Version: 1.0 3rd-Party support link
    3rd Party Preference Panes:
        Carbonite  3rd-Party support link
        Flash Player  3rd-Party support link
        Flip4Mac WMV  3rd-Party support link
    Bad Fonts:
        None
    Old Applications:
        /Library/Application Support/Microsoft/MERP2.0
            Microsoft Error Reporting:    Version: 2.2.9 - SDK 10.4 3rd-Party support link
            Microsoft Ship Asserts:    Version: 1.1.4 - SDK 10.4 3rd-Party support link
        Solver:    Version: 1.0 - SDK 10.5 3rd-Party support link
            /Applications/Microsoft Office 2011/Office/Add-Ins/Solver.app
        /Library/Application Support/Carbonite
            CarboniteDaemon:    Version: 1.1.14 build 604 - SDK 10.5 3rd-Party support link
            CarboniteStatus:    Version: 1.1.14 build 604 - SDK 10.5 3rd-Party support link
            CarboniteAlerts:    Version: 1.1.14 build 604 - SDK 10.5 3rd-Party support link
        /Applications/Microsoft Office 2011/Office
            Microsoft Graph:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Database Utility:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Office Reminders:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Upload Center:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            My Day:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            SyncServicesAgent:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Open XML for Excel:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Alerts Daemon:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Database Daemon:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Chart Converter:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Clip Gallery:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
        /Applications/Microsoft Office 2011
            Microsoft PowerPoint:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Excel:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Outlook:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Word:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            Microsoft Document Connection:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
        Microsoft Language Register:    Version: 14.3.9 - SDK 10.5 3rd-Party support link
            /Applications/Microsoft Office 2011/Additional Tools/Microsoft Language Register/Microsoft Language Register.app
        Microsoft AutoUpdate:    Version: 2.3.6 - SDK 10.4 3rd-Party support link
            /Library/Application Support/Microsoft/MAU2.0/Microsoft AutoUpdate.app
    Time Machine:
        Auto backup: YES
        Volumes being backed up:
            Macintosh HD: Disk size: 364.60 GB Disk used: 135.61 GB
        Destinations:
            Time Machine Backups [Local] (Last used)
            Total size: 2 
            Total number of backups: 169
            Oldest backup: 2011-04-10 20:10:19 +0000
            Last backup: 2014-02-04 22:28:22 +0000
            Size of backup disk: Excellent
                Backup size 2  > (Disk size 364.60 GB X 3)
        Time Machine details may not be accurate.
        All volumes being backed up may not be listed.
    Top Processes by CPU:
            16%    Solavant Demo
             9%    mds
             3%    CarboniteDaemon
             2%    WindowServer
             2%    EtreCheck
    Top Processes by Memory:
        348 MB    firefox
        217 MB    clamd
        135 MB    mds_stores
        106 MB    Mail
        102 MB    softwareupdated
    Virtual Memory Information:
        794 MB    Free RAM
        1.70 GB    Active RAM
        443 MB    Inactive RAM
        587 MB    Wired RAM
        1.13 GB    Page-ins
        896 KB    Page-outs

    Fixing a Mavericks Installation Problem
    How to manage a failed OS X Mavericks installation | MacFixIt - CNET Reviews.
    Try these in order:
    1. a. Resetting your Mac's PRAM and NVRAM
        b. Intel-based Macs: Resetting the System Management Controller (SMC)
    2. Restart the computer in Safe Mode, then restart again, normally. If this doesn't help, then:
         Boot to the Recovery HD: Restart the computer and after the chime press and hold down the
         COMMAND and R keys until the Utilities menu screen appears. Alternatively, restart the computer and
         after the chime press and hold down the OPTION key until the boot manager screen appears.
         Select the Recovery HD and click on the downward pointing arrow button.
    3. Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the Utilities menu. Repair the Hard Drive and Permissions as follows.
    When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the main menu. Select Restart from the Apple menu.
    4. Reinstall Lion/Mountain Lion, Mavericks: Reboot from the Recovery HD. Select Reinstall Lion/Mountain Lion, Mavericks from the Utilities menu, and click on the Continue button.
    Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.

  • Should I do a clean install of Mountain Lion on a late 2009 iMac or will I find hardware/driver issues?

    I have a late 2009 iMac (2.93 Ghz Intel Core Duo, 4GB of ram, model id is 9.1) running Lion right now. I upgraded it all the way from Leopard using the standard keep-all-your-apps-and-settings way. After looking at the hardware requirements for Mountain Lion (and my success with running Lion) it seems that my good ol' iMac is still capable of running it fairly well. But I don't like the idea of "stacking" upgrade after upgrade (*coughs*, clean freak!). I like the idea of starting out clean this time because so many years of use has filled my mac with a lot of crap I no longer use.
    So I would like to know your sane advice, and if there's anything I should check out before attempting this. Especially I'm concerned about hardware/driver related issues like for example: the webcam or speakers no longer working. Also, if there's something I'm overlooking please point it out.
    Thank you in advance for any help you guys can give me. I'll be very grateful!

    If it wasn't a Mac computer that originally came with either Lion or Mt Lion Pre-Installed by Apple when new you would not be able to connect to the Online Internet Recovery system. It is a Feature of the Mac EFI Firmware system. And it will only install whichever version of the Download only version of OS X that originally came on that system.
    My MBP came with Lion Preinstalled. Even if I have Mt Lion installed on the hard drive the Online Internet Recovery system would always point my MBP to the Lion download as that was the original version of OS X that came on my Mac.
    No real authentication needed. Since your Mac came with Mt Lion no matter what newer versionof OS X you ever install the OIRS will always point you to Mt Lion and ONLY Mt Lion.
    It is something different, but not completely different, from the built in Recovery HD partition on the internal drive.
    No worries as during the install of MT Lion on your SSD the installer will Recreate the Mt Lion Recovery HD partition on your SSD.

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