Fontd process causing Mac to lock up for minutes at a time

Here is a problem and also the solution, (in case you have the same problem):
My Mac (running OS X Lion) was exhibiting a problem whereby it paused for minutes at a time; the mouse moved, but no applications could respond (and they all showed the spinning beachball). Turned out to be a rogue ‘fontd’ process. This is how I fixed it.
So the symptoms were that occasionally applications would stop responding for a minute or two. This would especially happen when I launched a new app or browser window, and also occurred when I logged in after rebooting: it would hang with a near-empty screen, slowly opening my apps, waiting a(n agonising) couple of minutes between each one.
To cut a long story short (long version here: http://dysphoria.net/2012/02/18/mac-keeps-pausing-fontd-run-amuck/ ), the solution was to flush the font cache, as described in a Macworld article here: http://www.macworld.com/article/139383/2009/03/fontcacheclear.html
At the command line:
atsutil databases -removeUser
atsutil databases -remove
atsutil server -shutdown
atsutil server -ping

The next time you have the problem, note the exact times when it starts and ends: hour, minute, second.
If you have more than one user account, these instructions must be carried out as an administrator.
Launch the Console application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Console in the icon grid.
Make sure the title of the Console window is All Messages. If it isn't, select All Messages from the SYSTEM LOG QUERIES menu on the left.
Scroll back in the log to the time you noted above. Post any messages timestamped during that interval – the text, please, not a screenshot.
When posting a log extract, be selective. In most cases, a few dozen lines are more than enough.
Please do not indiscriminately dump thousands of lines from the log into a message.
Important: Some private information, such as your name, may appear in the log. Edit it out by search-and-replace in a text editor before posting.

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    Please do not indiscriminately dump thousands of lines from the log into a message.
    Important: Some private information, such as your name, may appear in the log. Edit it out by search-and-replace in a text editor before posting.

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              0   CoreFoundation                      0x00007fff86cb641c __exceptionPreprocess + 172
              1   libobjc.A.dylib                     0x00007fff8fa24e75 objc_exception_throw + 43
              2   CoreFoundation                      0x00007fff86cb5fc9 -[NSException raise] + 9
              3   personalbackup                      0x00000001030298e6 personalbackup + 10470
              4   Foundation                          0x00007fff8c3f9094 __NSFireTimer + 96
              5   CoreFoundation                      0x00007fff86c1d724 __CFRUNLOOP_IS_CALLING_OUT_TO_A_TIMER_CALLBACK_FUNCTION__ + 20
              6   CoreFoundation                      0x00007fff86c1d25f __CFRunLoopDoTimer + 1151
              7   CoreFoundation                      0x00007fff86c8e76a __CFRunLoopDoTimers + 298
              8   CoreFoundation                      0x00007fff86bd8aa5 __CFRunLoopRun + 1525
              9   CoreFoundation                      0x00007fff86bd8275 CFRunLoopRunSpecific + 309
              10  HIToolbox                           0x00007fff8930ff0d RunCurrentEventLoopInMode + 226
              11  HIToolbox                           0x00007fff8930fcb7 ReceiveNextEventCommon + 479
              12  HIToolbox                           0x00007fff8930fabc _BlockUntilNextEventMatchingListInModeWithFilter + 65
              13  AppKit                              0x00007fff8799d28e _DPSNextEvent + 1434
              14  AppKit                              0x00007fff8799c8db -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 122
              15  AppKit                              0x00007fff879909cc -[NSApplication run] + 553
              16  AppKit                              0x00007fff8797b803 NSApplicationMain + 940
              17  IntegoMenu                          0x0000000100001aa8 start + 52
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        "X-Mme-Country" = AU;
        "X-Mme-Nac-Version" = 11A457;
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        "X-Mme-Client-Info" = "<MacBookPro5,1> <Mac OS X;10.9.1;13B42> <com.apple.AOSKit/176>";
        "X-Mme-Country" = AU;
        "X-Mme-Nac-Version" = 11A457;
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    (null),
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        DialogType = Unknown;
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    (null),
    responseBody=
    (null)
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    21/12/2013 12:52:24.813 pm com.apple.backupd[562]: Starting automatic backup
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    21/12/2013 12:52:24.960 pm com.apple.mtmd[40]: Set snapshot time: 2013-12-21 12:52:26 +1100 (current time: 2013-12-21 12:52:24 +1100)
    21/12/2013 12:52:25.070 pm netbarrierd[80]: Switched to Network (Router IP(192.168.0.1) MAC(00:24:b2:a3:4a:d0) Name(BigPond4447)
    21/12/2013 12:52:25.070 pm netbarrierd[80]: Known network detected. Switch to profile "Home"
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    21/12/2013 12:52:29.625 pm CalendarAgent[230]: [com.apple.calendar.store.log.subscription] [Failed to refresh <CalManagedSubscriptionInfo: 0x7ff26e51c7a0> (entity: SubscriptionInfo; id: 0x40012b <x-coredata://46AC892B-FBE5-404E-98CB-56251B43F9AA/SubscriptionInfo/p1> ; data: {
        calendar = "0x14000eb <x-coredata://46AC892B-FBE5-404E-98CB-56251B43F9AA/CalDAVSubscribedCalendar/p5> ";
        hasAlarmFilter = 0;
        hasAttachmentFilter = 0;
        hasTaskFilter = 0;
        isAutoProvisioned = 0;
        isAutoRefreshed = 0;
        languageCode = nil;
        lastError = "0x5680016b <x-coredata://46AC892B-FBE5-404E-98CB-56251B43F9AA/SubscriptionError/p346>";
        locationCode = nil;
        needsRefresh = 0;
        refreshDate = nil;
        refreshInterval = 0;
        subscriptionID = nil;
        subscriptionNotes = nil;
        subscriptionTitle = nil;
        subscriptionURL = "(...not nil..)";
        subscriptionURLString = "webcal://ical.me.com/alexyim/Holidays.ics";
    }) with error Error Domain=CalSubscriptionErrorDomain Code=-1 "The operation couldn’t be completed. (CalSubscriptionErrorDomain error -1.)"]
    21/12/2013 12:52:29.000 pm kernel[0]: wlEvent: en1 en1 Link DOWN virtIf = 0
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    21/12/2013 12:52:30.000 pm kernel[0]: wlEvent: en1 en1 Link UP virtIf = 0
    21/12/2013 12:52:30.000 pm kernel[0]: AirPort: Link Up on en1
    21/12/2013 12:52:30.000 pm kernel[0]: en1: BSSID changed to 20:c9:d0:a8:60:47
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    21/12/2013 12:52:30.263 pm UserEventAgent[11]: Captive: CNPluginHandler en1: Authenticated
    21/12/2013 12:52:30.321 pm configd[17]: network changed: v4(en1!:192.168.0.6) DNS+ Proxy+ SMB
    21/12/2013 12:52:30.328 pm netbarrierd[80]: Switched to Network (Router IP(192.168.0.1) MAC(00:24:b2:a3:4a:d0) Name(Time Machine)
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        calendar = "0x14000eb <x-coredata://46AC892B-FBE5-404E-98CB-56251B43F9AA/CalDAVSubscribedCalendar/p5> ";
        hasAlarmFilter = 0;
        hasAttachmentFilter = 0;
        hasTaskFilter = 0;
        isAutoProvisioned = 0;
        isAutoRefreshed = 0;
        languageCode = nil;
        lastError = "0x5700016b <x-coredata://46AC892B-FBE5-404E-98CB-56251B43F9AA/SubscriptionError/p348>";
        locationCode = nil;
        needsRefresh = 0;
        refreshDate = nil;
        refreshInterval = 0;
        subscriptionID = nil;
        subscriptionNotes = nil;
        subscriptionTitle = nil;
        subscriptionURL = "(...not nil..)";
        subscriptionURLString = "webcal://ical.me.com/alexyim/Holidays.ics";
    }) with error Error Domain=CalSubscriptionErrorDomain Code=-1 "The operation couldn’t be completed. (CalSubscriptionErrorDomain error -1.)"]
    21/12/2013 12:53:08.000 pm kernel[0]: **** [IOBluetoothHostControllerUSBTransport][SuspendDevice] -- Suspend -- suspendDeviceCallResult = 0x0000 (kIOReturnSuccess) -- 0xa000 ****
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    21/12/2013 12:55:13.000 pm kernel[0]: disk0s2: I/O error.
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    21/12/2013 12:56:34.567 pm WindowServer[165]: disable_update_timeout: UI updates were forcibly disabled by application "Finder" for over 1.00 seconds. Server has re-enabled them.
    21/12/2013 12:56:35.086 pm WindowServer[165]: common_reenable_update: UI updates were finally reenabled by application "Finder" after 1.52 seconds (server forcibly re-enabled them after 1.00 seconds)
    21/12/2013 12:56:39.000 pm kernel[0]: jnl: disk2s2: replay_journal: from: 3809280 to: 4624384 (joffset 0x3a28000)
    21/12/2013 12:56:42.000 pm kernel[0]: jnl: disk2s2: journal replay done.
    21/12/2013 12:56:42.000 pm kernel[0]: hfs: mounted Time Machine Backups on device disk2s2
    21/12/2013 12:56:43.769 pm com.apple.backupd[562]: Disk image /Volumes/Data/Christopher Molloy’s PowerBook G4 15".sparsebundle mounted at: /Volumes/Time Machine Backups
    21/12/2013 12:56:44.601 pm com.apple.backupd[562]: Backing up to /dev/disk2s2: /Volumes/Time Machine Backups/Backups.backupdb
    21/12/2013 12:56:44.633 pm mds[41]: (Error) Volume: Root store set to FSOnly with matching create! (loaded:1)
    21/12/2013 12:58:01.000 pm kernel[0]: disk0s2: I/O error.
    21/12/2013 12:58:03.968 pm com.apple.backupd[562]: Event store UUIDs don't match for volume: Macintosh HD
    21/12/2013 12:58:08.287 pm com.apple.backupd[562]: Deep event scan at path:/ reason:must scan subdirs|new event db|
    21/12/2013 12:59:24.000 pm kernel[0]: disk0s2: I/O error.
    21/12/2013 1:00:01.882 pm SystemUIServer[273]: Metadata.framework [Error]: mdsCopyStoreInformation failed: (268451843) (ipc/rcv) timed out
    21/12/2013 1:00:11.885 pm SystemUIServer[273]: Metadata.framework [Error]: mdsCopyStoreInformation failed: (268451843) (ipc/rcv) timed out
    21/12/2013 1:00:34.913 pm SystemUIServer[273]: Metadata.framework [Error]: mdsCopyStoreInformation failed: (268451843) (ipc/rcv) timed out
    21/12/2013 1:00:50.000 pm kernel[0]: disk0s2: I/O error.
    21/12/2013 1:02:11.000 pm kernel[0]: disk0s2: I/O error.
    21/12/2013 1:02:12.651 pm Console[599]: setPresentationOptions called with NSApplicationPresentationFullScreen when there is no visible fullscreen window; this call will be ignored.
    21/12/2013 1:03:32.000 pm kernel[0]: disk0s2: I/O error.
    21/12/2013 1:04:51.000 pm kernel[0]: disk0s2: I/O error.

    One thing our logs have in common is the "SystemUIServer[...]: Metadata.framework [Error]: mdsCopyStoreInformation failed: (268451843) (ipc/rcv) timed out" part ...

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    It says "Pauses can be minimized by using a small young generation and incremental collection, at the expense of throughput."
    Well, I AM using incremental collection, and the young generation is the default size, which is quite small I believe. (32 MB max?)
    It also says "Unless you have problems with pauses, try granting as much memory as possible to the JVM. The default size (64MB) is often too small."
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    It also says "Unless you find problems with excessive major collection or pause times, grant plenty of memory to the young generation. The default MaxNewSize (32MB) is generally too small."
    I AM having problems with excessive major collections and pause times, so according to this I should NOT grant more memory to young generation (eden).
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    What should I do? The Tuning guide essentially says to screw around with generation sizes, but none of its specific tips seem to apply to me! This is a production server and I am worried about making things worse by playing around, so I was hoping someone out there might have some experience with this and concrete advice before I just start messing around with the memory map. Should I increase the young generation size? Decrease it? Something else altogether? HELP!

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    HOWEVER...
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    An unexpected exception has been detected in native code outside the VM.
    Unexpected Signal : 11 occurred at PC=0x40573aa7
    Function name=malloc
    Library=/lib/libc.so.6
    Current Java thread:
    Dynamic libraries:
    011121:231738.194: Search ( pizzala, lzh ) returned 50 results (28 ms)
    08048000-0804c000 r-xp 00000000 08:06 376904 /usr/local/java/jre1.3.1_01/bin/i386/native_threads/java
    0804c000-0804d000 rw-p 00003000 08:06 376904 /usr/local/java/jre1.3.1_01/bin/i386/native_threads/java
    40000000-40013000 r-xp 00000000 08:06 311298 /lib/ld-2.1.3.so
    40013000-40014000 rw-p 00012000 08:06 311298 /lib/ld-2.1.3.so
    40015000-40016000 r--p 00000000 08:06 2424834 /usr/share/locale/en_US/LC_MESSAGES/SYS_LC_MESSAGES
    40016000-40017000 r--p 00000000 08:06 2408452 /usr/share/locale/en_US/LC_MONETARY
    40017000-40018000 r--p 00000000 08:06 2408454 /usr/share/locale/en_US/LC_TIME
    40018000-40023000 r-xp 00000000 08:06 311344 /lib/libpthread-0.8.so
    40023000-4002a000 rw-p 0000a000 08:06 311344 /lib/libpthread-0.8.so
    4002b000-40034000 r-xp 00000000 08:06 1081477 /usr/local/java/jre1.3.1_01/lib/i386/native_threads/libhpi.so
    40034000-40035000 rw-p 00008000 08:06 1081477 /usr/local/java/jre1.3.1_01/lib/i386/native_threads/libhpi.so
    40035000-403b0000 r-xp 00000000 08:06 2769091 /usr/local/java/jre1.3.1_01/lib/i386/server/libjvm.so
    403b0000-403b1000 ---p 0037b000 08:06 2769091 /usr/local/java/jre1.3.1_01/lib/i386/server/libjvm.so
    403b1000-404fd000 rw-p 0037b000 08:06 2769091 /usr/local/java/jre1.3.1_01/lib/i386/server/libjvm.so
    40515000-40517000 r-xp 00000000 08:06 311314 /lib/libdl-2.1.3.so
    40517000-40519000 rw-p 00001000 08:06 311314 /lib/libdl-2.1.3.so
    4051a000-40607000 r-xp 00000000 08:06 311305 /lib/libc-2.1.3.so
    40607000-4060b000 rw-p 000ec000 08:06 311305 /lib/libc-2.1.3.so
    4060f000-40621000 r-xp 00000000 08:06 311318 /lib/libnsl-2.1.3.so
    40621000-40623000 rw-p 00011000 08:06 311318 /lib/libnsl-2.1.3.so
    40625000-40641000 r-xp 00000000 08:06 311316 /lib/libm-2.1.3.so
    40641000-40642000 rw-p 0001b000 08:06 311316 /lib/libm-2.1.3.so
    40642000-40676000 r-xp 00000000 08:06 704575 /usr/lib/libstdc++-2-libc6.1-1-2.9.0.so
    40676000-40682000 rw-p 00033000 08:06 704575 /usr/lib/libstdc++-2-libc6.1-1-2.9.0.so
    40684000-40695000 r-xp 00000000 08:06 1081479 /usr/local/java/jre1.3.1_01/lib/i386/libverify.so
    40695000-40697000 rw-p 00010000 08:06 1081479 /usr/local/java/jre1.3.1_01/lib/i386/libverify.so
    40697000-406b8000 r-xp 00000000 08:06 1081480 /usr/local/java/jre1.3.1_01/lib/i386/libjava.so
    406b8000-406ba000 rw-p 00020000 08:06 1081480 /usr/local/java/jre1.3.1_01/lib/i386/libjava.so
    406bb000-406cf000 r-xp 00000000 08:06 1081481 /usr/local/java/jre1.3.1_01/lib/i386/libzip.so
    406cf000-406d2000 rw-p 00013000 08:06 1081481 /usr/local/java/jre1.3.1_01/lib/i386/libzip.so
    406d2000-41400000 r--s 00000000 08:06 1081510 /usr/local/java/jre1.3.1_01/lib/rt.jar
    4142d000-416d2000 r--s 00000000 08:06 1081511 /usr/local/java/jre1.3.1_01/lib/i18n.jar
    416d2000-416e8000 r--s 00000000 08:06 1081498 /usr/local/java/jre1.3.1_01/lib/sunrsasign.jar
    77a9f000-77ab5000 r--p 00000000 08:06 2408451 /usr/share/locale/en_US/LC_CTYPE
    77ab5000-77abd000 r--p 00000000 08:06 2408450 /usr/share/locale/en_US/LC_COLLATE
    77abd000-77abe000 r--p 00000000 08:06 2408453 /usr/share/locale/en_US/LC_NUMERIC
    77abe000-77abf000 r-xp 00000000 08:06 1622117 /usr/lib/gconv/ISO8859-1.so
    77abf000-77ac0000 rw-p 00000000 08:06 1622117 /usr/lib/gconv/ISO8859-1.so
    77ac1000-77ac9000 r-xp 00000000 08:06 311336 /lib/libnss_files-2.1.3.so
    77ac9000-77aca000 rw-p 00007000 08:06 311336 /lib/libnss_files-2.1.3.so
    77b37000-77b40000 r-xp 00000000 08:06 1081484 /usr/local/java/jre1.3.1_01/lib/i386/libnet.so
    77b40000-77b41000 rw-p 00008000 08:06 1081484 /usr/local/java/jre1.3.1_01/lib/i386/libnet.so
    77b41000-77b45000 r-xp 00000000 08:06 1081513 /usr/local/java/jre1.3.1_01/lib/i386/libNBIO.so
    77b45000-77b46000 rw-p 00003000 08:06 1081513 /usr/local/java/jre1.3.1_01/lib/i386/libNBIO.so
    77b46000-77b4f000 r-xp 00000000 08:06 311342 /lib/libnss_nisplus-2.1.3.so
    77b4f000-77b51000 rw-p 00008000 08:06 311342 /lib/libnss_nisplus-2.1.3.so
    77b51000-77b59000 r-xp 00000000 08:06 311340 /lib/libnss_nis-2.1.3.so
    77b59000-77b5b000 rw-p 00007000 08:06 311340 /lib/libnss_nis-2.1.3.so
    77b5b000-77b5e000 r-xp 00000000 08:06 311334 /lib/libnss_dns-2.1.3.so
    77b5e000-77b5f000 rw-p 00002000 08:06 311334 /lib/libnss_dns-2.1.3.so
    77b5f000-77b6b000 r-xp 00000000 08:06 311346 /lib/libresolv-2.1.3.so
    77b6b000-77b6c000 rw-p 0000b000 08:06 311346 /lib/libresolv-2.1.3.so
    Local Time = Wed Nov 21 23:17:38 2001
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    # Java VM: Java HotSpot(TM) Server VM (1.3.1_01 mixed mode)
    # An error report file has been saved as hs_err_pid20055.log.
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