Breakpoints are ignored in qt creator 3.0.1

Set a breakpoint, run in qtcreator. Program runs without stopping. (breakpoint at main).
Am able to debug using plain GDB so is not a compile issue.
Deleting the ~/.config/QtProject or the ~/.config/QtProject.conf did not fix.

t14:33:25.570 [371647ms]
sStarting debugger "GdbEngine" for ABI "x86-linux-generic-elf-64bit"...
t14:33:25.570
dStart parameters: 'elasticnodes' mode: 1
dABI: x86-linux-generic-elf-64bit
dLanguages: c++
dExecutable: /home/chris/qt/workspace/build-elasticnodes-Desktop_Qt_5_2_1_GCC_64bit-Debug/elasticnodes
dDirectory: /home/chris/qt/workspace/build-elasticnodes-Desktop_Qt_5_2_1_GCC_64bit-Debug
dDebugger: /usr/bin/gdb
dProject: /home/chris/qt/workspace/elasticnodes (built: /home/chris/qt/workspace/build-elasticnodes-Desktop_Qt_5_2_1_GCC_64bit-Debug)
dQML server: 127.0.0.1:3768
dRemote: :0
dSysroot:
dDebug Source Location: /usr/src/debug/qt5base/src/corelib:/usr/src/debug/qt5base/src/gui:/usr/src/debug/qt5base/src/network
dDumper libraries: /home/chris/qt/Qt5.2.1/5.2.1/gcc_64//qtc-debugging-helper/ /home/chris/qt/Qt5.2.1/Tools/QtCreator/qtc-debugging-helper/749905821/ /home/chris/.local/share/data/QtProject/QtCreator/qtc-debugging-helper/749905821/
t14:33:25.570
dDebugger settings:
dIgnoreFirstChanceAccessViolation: false (default: false)
dLoadGdbInit: true (default: true)
dCDB_Console: false (default: false)
dBreakpointCorrection: true (default: true)
dBreakEvent: (default: )
dBreakOnCrtDbgReport: false (default: false)
dSymbolPaths: (default: )
dSourcePaths: (default: )
dAdditionalArguments: (default: )
dUseAddressInBreakpointsView: false (default: false)
dUseAddressInStackView: false (default: false)
dUseToolTipsInBreakpointsView: false (default: false)
dUseToolTipsInBreakpointsView: false (default: true) ***
dUseToolTips: false (default: true) ***
dUseToolTipsInLocalsView: false (default: false)
dUseCodeModel: true (default: true)
dShowThreadNames: false (default: false)
dRaiseOnInterrupt: true (default: true)
dUseDebuggingHelper: true (default: true)
dSwitchModeOnExit: false (default: false)
dBreakpointsFullPath: false (default: false)
dCloseBuffersOnExit: false (default: false)
dLogTimeStamps: true (default: false) ***
dVerboseLog: true (default: false) ***
dAutoQuit: false (default: false)
dFontSizeFollowsEditor: false (default: false)
dUseMessageBoxForSignals: true (default: true)
dUseAlternatingRowColours: false (default: false)
dAlwaysAdjustBreakpointsColumnWidths: false (default: false)
dNoPluginBreakpoints: false (default: false)
dSelectedPluginBreakpoints: false (default: false)
dAdjustBreakpointLocations: true (default: true)
dAllPluginBreakpoints: true (default: true)
dSkipKnownFrames: false (default: false)
dEnableReverseDebugging: false (default: false)
dMaximalStringLength: 10000 (default: 10000)
dListSourceFiles: false (default: false)
dAutoDerefPointers: true (default: true)
dAlwaysAdjustLocalsColumnWidths: false (default: false)
dShowQtNamespace: true (default: true)
dSortStructMembers: true (default: true)
dAlwaysAdjustStackColumnWidths: false (default: false)
dShowStandardNamespace: true (default: true)
dIdentifyDebugInfoPackages: false (default: false)
dMaximalStackDepth: 20 (default: 20)
dMultiInferior: false (default: false)
dIntelFlavor: false (default: false)
dTargetAsync: false (default: false)
dWarnOnReleaseBuilds: true (default: true)
dAutoEnrichParameters: false (default: true) ***
dUseDynamicType: true (default: true)
dGdbPostAttachCommands: (default: )
dWatchdogTimeout: 20 (default: 20)
dGdbStartupCommands: (default: )
dGdbCustomDumperCommands: (default: )
dLoadGdbDumpers: false (default: true) ***
dAttemptQuickStart: false (default: false)
dQmlInspector.FromQml: false (default: false)
dShowQmlObjectTree: true (default: true)
dQmlInspector.ShowAppOnTop: false (default: false)
dAlwaysAdjustThreadsColumnWidths: false (default: false)
dAlwaysAdjustModulesColumnWidths: false (default: false)
dAlwaysAdjustRegistersColumnWidths: false (default: false)
dAlwaysAdjustSnapshotsColumnWidths: false (default: false)
dBreakOnFatal: false (default: false)
dBreakOnAbort: false (default: false)
dBreakOnCatch: false (default: false)
dBreakOnWarning: false (default: false)
dSelectedPluginBreakpointsPattern: .* (default: .*)
dBreakOnThrow: false (default: false)
t14:33:25.580 [10ms]
dState changed from DebuggerNotReady(0) to EngineSetupRequested(1) [master]
t14:33:25.580
dQUEUE: SETUP ENGINE
t14:33:25.583 [3ms]
dCALL: SETUP ENGINE
t14:33:25.584 [1ms]
dEXAMINING /home/chris/qt/workspace/build-elasticnodes-Desktop_Qt_5_2_1_GCC_64bit-Debug/elasticnodes
t14:33:25.584
dELF SECTIONS: .interp .note.ABI-tag .note.gnu.build-id .gnu.hash .dynsym .dynstr .gnu.version .gnu.version_r .rela.dyn .rela.plt .init .plt .text .fini .rodata .eh_frame_hdr .eh_frame .gcc_except_table .init_array .fini_array .jcr .data.rel.ro .dynamic .got .got.plt .data .bss .comment .debug_aranges .debug_info .debug_abbrev .debug_line .debug_str .debug_ranges .gdb_index .shstrtab .symtab .strtab
t14:33:25.584
dTRYING TO START ADAPTER
t14:33:25.584
dENABLING TEST CASE: 0
t14:33:25.584
dSTARTING /usr/bin/gdb -i mi --tty=/tmp/QtCreator.wy3389
t14:33:25.591 [7ms]
dGDB STARTED, INITIALIZING IT
t14:33:25.591
<41show version
t14:33:25.591
<42show debug-file-directory
t14:33:25.592 [1ms]
<43set print object on
t14:33:25.592
<44set breakpoint pending on
t14:33:25.592
<45set print elements 10000
t14:33:25.593 [1ms]
<46handle SIGSEGV nopass stop print
t14:33:25.593
<47set unwindonsignal on
t14:33:25.593
<48set width 0
t14:33:25.593
<49set height 0
t14:33:25.593
sSetting up inferior...
t14:33:25.612
<50set substitute-path /var/tmp/qt-src /home/chris/qt/Qt5.2.1/5.2.1/gcc_64
t14:33:25.613
<# directory does not exist: /usr/src/debug/qt5base/src/corelib
t14:33:25.613
<# directory does not exist: /usr/src/debug/qt5base/src/gui
t14:33:25.614 [1ms]
<# directory does not exist: /usr/src/debug/qt5base/src/network
t14:33:25.614
<51-interpreter-exec console "set auto-solib-add on"
t14:33:25.614
<52pwd
t14:33:25.646 [32ms]
>=thread-group-added,id="i1"
>~"GNU gdb (GDB) 7.6.1-ubuntu\n"
>~"Copyright (C) 2013 Free Software Foundation, Inc.\n"
>~"License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\nThis is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law. Type \"show copying\"\nand \"show warranty\" for details.\n"
>~"This GDB was configured as \"x86_64-linux-gnu\".\nFor bug reporting instructions, please see:\n"
>~"<http://www.gnu.org/software/gdb/bugs/>.\n"
t14:33:25.647 [1ms]
t14:33:25.647
>&"show version\n"
>~"GNU gdb (GDB) 7.6.1-ubuntu\n"
>~"Copyright (C) 2013 Free Software Foundation, Inc.\n"
>~"License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\nThis is free software: you are free to change and redistribute it.\nThere is NO WARRANTY, to the extent permitted by law. Type \"show copying\"\nand \"show warranty\" for details.\n"
>~"This GDB was configured as \"x86_64-linux-gnu\".\nFor bug reporting instructions, please see:\n"
>~"<http://www.gnu.org/software/gdb/bugs/>.\n"
t14:33:25.647
>41^done
t14:33:25.647
tResponse time: show version: 0.056 s
t14:33:25.647
dPARSING VERSION: 41^done
t14:33:25.647
dSUPPORTED GDB VERSION GNU gdb (GDB) 7.6.1-ubuntu
dCopyright (C) 2013 Free Software Foundation, Inc.
dLicense GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
dThis is free software: you are free to change and redistribute it.
dThere is NO WARRANTY, to the extent permitted by law. Type "show copying"
dand "show warranty" for details.
dThis GDB was configured as "x86_64-linux-gnu".
dFor bug reporting instructions, please see:
d<http://www.gnu.org/software/gdb/bugs/>.
dGNU gdb (GDB) 7.6.1-ubuntu
dCopyright (C) 2013 Free Software Foundation, Inc.
dLicense GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
dThis is free software: you are free to change and redistribute it.
dThere is NO WARRANTY, to the extent permitted by law. Type "show copying"
dand "show warranty" for details.
dThis GDB was configured as "x86_64-linux-gnu".
dFor bug reporting instructions, please see:
d<http://www.gnu.org/software/gdb/bugs/>.
t14:33:25.647
dUSING GDB VERSION: 70601, BUILD: 2013
t14:33:25.647
<53-interpreter-exec console "set target-async off"
t14:33:25.648 [1ms]
<54-interpreter-exec console "python print(sys.version)"
t14:33:25.648
t14:33:25.649 [1ms]
>&"show debug-file-directory\n"
>~"The directory where separate debug symbols are searched for is \"/usr/lib/debug\".\n"
t14:33:25.649
>42^done
t14:33:25.649
tResponse time: show debug-file-directory: 0.058 s
t14:33:25.650 [1ms]
<55set debug-file-directory /usr/lib/debug:/usr/lib/debug
t14:33:25.650
t14:33:25.650
>&"set print object on\n"
t14:33:25.650
>=cmd-param-changed,param="print object",value="on"
t14:33:25.650
>43^done
t14:33:25.650
tResponse time: set print object on: 0.059 s
t14:33:25.650
t14:33:25.650
>&"set breakpoint pending on\n"
t14:33:25.650
>=cmd-param-changed,param="breakpoint pending",value="on"
t14:33:25.650
>44^done
t14:33:25.650
tResponse time: set breakpoint pending on: 0.058 s
t14:33:25.650
t14:33:25.650
>&"set print elements 10000\n"
t14:33:25.650
>=cmd-param-changed,param="print elements",value="10000"
t14:33:25.650
>45^done
t14:33:25.650
tResponse time: set print elements 10000: 0.058 s
t14:33:25.650
t14:33:25.650
>&"handle SIGSEGV nopass stop print\n"
>~"Signal Stop\tPrint\tPass to program\tDescription\n"
>~"SIGSEGV Yes\tYes\tNo\t\tSegmentation fault\n"
t14:33:25.650
>46^done
t14:33:25.650
tResponse time: handle SIGSEGV nopass stop print: 0.058 s
t14:33:25.650
t14:33:25.650
>&"set unwindonsignal on\n"
t14:33:25.650
>=cmd-param-changed,param="unwindonsignal",value="on"
t14:33:25.650
>47^done
t14:33:25.650
tResponse time: set unwindonsignal on: 0.057 s
t14:33:25.650
t14:33:25.650
>&"set width 0\n"
t14:33:25.650
>=cmd-param-changed,param="width",value="4294967295"
t14:33:25.650
>48^done
t14:33:25.650
tResponse time: set width 0: 0.057 s
t14:33:25.650
t14:33:25.650
>&"set height 0\n"
t14:33:25.650
>49^done
t14:33:25.650
tResponse time: set height 0: 0.057 s
t14:33:25.650
t14:33:25.650
>&"set substitute-path /var/tmp/qt-src /home/chris/qt/Qt5.2.1/5.2.1/gcc_64\n"
t14:33:25.650
>50^done
t14:33:25.650
tResponse time: set substitute-path /var/tmp/qt-src /home/chris/qt/Qt5.2.1/5.2.1/gcc_64: 0.038 s
t14:33:25.650
t14:33:25.650
>51^done
t14:33:25.650
tResponse time: set auto-solib-add on: 0.036 s
t14:33:25.650
t14:33:25.650
>&"pwd\n"
>~"Working directory /home/chris/qt/workspace/build-elasticnodes-Desktop_Qt_5_2_1_GCC_64bit-Debug.\n"
t14:33:25.650
>52^done
t14:33:25.650
tResponse time: pwd: 0.036 s
t14:33:25.650
dENGINE SUCCESSFULLY STARTED
t14:33:25.650
dNOTE: ENGINE SETUP OK
t14:33:25.650
dState changed from EngineSetupRequested(1) to EngineSetupOk(3) [master]
t14:33:25.650
dQUEUE: SETUP INFERIOR
t14:33:25.650
dState changed from EngineSetupOk(3) to InferiorSetupRequested(4) [master]
t14:33:25.650
dQUEUE: SETUP INFERIOR
t14:33:25.650
t14:33:25.650
dCALL: SETUP INFERIOR
t14:33:25.651 [1ms]
<56-file-exec-and-symbols "/home/chris/qt/workspace/build-elasticnodes-Desktop_Qt_5_2_1_GCC_64bit-Debug/elasticnodes"
t14:33:25.652 [1ms]
>53^done
t14:33:25.652
tResponse time: set target-async off: 0.005 s
t14:33:25.652
>~"3.3.2+ (default, Feb 28 2014, 00:56:04) \n[GCC 4.8.1]"
>~"\n"
t14:33:25.652
>54^done
t14:33:25.652
tResponse time: python print(sys.version): 0.005 s
t14:33:25.652
t14:33:25.652
>&"set debug-file-directory /usr/lib/debug:/usr/lib/debug\n"
t14:33:25.652
>=cmd-param-changed,param="debug-file-directory",value="/usr/lib/debug:/usr/lib/debug"
t14:33:25.652
>55^done
t14:33:25.652
tResponse time: set debug-file-directory /usr/lib/debug:/usr/lib/debug: 0.003 s
t14:33:25.652
t14:33:25.654 [2ms]
>56^done
t14:33:25.654
tResponse time: -file-exec-and-symbols "/home/chris/qt/workspace/build-elasticnodes-Desktop_Qt_5_2_1_GCC_64bit-Debug/elasticnodes": 0.004 s
t14:33:25.654
sSetting breakpoints...
t14:33:25.654
dSetting breakpoints...
t14:33:25.654
dATTEMPT BREAKPOINT SYNCHRONIZATION
t14:33:25.654
dTAKING OWNERSHIP OF BREAKPOINT 1 IN STATE 0
t14:33:25.656 [1ms]
<57-break-insert -f "\"main.cpp\":47"
t14:33:25.656
dBREAKPOINTS ARE NOT FULLY SYNCHRONIZED
t14:33:25.656
t14:33:25.665 [9ms]
dATTEMPT SYNC
t14:33:25.665
dATTEMPT BREAKPOINT SYNCHRONIZATION
t14:33:25.665
dBREAKPOINTS ARE NOT FULLY SYNCHRONIZED
t14:33:25.672 [7ms]
>57^done,bkpt=

{number="1",type="breakpoint",disp="keep",enabled="y",addr="0x000000000040823c",func="main(int, char**)",file="../elasticnodes/main.cpp",fullname="/home/chris/qt/workspace/elasticnodes/main.cpp",line="47",thread-groups=["i1"],times="0",original-location="main.cpp:47"}

t14:33:25.672
tResponse time: -break-insert -f "\"main.cpp\":47": 0.017 s
t14:33:25.673 [1ms]
dATTEMPT BREAKPOINT SYNCHRONIZATION
t14:33:25.673
dBREAKPOINTS ARE SYNCHRONIZED
t14:33:25.673
dALL COMMANDS DONE; INVOKING CALLBACK
t14:33:25.674 [1ms]
<58maint print msymbols "/tmp/gdb_ns_.Om3389"
t14:33:25.674
t14:33:25.681 [7ms]
>&"maint print msymbols \"/tmp/gdb_ns_.Om3389\"\n"
t14:33:25.682 [1ms]
>58^done
t14:33:25.682
tResponse time: maint print msymbols "/tmp/gdb_ns_.Om3389": 0.009 s
t14:33:25.682
dFOUND NON-NAMESPACED QT
t14:33:25.682
dNOTE: INFERIOR SETUP OK
t14:33:25.682
dState changed from InferiorSetupRequested(4) to InferiorSetupOk(6) [master]
t14:33:25.683 [1ms]
dState changed from InferiorSetupOk(6) to EngineRunRequested(7) [master]
t14:33:25.683
dQUEUE: RUN ENGINE
t14:33:25.683
t14:33:25.683
dCALL: RUN ENGINE
t14:33:25.683
<59-exec-run
t14:33:25.684 [1ms]
&"warning: GDB: Failed to set controlling terminal: Inappropriate ioctl for device\n"
t14:33:25.685 [1ms]
>=thread-group-started,id="i1",pid="3736"
t14:33:25.685
sThread group i1 created
t14:33:25.685
dTaking notice of pid 3736
t14:33:25.685
>=thread-created,id="1",group-id="i1"
t14:33:25.685
sThread 1 created

t14:33:29.748 [4063ms]
>=thread-exited,id="1",group-id="i1"
t14:33:29.748
sThread 1 in group i1 exited
t14:33:29.749 [1ms]
>=thread-group-exited,id="i1"
t14:33:29.749
sThread group i1 exited
t14:33:29.749
>59^error,msg="During startup program exited normally."
t14:33:29.749
tResponse time: -exec-run: 4.066 s
t14:33:29.749
dDuring startup program exited normally.
t14:33:29.749
dNOTE: ENGINE RUN FAILED
t14:33:29.749
sRun failed.
t14:33:29.749
dState changed from EngineRunRequested(7) to EngineRunFailed(8) [master]
t14:33:29.749
dState changed from EngineRunFailed(8) to EngineShutdownRequested(20) [master]
t14:33:29.749
dQUEUE: SHUTDOWN ENGINE
t14:33:29.749
t14:33:29.750 [1ms]
dCALL: SHUTDOWN ENGINE
t14:33:29.750
dPLAIN ADAPTER SHUTDOWN 20
t14:33:29.750
dINITIATE GDBENGINE SHUTDOWN IN STATE 0, PROC: 2
t14:33:29.750
<60-gdb-exit
t14:33:29.762 [12ms]
>60^exit
t14:33:29.762
tResponse time: -gdb-exit: 0.012 s
t14:33:29.762
dGDB CLAIMS EXIT; WAITING
t14:33:29.762
dGDB PROCESS FINISHED, status 0, code 0
t14:33:29.762
dNOTE: ENGINE SHUTDOWN OK
t14:33:29.762
dState changed from EngineShutdownRequested(20) to EngineShutdownOk(22) [master]
t14:33:29.763 [1ms]
dState changed from EngineShutdownOk(22) to DebuggerFinished(23) [master]
t14:33:29.763
dQUEUE: FINISH DEBUGGER
t14:33:29.763
dNOTE: FINISH DEBUGGER
t14:33:29.763
dHANDLE RUNCONTROL FINISHED
t14:33:29.763
sDebugger finished.