[Gate-users] GateApplicationMgr.cc Error

Siti Salasiah MusNMey ctsalasiah1950 at gmail.com
Mon Mar 11 01:51:28 CET 2013


Hi,
Please help me considering my simulation problem. I define my mac file with
the following simulation:

##################################
# EXPERIMENT
#
/gate/application/setTimeSlice     60.0 s
/gate/application/setTimeStart     0 s
/gate/application/setTimeStop      60.0 s
/gate/application/startDAQ


After running for a week, I have this error
*/home/gate/Progs/Gate/gate_v6.2/source/general/src/GateApplicationMgr.cc
(l.220): Error in GateApplicationMgr::GetTimeSlice, run=2. *The same
problem happens when I simulate before for 1800 s after running for two
weeks. Is it because of memory or what? It has been a month but I cant get
correct GATE simulation. Please help me.

Siti



List of initialized processes:
[Core-0] Initialization of geometry
[Physic-1]
[Physic-1]  ----------------------------------------------------------
[Physic-1]                      Ionization potential
[Physic-1]   - worldDefaultAir defaut value: I = 85.7031 eV
[Physic-1]   - Air defaut value: I = 85.6694 eV
[Physic-1]   - Vacuum defaut value: I = 19.2 eV
[Physic-1]   - BGO defaut value: I = 473.785 eV
[Physic-1]   - Tungsten defaut value: I = 727 eV
[Physic-1]   - Lung defaut value: I = 69.7265 eV
[Physic-1]   - Body defaut value: I = 69.0157 eV
[Physic-1]   - SpineBone defaut value: I = 85.2598 eV
[Physic-1]   - RibBone defaut value: I = 102.82 eV
[Physic-1]  ----------------------------------------------------------
[Core-0] Initialization of physics
[Physic-2]   GatePhysicsList::ConstructProcess
[Physic-3]    mLoadState = 1
[Physic-3]    mListOfStepLimiter.size = 0
[Core-0] Initialization of actors
Nof Higher level 2

GATE object:        'digitizer/Coincidences'
Is enabled?         Yes
Coincidence window: 1.000e+01 ns
Coincidence window jitter: 0.000e+00 ps
Coincidence offset: 0.000e+00 ps
Coincidence offset jitter: 0.000e+00 ps
Min sector diff.:   2
Input:              'Singles'
Output:             'Coincidences'

GATE object:        'digitizer/delay'
Is enabled?         Yes
Coincidence window: 1.000e+01 ns
Coincidence window jitter: 0.000e+00 ps
Coincidence offset: 5.000e+02 ns
Coincidence offset jitter: 0.000e+00 ps
Min sector diff.:   2
Input:              'Singles'
Output:             'delay'
 in GateCoincidencePulseProcessorChain call new GateCoincidenceDigiMaker

GATE object:        'digitizer/finalCoinc'
Is enabled?         Yes
Nb of elements:     0
Attached to:        'digitizer'
Output:             'finalCoinc'

Output module: 'sinogram'
 >> Job:                                 build a set of 2D sinograms from a
PET simulation
 >> Is enabled ?                         Yes
 >> Number of crystals per crystal ring: 0
 >> Number of crystal rings:             0
 >> Number of radial sinogram bins:      0
 >> Filled ?                             No
 >> Attached to system:                  systems/ecat
 >> Input data:                          finalCoinc
Output module: 'ecat7'
 >> Job:                   write a set of 2D sinograms into an Ecat7 output
file
 >> Is enabled ?           Yes
 >> File name:             NCATSinogramEcat.S
 >> Attached to system:    systems/ecat
 Range Translator
Range   0 : imageValue in [    0.000e+00 , 0.000e+00 ]  ---> activity (Bq)
0.000e+00
Range   1 : imageValue in [    2.000e+00 , 2.000e+00 ]  ---> activity (Bq)
8.000e+03
Range   2 : imageValue in [    4.000e+00 , 4.000e+00 ]  ---> activity (Bq)
2.400e+03
Range   3 : imageValue in [    6.000e+01 , 6.000e+01 ]  ---> activity (Bq)
6.000e+04
Range   4 : imageValue in [    7.500e+01 , 7.500e+01 ]  ---> activity (Bq)
8.400e+04
GateSourceVoxelImageReader::ReadFile : fileName: ncat_header_act.h33
 Header read from       'ncat_header_act.h33'
 Data file name         'Section1_act.i33'
 Nb of planes:           21
 Nb of pixels per plane: 64 64
 Pixel size:             6.250e+00 6.250e+00
 Slice thickness:        6.250e+00
 Matrix size:            4.000e+02 4.000e+02
 Data type:              UNSIGNED INTEGER
 Data byte order: LITTLEENDIAN

 **** Error: Volume does not exist ****
 Ignoring confine condition
Source ---------------> voxel_NCAT
  ID                  : 0
  type                : backtoback
  startTime (s)       : 0.000e+00
  time (s)            : 0.000e+00
  forcedUnstable      : 1
  forcedLifetime (s)  : 9.502e+03
  verboseLevel        : 0
-----------------------
  Voxel reader ---------->   number of voxels       : 44735
  total activity (Bq)    : 8.224e+08
  position  (mm)         : 0.000e+00 0.000e+00 0.000e+00
  voxel size  (mm)    : 6.250e+00 6.250e+00 6.250e+00
Source --------------> voxel_NCAT
  ID                 : 0
  type               : backtoback
  activity (Bq)      : 0.000e+00
  startTime (s)      : 0.000e+00
  time (s)           : 0.000e+00
  forcedUnstable     : 1
  forcedHalfLife (s) : 6.586e+03
  verboseLevel       : 0
  relative to vol    : World
----------------------

    GPS info ---------------->
    particle                 : gamma
    SourcePosType            : Point
    Shape                    : NULL
    halfx,halfy,halfz  (mm)  : 0.000e+00 0.000e+00 0.000e+00
    Radius             (mm)  : 0.000e+00
    CentreCoords       (mm)  : 0.000e+00 0.000e+00 0.000e+00
    EnergyDisType            : Mono
    AngleDisType            : iso
    MinTheta, MaxTheta (deg) : 0.000e+00 1.800e+02
    MinPhi, MaxPhi     (deg) : 0.000e+00 3.600e+02
    --------------------------

GateSourceMgr::ListSources: List of the sources in the source manager
Source ---------------> voxel_NCAT
  ID                  : 0
  type                : backtoback
  startTime (s)       : 0.000e+00
  time (s)            : 0.000e+00
  forcedUnstable      : 1
  forcedLifetime (s)  : 9.502e+03
  verboseLevel        : 0
-----------------------
GateSourceMgr::ListSources: List of the sources in the source manager
Source ---------------> voxel_NCAT
  ID                  : 0
  type                : backtoback
  startTime (s)       : 0.000e+00
  time (s)            : 0.000e+00
  forcedUnstable      : 1
  forcedLifetime (s)  : 9.502e+03
  verboseLevel        : 0
-----------------------
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time   = 60 sec
[Acquisition-0] Simulation will have  = 1 run(s)

----- HepJamesRandom engine status -----
 Initial seed = 669708517
 u[] = 0.313493 0.22101 0.720638 0.288275 0.209104 0.961876 0.0185378
0.767277 0.570899 0.11677 0.585697 0.361668 0.499346 0.969958 0.659357
0.470614 0.232287 0.851241 0.27455 0.788571 0.407255 0.205312 0.558045
0.841456 0.443543 0.0437512 0.20597 0.975022 0.180286 0.842097 0.240617
0.115375 0.0104213 0.86239 0.254429 0.284886 0.114014 0.250714 0.477909
0.527364 0.887455 0.402326 0.5341 0.418133 0.107406 0.124517 0.302133
0.489961 0.8011 0.598657 0.398494 0.285134 0.133646 0.956609 0.548981
0.0394724 0.830412 0.922722 0.527004 0.588913 0.129604 0.169863 0.043967
0.0808861 0.801898 0.583084 0.269808 0.84379 0.235689 0.208139 0.683603
0.275 0.411587 0.134052 0.253045 0.356203 0.629278 0.233236 0.444437
0.502942 0.77252 0.00816381 0.210178 0.938382 0.894515 0.511199 0.913346
0.907528 0.240269 0.448999 0.814368 0.13479 0.692496 0.707161 0.983838
0.703152 0.403158
 c = 0.652903, cd = 0.456233, cm = 1
 i97 = 93, u[i97] = 0.707161
 j97 = 29, u[j97] = 0.842097
----------------------------------------
 >> entering [GateToSinogram::RecordBeginOfAcquisition]
    Acquisition start time: 0.000e+00
    Number of frames: 1
    Total number of crystals per crystal rings: 576
    Number of crystal rings: 32
    Number of radial sinogram bins:    288
    Number of azimuthal sinogram bins: 288
    Crystal location blurring in tangential direction: 1.800e+00 mm
    Crystal location blurring in axial direction: 1.800e+00 mm
    Prompt coincidences are recorded in data = 0
    Delayed coincidences (if simulated) are recorded in data = 1
    True scattered coincidences (eventID1 = eventID2) are recorded in data
= 4
 >> leaving [GateToSinogram::RecordBeginOfAcquisition]
 >> entering [GateSinoToEcat7::RecordBeginOfAcquisition]
    Number of crystal rings: 32
    crystal axial pitch: 4.850e+00 mm
    crystal transverse pitch: 4.494e+00 mm
    ECAT7 file NCATSinogramEcat.S created
 >> leaving [GateSinoToEcat7::RecordBeginOfAcquisition]
[Acquisition-0]
[Acquisition-0] Slice 0 from 0 to 60 s [slice=60 s], final stop at 60 s.

RayleighScattering:   for  gamma    SubType= 11
      Lambda tables from 1.000e+02 eV  to 1.000e+01 TeV in 200 bins,
spline: 1
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
         PenRayleigh :  Emin= 0.000e+00 eV    Emax= 1.000e+02 GeV

Compton:   for  gamma    SubType= 13
      Lambda tables from 1.000e+02 eV  to 1.000e+01 TeV in 77 bins, spline:
1
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
       Klein-Nishina :  Emin= 0.000e+00 eV    Emax= 1.000e+01 TeV

PhotoElectric:   for  gamma    SubType= 12
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
       PhotoElectric :  Emin= 0.000e+00 eV    Emax= 1.000e+01 TeV

ElectronIonisation:   for  e-    SubType= 2
      dE/dx and range tables from 1.000e+02 eV  to 1.000e+01 TeV in 77 bins
      Lambda tables from threshold to 1.000e+01 TeV in 77 bins, spline: 1
      finalRange(mm)= 1.000e+00, dRoverRange= 2.000e-01, integral: 1,
fluct: 1, linLossLimit= 1.000e-02
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
        MollerBhabha :  Emin= 0.000e+00 eV    Emax= 1.000e+01 TeV

Bremsstrahlung:   for  e-    SubType= 3
      dE/dx and range tables from 1.000e+02 eV  to 1.000e+01 TeV in 77 bins
      Lambda tables from threshold to 1.000e+01 TeV in 77 bins, spline: 1
      LPM flag: 1 for E > 1.000e+00 GeV
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
             eBremSB :  Emin= 0.000e+00 eV    Emax= 1.000e+00 GeV
AngularGenUrban
            eBremLPM :  Emin= 1.000e+00 GeV   Emax= 1.000e+01 TeV
AngularGenUrban

ElectronIonisation:   for  e+    SubType= 2
      dE/dx and range tables from 1.000e+02 eV  to 1.000e+01 TeV in 77 bins
      Lambda tables from threshold to 1.000e+01 TeV in 77 bins, spline: 1
      finalRange(mm)= 1.000e+00, dRoverRange= 2.000e-01, integral: 1,
fluct: 1, linLossLimit= 1.000e-02
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
        MollerBhabha :  Emin= 0.000e+00 eV    Emax= 1.000e+01 TeV

Bremsstrahlung:   for  e+    SubType= 3
      dE/dx and range tables from 1.000e+02 eV  to 1.000e+01 TeV in 77 bins
      Lambda tables from threshold to 1.000e+01 TeV in 77 bins, spline: 1
      LPM flag: 1 for E > 1.000e+00 GeV
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
             eBremSB :  Emin= 0.000e+00 eV    Emax= 1.000e+00 GeV
AngularGenUrban
            eBremLPM :  Emin= 1.000e+00 GeV   Emax= 1.000e+01 TeV
AngularGenUrban

annihil:   for  e+    SubType= 5
      ===== EM models for the G4Region  DefaultRegionForTheWorld ======
            eplus2gg :  Emin= 0.000e+00 eV    Emax= 1.000e+01 TeV
 >> entering [GateToSinogram::RecordBeginOfRun]
    Frame ID = 1
 >> leaving [GateToSinogram::RecordBeginOfRun]
 >> entering [GateSinoToEcat7::RecordBeginOfRun]
    Frame ID:     1
    Gate ID:      1
    Bed position: 0
    Prompt coincidences are recorded with data = 0
    Delayed coincidences (if simulated) are recorded with data = 1
    True scattered coincidences are recorded with data = 4
 >> leaving [GateSinoToEcat7::RecordBeginOfRun]
WARNING: Scene "refresh" not found.
  /vis/scene/list to see scenes.
 >> entering [GateToSinogram::RecordEndOfRun]
    Number of prompt coincidences for all ring combinations        2889636
      Number of true coincidences for all ring combinations          513257
        Number of scattered coincidences for all ring combinations     8
      Number of random coincidences for all ring combinations        2376379
    Number of delayed coincidences for all ring combinations       2273250
    sinograms 1,1,1,0,0 written to the raw file NCATSinogram_1.ima
    sinograms 1,1,1,1,0 written to the raw file NCATSinogram_1_del.ima
    sinograms 1,1,1,4,0 written to the raw file NCATSinogram_1_sct.ima
 >> leaving [GateToSinogram::RecordEndOfRun]
 >> entering [GateSinoToEcat7::RecordEndOfRun]
    Frame ID:                             1
    Gate ID:                             1
    Data ID:                             0
    Bed ID:                             0
    Number of sinogram radial elements:   288
    Number of sinogram azimutal elements: 144
    Maximum ring difference:              22
    Span factor:                          9
     ==> Number of segments               5
              Segment 0 is for ring difference -4 to 4
                and goes from slice 0 to slice 62
              Segment 1 is for ring difference 5 to 13
                and goes from slice 5 to slice 57
              Segment -1 is for ring difference -13 to -5
                and goes from slice 5 to slice 57
              Segment 2 is for ring difference 14 to 22
                and goes from slice 14 to slice 48
              Segment -2 is for ring difference -22 to -14
                and goes from slice 14 to slice 48
    Frame start time:                       0 msec
    Frame duration:                       60000 msec
    Number of prompts in ECAT sinogram                    2613153
    Number of delayeds in ECAT sinogram                   2064498
    Number of net trues in ECAT sinogram                  548655
    Maximum bin content:                  8
    Frame ID:                             1
    Gate ID:                             1
    Data ID:                             1
    Bed ID:                             0
    Number of sinogram radial elements:   288
    Number of sinogram azimutal elements: 144
    Maximum ring difference:              22
    Span factor:                          9
     ==> Number of segments               5
              Segment 0 is for ring difference -4 to 4
                and goes from slice 0 to slice 62
              Segment 1 is for ring difference 5 to 13
                and goes from slice 5 to slice 57
              Segment -1 is for ring difference -13 to -5
                and goes from slice 5 to slice 57
              Segment 2 is for ring difference 14 to 22
                and goes from slice 14 to slice 48
              Segment -2 is for ring difference -22 to -14
                and goes from slice 14 to slice 48
    Frame start time:                       0 msec
    Frame duration:                       60000 msec
    Number of prompts in ECAT sinogram                    2613153
    Number of delayeds in ECAT sinogram                   2064498
    Number of net trues in ECAT sinogram                  548655
    Maximum bin content:                  6
    Frame ID:                             1
    Gate ID:                             1
    Data ID:                             4
    Bed ID:                             0
    Number of sinogram radial elements:   288
    Number of sinogram azimutal elements: 144
    Maximum ring difference:              22
    Span factor:                          9
     ==> Number of segments               5
              Segment 0 is for ring difference -4 to 4
                and goes from slice 0 to slice 62
              Segment 1 is for ring difference 5 to 13
                and goes from slice 5 to slice 57
              Segment -1 is for ring difference -13 to -5
                and goes from slice 5 to slice 57
              Segment 2 is for ring difference 14 to 22
                and goes from slice 14 to slice 48
              Segment -2 is for ring difference -22 to -14
                and goes from slice 14 to slice 48
    Frame start time:                       0 msec
    Frame duration:                       60000 msec
    Number of prompts in ECAT sinogram                    2613153
    Number of delayeds in ECAT sinogram                   2064498
    Number of net trues in ECAT sinogram                  548655
    Maximum bin content:                  1
 >> leaving [GateSinoToEcat7::RecordEndOfRun]
ERROR: G4VisCommandsViewerUpdate::SetNewValue: no current viewer.
[Acquisition-0]
[Acquisition-0] Slice 1 from 60 to 60 s [slice=5.2865e-322 s], final stop
at 60 s.
 >> entering [GateToSinogram::RecordBeginOfRun]
    Frame ID = 2
 >> leaving [GateToSinogram::RecordBeginOfRun]
 >> entering [GateSinoToEcat7::RecordBeginOfRun]
    Frame ID:     2
    Gate ID:      1
    Bed position: 0
    Prompt coincidences are recorded with data = 0
    Delayed coincidences (if simulated) are recorded with data = 1
    True scattered coincidences are recorded with data = 4
 >> leaving [GateSinoToEcat7::RecordBeginOfRun]
WARNING: Scene "refresh" not found.
  /vis/scene/list to see scenes.
 >> entering [GateToSinogram::RecordEndOfRun]
    Number of prompt coincidences for all ring combinations        2893393
      Number of true coincidences for all ring combinations          514122
        Number of scattered coincidences for all ring combinations     15
      Number of random coincidences for all ring combinations        4755650
    Number of delayed coincidences for all ring combinations       2276450
    sinograms 2,1,1,0,0 written to the raw file NCATSinogram_2.ima
    sinograms 2,1,1,1,0 written to the raw file NCATSinogram_2_del.ima
    sinograms 2,1,1,4,0 written to the raw file NCATSinogram_2_sct.ima
 >> leaving [GateToSinogram::RecordEndOfRun]
 >> entering [GateSinoToEcat7::RecordEndOfRun]
    Frame ID:                             2
    Gate ID:                             1
    Data ID:                             0
    Bed ID:                             0
    Number of sinogram radial elements:   288
    Number of sinogram azimutal elements: 144
    Maximum ring difference:              22
    Span factor:                          9
     ==> Number of segments               5
              Segment 0 is for ring difference -4 to 4
                and goes from slice 0 to slice 62
              Segment 1 is for ring difference 5 to 13
                and goes from slice 5 to slice 57
              Segment -1 is for ring difference -13 to -5
                and goes from slice 5 to slice 57
              Segment 2 is for ring difference 14 to 22
                and goes from slice 14 to slice 48
              Segment -2 is for ring difference -22 to -14
                and goes from slice 14 to slice 48
    Frame start time:                       60000 msec
    Frame duration:                       60000 msec
    Number of prompts in ECAT sinogram                    2617690
    Number of delayeds in ECAT sinogram                   2067230
    Number of net trues in ECAT sinogram                  550460
    Maximum bin content:                  7
    Frame ID:                             2
    Gate ID:                             1
    Data ID:                             1
    Bed ID:                             0
    Number of sinogram radial elements:   288
    Number of sinogram azimutal elements: 144
    Maximum ring difference:              22
    Span factor:                          9
     ==> Number of segments               5
              Segment 0 is for ring difference -4 to 4
                and goes from slice 0 to slice 62
              Segment 1 is for ring difference 5 to 13
                and goes from slice 5 to slice 57
              Segment -1 is for ring difference -13 to -5
                and goes from slice 5 to slice 57
              Segment 2 is for ring difference 14 to 22
                and goes from slice 14 to slice 48
              Segment -2 is for ring difference -22 to -14
                and goes from slice 14 to slice 48
    Frame start time:                       60000 msec
    Frame duration:                       60000 msec
    Number of prompts in ECAT sinogram                    2617690
    Number of delayeds in ECAT sinogram                   2067230
    Number of net trues in ECAT sinogram                  550460
    Maximum bin content:                  5
    Frame ID:                             2
    Gate ID:                             1
    Data ID:                             4
    Bed ID:                             0
    Number of sinogram radial elements:   288
    Number of sinogram azimutal elements: 144
    Maximum ring difference:              22
    Span factor:                          9
     ==> Number of segments               5
              Segment 0 is for ring difference -4 to 4
                and goes from slice 0 to slice 62
              Segment 1 is for ring difference 5 to 13
                and goes from slice 5 to slice 57
              Segment -1 is for ring difference -13 to -5
                and goes from slice 5 to slice 57
              Segment 2 is for ring difference 14 to 22
                and goes from slice 14 to slice 48
              Segment -2 is for ring difference -22 to -14
                and goes from slice 14 to slice 48
    Frame start time:                       60000 msec
    Frame duration:                       60000 msec
    Number of prompts in ECAT sinogram                    2617690
    Number of delayeds in ECAT sinogram                   2067230
    Number of net trues in ECAT sinogram                  550460
    Maximum bin content:                  1
 >> leaving [GateSinoToEcat7::RecordEndOfRun]
ERROR: G4VisCommandsViewerUpdate::SetNewValue: no current viewer.
[Acquisition-0]
[Acquisition-0] Slice 2 from 60 to 7.01573e-322 s [slice=1.14623e-321 s],
final stop at 60 s.
 >> entering [GateToSinogram::RecordBeginOfRun]
    Frame ID = 3
 >> leaving [GateToSinogram::RecordBeginOfRun]
 >> entering [GateSinoToEcat7::RecordBeginOfRun]
    Frame ID:     3
    Gate ID:      1
    Bed position: 0
    Prompt coincidences are recorded with data = 0
    Delayed coincidences (if simulated) are recorded with data = 1
    True scattered coincidences are recorded with data = 4
 >> leaving [GateSinoToEcat7::RecordBeginOfRun]
WARNING: Scene "refresh" not found.
  /vis/scene/list to see scenes.
*/home/gate/Progs/Gate/gate_v6.2/source/general/src/GateApplicationMgr.cc
(l.220): Error in GateApplicationMgr::GetTimeSlice, run=2*

WARNING - Attempt to delete the physical volume store while geometry closed
!
WARNING - Attempt to delete the logical volume store while geometry closed !
WARNING - Attempt to delete the solid store while geometry closed !
WARNING - Attempt to delete the region store while geometry closed !
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