[Gate-users] Simulation hangs with certain Mersenne-Twister Seeds
Hermann Fuchs
hermann.fuchs at meduniwien.ac.at
Fri Feb 24 10:11:54 CET 2012
Hello
We have found a strange behavior of GATE in certain situations.
Using the random generator MersenneTwister we have found that certain
seeds cause the simulation to hang. No error is issued, but the
simulation is never finished.
I've attached the output of GATE and a mac file which creates such a
hanging simulation.
We use the GATE gjs splitter to split a given macro into smaller units
suitable for cluster processing.
The problem seems to occur rather frequently, of 300 randomly chosen
seeds, 20 seem to cause simulation hangups. This failure rate of 7 % is
pretty high.
The problem is not limited to this specific macfile.
Manually opening the macfile and selecting a different seed solves the
problem.
However, a failure of 7 % of all simulations within the cluster and the
manual intervention required is not a desirable situation.
Switching to a different random generator does not seem to be an option
as a poorer random generator such as Ranlux cause simulation artifacts.
Could someone please have a look at it.
Cheers,
Hermann
--
-------------
DI Hermann Fuchs
Christian Doppler Laboratory for Medical Radiation Research for Radiation Oncology
Department of Radiation Oncology
Medical University Vienna
Währinger Gürtel 18-20
A-1090 Wien
Tel. + 43 / 1 / 40 400 7271
Mail. hermann.fuchs at meduniwien.ac.at
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/vis/disable
/gate/geometry/setMaterialDatabase /home/runhere/bknaeusl/23122011_2artefacts_05cm05cm/23122011_artefacts2cm6cm_02x05x05_100MBq/SystemFiles/GateMaterials.db
/gate/world/geometry/setXLength 100 cm
/gate/world/geometry/setYLength 100 cm
/gate/world/geometry/setZLength 100 cm
/gate/world/daughters/name SPECThead
/gate/world/daughters/insert box
/gate/SPECThead/geometry/setXLength 8.59 cm
/gate/SPECThead/geometry/setYLength 21. cm
/gate/SPECThead/geometry/setZLength 30. cm
/gate/SPECThead/placement/setTranslation 20.0 0. 0. cm
/gate/SPECThead/setMaterial Air
/gate/SPECThead/repeaters/insert ring
/gate/SPECThead/ring/setRepeatNumber 2
/gate/SPECThead/moves/insert orbiting
/gate/SPECThead/orbiting/setSpeed 0.3 deg/s
/gate/SPECThead/orbiting/setPoint1 0 0 0 cm
/gate/SPECThead/orbiting/setPoint2 0 0 1 cm
/gate/SPECThead/vis/forceWireframe
/gate/SPECThead/daughters/name shielding
/gate/SPECThead/daughters/insert box
/gate/shielding/geometry/setXLength 8.59 cm
/gate/shielding/geometry/setYLength 21. cm
/gate/shielding/geometry/setZLength 30. cm
/gate/shielding/placement/setTranslation 0. 0. 0. cm
/gate/shielding/setMaterial Lead
/gate/shielding/vis/setColor red
/gate/shielding/vis/forceWireframe
/gate/SPECThead/daughters/name crystal
/gate/SPECThead/daughters/insert box
/gate/crystal/geometry/setXLength 1.59 cm
/gate/crystal/geometry/setYLength 19. cm
/gate/crystal/geometry/setZLength 28. cm
/gate/crystal/placement/setTranslation 0. 0. 0. cm
/gate/crystal/setMaterial NaI
/gate/crystal/vis/setColor yellow
/gate/SPECThead/daughters/name compartment
/gate/SPECThead/daughters/insert box
/gate/compartment/geometry/setXLength 2.5 cm
/gate/compartment/geometry/setYLength 19. cm
/gate/compartment/geometry/setZLength 28. cm
/gate/compartment/placement/setTranslation 2.045 0. 0. cm
/gate/compartment/setMaterial Glass
/gate/compartment/vis/setColor grey
/gate/SPECThead/daughters/name collimator
/gate/SPECThead/daughters/insert box
/gate/collimator/geometry/setXLength 3.5 cm
/gate/collimator/geometry/setYLength 19. cm
/gate/collimator/geometry/setZLength 28. cm
/gate/collimator/placement/setTranslation -2.545 0. 0. cm
/gate/collimator/setMaterial Lead
/gate/collimator/vis/setColor red
/gate/collimator/vis/forceWireframe
/gate/collimator/daughters/name hole
/gate/collimator/daughters/insert hexagone
/gate/hole/geometry/setHeight 3.5 cm
/gate/hole/geometry/setRadius 0.075 cm
/gate/hole/placement/setRotationAxis 0 1 0
/gate/hole/placement/setRotationAngle 90 deg
/gate/hole/setMaterial Air
/gate/hole/repeaters/insert cubicArray
/gate/hole/cubicArray/setRepeatNumberX 1
/gate/hole/cubicArray/setRepeatNumberY 111
/gate/hole/cubicArray/setRepeatNumberZ 95
/gate/hole/cubicArray/setRepeatVector 0. 0.17 0.294 cm
/gate/hole/repeaters/insert linear
/gate/hole/linear/setRepeatNumber 2
/gate/hole/linear/setRepeatVector 0. 0.085 0.147 cm
/gate/world/daughters/name Phantom
/gate/world/daughters/insert cylinder
/gate/Phantom/geometry/setRmax 10.8 cm
/gate/Phantom/geometry/setRmin 0. cm
/gate/Phantom/geometry/setHeight 5 cm
/gate/Phantom/placement/setTranslation 0. 0. 0. cm
/gate/Phantom/setMaterial Water
/gate/Phantom/vis/setColor blue
/gate/Phantom/vis/forceWireframe
/gate/world/daughters/name artefact1
/gate/world/daughters/insert box
/gate/artefact1/geometry/setXLength 0.2 cm
/gate/artefact1/geometry/setYLength 0.5 cm
/gate/artefact1/geometry/setZLength 0.5 cm
/gate/artefact1/placement/setTranslation 15.705 2.0 0. cm
/gate/artefact1/moves/insert orbiting
/gate/artefact1/orbiting/setSpeed 0.30 deg/s
/gate/artefact1/orbiting/setPoint1 0 0 0 cm
/gate/artefact1/orbiting/setPoint2 0 0 1 cm
/gate/artefact1/setMaterial Copper
/gate/artefact1/vis/setColor blue
/gate/world/daughters/name artefact2
/gate/world/daughters/insert box
/gate/artefact2/geometry/setXLength 0.2 cm
/gate/artefact2/geometry/setYLength 0.5 cm
/gate/artefact2/geometry/setZLength 0.5 cm
/gate/artefact2/placement/setTranslation 15.705 6.0 0. cm
/gate/artefact2/moves/insert orbiting
/gate/artefact2/orbiting/setSpeed 0.30 deg/s
/gate/artefact2/orbiting/setPoint1 0 0 0 cm
/gate/artefact2/orbiting/setPoint2 0 0 1 cm
/gate/artefact2/setMaterial Copper
/gate/artefact2/vis/setColor blue
/gate/systems/SPECThead/crystal/attach crystal
/gate/systems/SPECThead/describe
/gate/crystal/attachCrystalSD
/gate/Phantom/attachPhantomSD
/gate/compartment/attachPhantomSD
/gate/shielding/attachPhantomSD
/gate/SPECThead/attachPhantomSD
/gate/collimator/attachPhantomSD
/gate/physics/addProcess PhotoElectric
/gate/physics/processes/PhotoElectric/setModel StandardModel
/gate/physics/addProcess Compton
/gate/physics/processes/Compton/setModel PenelopeModel
/gate/physics/addProcess RayleighScattering
/gate/physics/processes/RayleighScattering/setModel PenelopeModel
/gate/physics/addProcess ElectronIonisation
/gate/physics/processes/ElectronIonisation/setModel StandardModel e-
/gate/physics/addProcess Bremsstrahlung
/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
/gate/physics/addProcess MultipleScattering e-
/gate/physics/processList Enabled
/gate/physics/processList Initialized
/gate/physics/Gamma/SetCutInRegion SPECThead 0.1 cm
/gate/physics/Electron/SetCutInRegion SPECThead 1.0 cm
/gate/run/initialize
/gate/source/addSource SourceConfinement1
/gate/source/SourceConfinement1/gps/type Volume
/gate/source/SourceConfinement1/gps/shape Cylinder
/gate/source/SourceConfinement1/gps/radius 10.8 cm
/gate/source/SourceConfinement1/gps/halfz 2.5 cm
/gate/source/SourceConfinement1/gps/centre 0. 0. 0. cm
/gate/source/SourceConfinement1/gps/particle gamma
/gate/source/SourceConfinement1/gps/energy 140. keV
/gate/source/SourceConfinement1/setActivity 100000000. Bq
/gate/source/SourceConfinement1/gps/angtype iso
/gate/digitizer/Singles/insert adder
/gate/digitizer/Singles/insert blurring
/gate/digitizer/Singles/blurring/setResolution 0.10
/gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV
/gate/digitizer/Singles/insert thresholder
/gate/digitizer/Singles/thresholder/setThreshold 120. keV
/gate/digitizer/Singles/insert upholder
/gate/digitizer/Singles/upholder/setUphold 160. keV
/gate/output/root/setFileName /home/runhere/bknaeusl/23122011_2artefacts_05cm05cm/23122011_artefacts2cm6cm_02x05x05_100MBq/Output/benchSPECT157
/gate/output/root/setRootSinglesAdderFlag 1
/gate/output/root/setRootSinglesBlurringFlag 1
/gate/output/root/setRootSinglesThresholderFlag 1
/gate/output/root/setRootSinglesUpholderFlag 1
/gate/output/ascii/setOutFileSinglesAdderFlag 0
/gate/output/ascii/setOutFileSinglesBlurringFlag 0
/gate/output/ascii/setOutFileSinglesThresholderFlag 0
/gate/output/ascii/setOutFileSinglesUpholderFlag 0
/gate/random/setEngineName MersenneTwister
/gate/random/setEngineSeed auto
/gate/random/verbose 1
/gate/output/projection/setFileName /home/runhere/bknaeusl/23122011_2artefacts_05cm05cm/23122011_artefacts2cm6cm_02x05x05_100MBq/Output/2artefacts2cm6cm_02x05x05_100MBq157
/gate/output/projection/pixelSizeX 3.32 mm
/gate/output/projection/pixelSizeY 3.32 mm
/gate/output/projection/pixelNumberX 128
/gate/output/projection/pixelNumberY 128
/gate/output/projection/projectionPlane YZ
/gate/application/setTimeSlice 2.4 s
/gate/application/setTimeStart 0. s
/gate/application/setTimeStop 600 s
/gate/verbose Physic 0
/gate/verbose Cuts 0
/gate/verbose SD 0
/gate/verbose Actions 0
/gate/verbose Actor 0
/gate/verbose Step 0
/gate/verbose Error 0
/gate/verbose Warning 0
/gate/verbose Output 0
/gate/verbose Beam 0
/gate/verbose Volume 0
/gate/verbose Image 0
/gate/verbose Geometry 0
/gate/verbose Core 0
/run/verbose 0
/event/verbose 0
/tracking/verbose 0
/gate/random/setEngineSeed 1164398721911993372
/gate/output/projection/enable
/gate/application/startDAQCluster 374.4 376.8 0 s
exit
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[G4]
[G4] *************************************************************
[G4] Geant4 version Name: geant4-09-04-patch-01 (18-February-2011)
[G4] Copyright : Geant4 Collaboration
[G4] Reference : NIM A 506 (2003), 250-303
[G4] WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4]
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Core-0] Initialization of actors
[Core-0]
[Core-0] **********************************************************************
[Core-0] GATE version name: gate_v6.1
[Core-0] Copyright : OpenGATE Collaboration
[Core-0] Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0] Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0] WWW : http://www.opengatecollaboration.org/
[Core-0] **********************************************************************
[Core-0]
[Core-0] Starting macro ./.Gate/MainSPECT/MainSPECT157.mac
[G4] GateDetectorConstruction::insertARFSD entered
[G4] created a ARF Sensivitive Detector
[G4] created command /gate/systems/SPECThead/arf/setARFStage
[G4] ABSLENGTH
[G4] MPV[0]: (1.84e-06, 50000)
[G4] MPV[1]: (4.08e-06, 50000)
[G4] Done DumpVector of 2 entries.
[G4] RINDEX
[G4] MPV[0]: (1.84e-06, 1.00028)
[G4] MPV[1]: (4.08e-06, 1.00028)
[G4] Done DumpVector of 2 entries.
[G4] GetDirectoryName()+ setHeight = /gate/hole/geometry/setHeight
[G4]
[G4] GATE object: 'systems/SPECThead'
[G4] Components:
[G4]
[G4] GATE object: 'systems/SPECThead/base'
[G4] Attached to volume: SPECThead
[G4] Nb of children: 1
[G4] GATE object: 'systems/SPECThead/crystal'
[G4] Attached to volume: crystal
[G4] Nb of children: 1
[G4] GATE object: 'systems/SPECThead/pixel'
[G4] Attached to volume: ---
List of Enabled processes:
=== Process: Bremsstrahlung ===
Particle: e+
* Model(s):
- <!> *** Warning *** <!> No model selected!
Particle: e-
* Model(s):
- StandardModel
=== Process: Compton ===
Particle: gamma
* Model(s):
- PenelopeModel
=== Process: ElectronIonisation ===
Particle: e+
* Model(s):
- <!> *** Warning *** <!> No model selected!
Particle: e-
* Model(s):
- StandardModel
=== Process: MultipleScattering ===
Particle: e-
=== Process: PhotoElectric ===
Particle: gamma
* Model(s):
- StandardModel
=== Process: RayleighScattering ===
Particle: gamma
* Model(s):
- PenelopeModel
List of initialized processes:
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Core-0] Initialization of actors
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time = 600 sec
[Acquisition-0] Simulation will have = 250 run(s)
--------- MTwist engine status ---------
Initial seed = 461655012
Current index = 128
Array status mt[] =
461655012 3943363834 321145631 3337432412 1711452315
1604478913 3477715902 2003259214 2414576711 2814167860
3503074952 1606516240 1856425965 1615167379 3858849264
1538912372 3177392701 822301966 3721728632 4246494168
4230000311 2709783251 447737763 3428883196 3516371143
1725285183 4196547424 826424760 3324659776 3648205334
3338186351 505727009 1961203785 453251883 2362823001
648907336 3714616616 1506014038 250681809 1225327282
103329883 1991673154 946619177 279958566 3339167062
452421280 2891459126 956251257 2202534065 2834359890
4075600546 168740054 3441085150 1708812032 3383961267
379814045 2320358365 4262070598 301220963 1022413528
661526016 1722137383 2594883684 830489251 2382125587
798727192 126739546 75469507 527963855 1305328138
2429716437 2762616944 444794518 1315470249 2935367714
2951217625 206515455 3034131186 1386835430 704742616
3096541228 3751087705 986522836 1638251957 1292496404
806148760 2217610470 1233247233 3613972812 157349526
3781700536 3479736912 2602105511 564518752 4211904038
1596887294 2944376607 2063098996 2837114507 787468622
6313990 3915287805 844207220 1979869153 2216356028
2382071601 2722068249 2874126144 2187026114 1064447767
2364042473 607451756 1067107440 3736108419 297537746
1447292075 1995680386 238761406 1894705220 4204216230
1147410565 3698135647 3659245110 3698564946 3715706525
2897344701 1830637025 2966267589 3202078055 2144791900
2315944915 1506399510 1666378483 3093502809 4161125541
1624825915 3271545470 2947221900 2232928608 3140013443
872159133 2819649320 3220809512 2247409447 3322078765
3811800217 952351828 2944598901 332633827 3199391678
1541596474 3784917524 4101893151 1367953175 1546622584
3146089254 688636828 3662861459 1523579478 426696024
512877308 3668415887 1303779422 2248828988 4180956406
502616392 1194922150 4161108704 3043347403 631266248
533902626 1095864419 1517506722 710860934 1834411956
1935800094 1951271439 1479244825 657540298 3516960611
1629748848 3017201252 358598956 4116911753 2429030462
620670935 3548248317 1434661087 1939414078 2429407138
3340801990 1604124030 3936415231 3061443759 237702819
2559235728 2515251642 1478036727 2426560524 24603171
4079120427 3752599331 165770586 2668677211 2133790901
3064114587 606978803 1749731892 726717373 973850628
1359007782 4124018836 3877780675 2159396239 1291288367
915722707 3121186987 1148043352 1167386823 1305635111
2053730054 557586186 36291288 1000337085 3149164309
3343625558 3591802731 3916805001 488964434 2464108441
280795717 4177558038 3443398437 570627353 3977910423
2461247773 1707820083 2321650161 495088981 2730194814
1325902912 3881744824 4255947001 4255544979 2055267488
4160575380 4026263521 3506132599 902689392 2793382939
3284501415 2920314493 4176522019 2228793735 1934026367
1700947099 1136159942 3279025126 2061727323 1315188099
1153527466 3674368950 498142055 2781620480 1189029926
1537229022 1855513365 228068797 875539017 1222091940
1557721647 1175597339 2500107094 3849453303 1682631958
1176068996 789520521 352947196 3226354426 1567625770
2246602051 475258576 997541402 4267238507 2652781744
4120517793 601941584 3818699669 1516889458 3992643330
1661314983 4187199455 2654982764 1131080293 1569636434
1623662972 3247715629 265199649 2575290719 1202747530
3032101199 580895288 2876772334 437502129 1227012649
4217590171 1140457674 1365717640 1097508381 1886958011
782957200 3622631677 2085499202 1280254010 1155500465
622956697 3635958373 2981213605 216765577 3273084946
1256499993 1298649179 2797973444 831515807 3411109403
1163958103 3213449324 1747110019 2867303910 2584078863
748578331 2578119456 4212862722 3477737436 2573110865
3506530196 723925063 1680522678 879514341 2743202218
472364856 2469968135 3081591879 4224648326 2044765637
2062028159 3067463648 4258313939 3914235480 4057910414
400966311 1511798184 627114449 1582795768 2922045311
3701222226 1952738165 2105555939 3273947880 258244948
3378363712 3646774378 1192364967 1341852695 3358861382
942243984 4136490790 3359727374 1857064757 4142667447
1181486134 2427636612 573939598 4195022933 3685391772
127023944 3512427380 3650189278 2386667867 752932454
810666470 2796641125 230406537 2080565586 2911653571
2653509320 18983476 33471941 2241330233 3764016646
1844792695 3532411723 1692326788 1211070708 2840495651
3842740158 2471752905 1870165742 843368417 2208514170
1143545740 2594439636 1621155104 2853626550 1903855700
180746008 2801192102 2945664001 14173787 1866642610
3643665353 3501028187 42537440 2889219047 1887608575
1328459707 1667641606 2663817670 25196982 3101886639
94313345 107404964 3463208466 2851156338 236879820
2797388951 635829347 2126931016 1977157445 2056521035
3558540008 1735403948 1358307477 4039823831 2874146838
3411771221 967762142 2852490533 3369278065 2850118151
1297998245 326864191 3936183717 3743387239 4086789372
2598736994 3691772038 1015081534 4018642970 3183997024
1854353868 692417858 625507882 2417922897 275800349
3754356718 2802489341 4195181430 31099619 201661672
3100444640 3583833921 2254489632 1149898911 2370642954
4159174555 1797619562 45336648 3037529304 1670112977
2295885534 3698828825 1772668206 3841189750 2809175795
3581323806 4149394681 1635167113 2588798254 3566947233
176124462 1665315305 735432970 2337940947 3924213877
341422765 1114254815 1931472467 1119080854 1732512494
4090113093 1651870647 2654282470 4078144427 2718136798
542506273 447513369 3050340240 148398060 2883801485
2982979963 380175244 3223617450 3695195258 2023873161
595490867 1222741417 3378267089 3905096994 4215526188
3013504401 1970125956 1844919933 3961270383 1404638238
1613855836 1833693265 1764863631 1216603108 610740054
808462634 2231896749 2486948645 632469724 2519783492
453208021 1239524639 2530425547 2939430945 2991023970
881801170 611406155 3993925095 104614595 3580145821
321799235 1105305627 4181878637 2687284304 1219751875
82662130 4092994785 4166674576 166380452 167950232
544423867 679180329 1561116462 1110411723 1843317201
738655790 4222152227 140911036 1748572359 642341496
161178129 1218561549 3906976851 3601672870 1087164750
3851014271 2266090143 4050325443 1297876433 25930272
3581300175 3953068842 1757462074 2638274739 269507360
1770595018 2853281152 1360961490 2477117446 1359870362
3089083820 1137814474 1493215898 2459468457 915493112
3060409016 325423265 1581331683 2206709959 3421897717
1207882889 2331449986 513606585 4243119893 217278501
4025259247 439958225 1025968617 1375535104 2788853207
2276359002 4214831784 2289166598 3455375010 2403193586
4064786428 1061880838 100690664 4155559537 3098369698
249234535 278685545 483681170 4268053598 2119706804
2611584459 130299790 44364102 3039970621 2284584537
2831306116 2061888122 3763967522 4160282783 761546597
1051584817 1428239852 756954775 2521490536 128
----------------------------------------
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