<html><body><div style="font-family: arial, helvetica, sans-serif; font-size: 12pt; color: #000000"><div>I think it's working ! </div><div>I just have some process that stop, not all of them go to the end. Maybe it's because of the number of cores the virtual machine has, I think a dual boot would be better :)</div><div><br data-mce-bogus="1"></div><div>Many thanks, you have been of great help!</div><div>Regards,</div><div>Sarah</div><div><br></div><div><span id="zwchr" data-marker="__DIVIDER__">----- Le 8 Mar 22, à 14:26, Dimitrios Thanasas <dthanas@uoa.gr> a écrit :<br></span></div><div data-marker="__QUOTED_TEXT__"><blockquote style="border-left:2px solid #1010FF;margin-left:5px;padding-left:5px;color:#000;font-weight:normal;font-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif;font-size:12pt;">Dear Sarah,<br><br>Yes you are right, using "auto" a new seed is generated every time you run<br>a different simulation. No you do not have to do something else.<br>You can confirm that you each run use a different cpu with the command<br>"top" when you run your simulations.<br>You do not have to install job splitter (I tried some months ago and I had<br>problems during the installation). I am not sure, but I think that using<br>job splitter you get one output file (based on the job splits) and without<br>it you get more output files and you have to find how to use them.<br><br>Regards,<br>Dimitris<br><br>-- <br>--------------------------<br>Dimitrios Thanasas, PhD<br>Medical Physicist<br>Medical Physics Lab<br>Medical School<br>National and Kapodistrian University of Athens<br>--------------------------<br><br><br>> Dear Dimitris,<br>><br>> Thank you so much for your response. I will try this right now!<br>><br>> What do you meen exactly by changing the engine seed ?<br>> I have set<br>><br>>> /gate/random/setEngineName MersenneTwister<br>>> /gate/random/setEngineSeed auto<br>><br>> I think a new seed is automaticallu generated that way?<br>><br>> I want to run my simulation for a specific number of primaries but not<br>> especially for a specific time.<br>><br>> Do I have to set something in order for Gate to use a different CPU for<br>> each simulation?<br>><br>> I use a DoseActor to produce a .hdr file, not a root file output.<br>><br>> Don't I need to install job splitter?<br>><br>> Thank you for your help,<br>> Sarah<br>><br>> ----- Le 8 Mar 22, à 13:15, Dimitrios Thanasas <dthanas@uoa.gr> a écrit :<br>><br>>> Dear Sarah,<br>><br>>> The general idea is to create different folders having the same mac<br>>> files<br>>> but changing the "Engine seed" and the time start and time stop also (if<br>>> you run the simulation for specific time and not for specific number of<br>>> primaries). Then, you open a different terminal in each folder and run<br>>> the<br>>> corresponding mac file. The number of the folders depends on the numbers<br>>> of CPUs that your machine has (each simulation run on a single CPU).<br>>> In order not to mix up the output files you can set diffrent name of<br>>> each<br>>> output file (eg outputname_1, outputname_2,....).<br>>> Then you can combine the results. Do you use a DoseActor to record the<br>>> dose (or energy deposited) in a output file or do you produce a root<br>>> file<br>>> as output?<br>>> In case you use a dose actor it is easy to sum up the dose of each run<br>>> but<br>>> it is not so easy to calculate the overall uncertainty. If your output<br>>> is<br>>> root files, you can merge them or load altogether in a root browser (I<br>>> do<br>>> not use root often so I cannot send you how to do this).<br>><br>>> I hope this will help you,<br>>> Dimitris<br>><br>>> --<br>>> --------------------------<br>>> Dimitrios Thanasas, PhD<br>>> Medical Physicist<br>>> Medical Physics Lab<br>>> Medical School<br>>> National and Kapodistrian University of Athens<br>>> --------------------------<br>><br>>> > Dear Dimitris Thanasas,<br>><br>>> > I come back to you about launching GATE with more than 10^9 primaries.<br>>> > I have tried to set an activity to my source and to run the simulation<br>>> for<br>>> > a certain time as you suggested.<br>>> > It allowed me to launch my simulation with 10^10 photons, but not<br>>> more.<br>><br>>> > Now I want to split my simulation, but I don't now how exactly and I<br>>> can't<br>>> > find any information about it, would you give me some advices ?<br>><br>>> > Thank you very much for your help,<br>>> > Regards,<br>>> > Sarah Blind<br>><br>>> > ----- Le 25 Fév 22, à 7:59, Dimitrios Thanasas <dthanas@uoa.gr> a<br>>> écrit :<br>><br>>> >> Dear Sarah,<br>><br>>> >> You could try to give an activity to your source, (e.g. 1 GBq -<br>>> without<br>>> >> half life) and then to run the simulation for a certain time (e.g.<br>>> 10s).<br>>> >> I<br>>> >> think that this wiil work (you may need a statactor to know exactly<br>>> the<br>>> >> number of the emitted particles).<br>>> >> If you try to split the simulation, you may need to change the engine<br>>> >> seed<br>>> >> in order not to have the same results in each simulation.<br>><br>>> >> Regards,<br>>> >> Dimitris<br>><br>>> >> > Dear Gate users,<br>><br>>> >> > I have the following model : 1 cell inside of which there are 12<br>>> >> clusters<br>>> >> > of 8000 nanoparticles each.<br>>> >> > My source is composed of a gamma beam of 5 keV.<br>>> >> > My simulation works fine up to 10^9 photons send. But with 10^10<br>>> >> primaries<br>>> >> > nothing happens anymore (there is no error message).<br>>> >> > Does someone have an idea what the problem might be ?<br>><br>>> >> > Thank you very much for your help,<br>>> >> > Regards,<br>>> >> > Sarah Blind<br>><br>>> >> > world.mac<br>><br>><br>><br>><br>>> >> > /gate/world/geometry/setXLength 30 um<br>>> >> > /gate/world/geometry/setYLength 30 um<br>>> >> > /gate/world/geometry/setZLength 30 um<br>>> >> > /gate/world/setMaterial Air<br>><br>>> >> > /gate/world/daughters/name cell<br>>> >> > /gate/world/daughters/insert sphere<br>>> >> > /gate/cell/geometry/setRmin 0.0 mm<br>>> >> > /gate/cell/geometry/setRmax 10 um<br>>> >> > /gate/cell/placement/setTranslation 0 0 0 um<br>>> >> > /gate/cell/setMaterial G4_WATER<br>>> >> > /gate/cell/vis/setVisible 1<br>>> >> > /gate/cell/vis/setColor blue<br>>> >> > /gate/cell/vis/forceSolid false<br>><br>>> >> > /gate/cell/daughters/name cluster<br>>> >> > /gate/cell/daughters/insert sphere<br>>> >> > /gate/cluster/geometry/setRmin 0.0 mm<br>>> >> > /gate/cluster/geometry/setRmax 500 nm<br>>> >> > /gate/cluster/placement/setTranslation 0 0 0 um<br>>> >> > /gate/cluster/setMaterial G4_WATER<br>>> >> > /gate/cluster/vis/setVisible 1<br>>> >> > /gate/cluster/vis/setColor yellow<br>>> >> > /gate/cluster/vis/forceSolid false<br>><br>>> >> > /gate/cluster/daughters/name NP<br>>> >> > /gate/cluster/daughters/insert sphere<br>>> >> > /gate/NP/geometry/setRmin 0 mm<br>>> >> > /gate/NP/geometry/setRmax 2 nm<br>>> >> > /gate/NP/placement/setTranslation 0 0 0 mm<br>>> >> > /gate/NP/setMaterial Bismuth<br>>> >> > /gate/NP/vis/setVisible 1<br>>> >> > /gate/NP/vis/setColor red<br>>> >> > /gate/NP/vis/forceSolid true<br>><br>><br>>> >> > /gate/NP/repeaters/insert cubicArray<br>>> >> > /gate/NP/cubicArray/setRepeatNumberX 20<br>>> >> > /gate/NP/cubicArray/setRepeatNumberY 20<br>>> >> > /gate/NP/cubicArray/setRepeatNumberZ 20<br>>> >> > /gate/NP/cubicArray/setRepeatVector 5 5 5 nm<br>><br>>> >> > /gate/cluster/repeaters/insert cubicArray<br>>> >> > /gate/cluster/cubicArray/setRepeatNumberX 3<br>>> >> > /gate/cluster/cubicArray/setRepeatNumberY 2<br>>> >> > /gate/cluster/cubicArray/setRepeatNumberZ 2<br>>> >> > /gate/cluster/cubicArray/setRepeatVector 5 5 5 um<br>><br>><br>><br>><br>>> >> > physics.mac<br>><br>>> >> > BQ_BEGIN<br>><br>><br>>> >> > /gate/physics/addPhysicsList QGSP_BERT_EMV<br>><br>>> >> > /gate/physics/Gamma/SetCutInRegion world 50 nm<br>>> >> > /gate/physics/Electron/SetCutInRegion world 50 nm<br>><br>>> >> > /gate/physics/Gamma/SetCutInRegion cell 20 nm<br>>> >> > /gate/physics/Electron/SetCutInRegion cell 20 nm<br>><br>>> >> > /gate/physics/Gamma/SetCutInRegion cluster 5 nm<br>>> >> > /gate/physics/Electron/SetCutInRegion cluster 5 nm<br>><br>>> >> > /gate/physics/Gamma/SetCutInRegion NP 0.5 nm<br>>> >> > /gate/physics/Electron/SetCutInRegion NP 0.5 nm<br>><br>>> >> > /gate/random/setEngineName MersenneTwister<br>><br>>> >> > /gate/physics/addAtomDeexcitation<br>><br>>> >> > /gate/physics/addProcess PhotoElectric gamma<br>>> >> > /gate/physics/processes/PhotoElectric/setModel LivermoreModel<br>>> >> > /gate/physics/processes/PhotoElectric/setAugerElectron true<br>>> >> > /gate/physics/processes/PhotoElectric/setDeltaRayCut 10 eV<br>>> >> > /gate/physics/processes/PhotoElectric/setXRayCut 10 eV<br>>> >> > /gate/physics/processes/PhotoElectric/setStepFunction e- 0.2 0.1 nm<br>><br>>> >> > /gate/physics/addProcess Compton gamma<br>>> >> > /gate/physics/processes/Compton/setModel LivermoreModel<br>>> >> > /gate/physics/processes/Compton/setStepFunction e- 0.2 0.1 nm<br>><br>>> >> > /gate/physics/addProcess RayleighScattering<br>>> >> > /gate/physics/processes/RayleighScattering/setModel LivermoreModel<br>><br>>> >> > /gate/physics/addProcess GammaConversion<br>>> >> > /gate/physics/processes/GammaConversion/setModel LivermoreModel<br>><br>>> >> > /gate/physics/addProcess ElectronIonisation<br>>> >> > /gate/physics/processes/ElectronIonisation/setModel LivermoreModel<br>>> e-<br>>> >> > /gate/physics/processes/ElectronIonisation/setModel PenelopeModel<br>>> e+<br>>> >> > /gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2<br>>> 0.1<br>>> >> nm<br>><br>>> >> > /gate/physics/addProcess Bremsstrahlung e-<br>>> >> > /gate/physics/addProcess Bremsstrahlung e+<br>>> >> > /gate/physics/processes/Bremsstrahlung/setModel LivermoreModel e-<br>>> >> > /gate/physics/processes/Bremsstrahlung/setModel PenelopeModel e+<br>><br>>> >> > /gate/physics/addProcess eMultipleScattering e-<br>>> >> > /gate/physics/addProcess eMultipleScattering e+<br>>> >> > /gate/physics/processes/eMultipleScattering/setModel UrbanModel e-<br>>> >> > /gate/physics/processes/eMultipleScattering/setModel UrbanModel e+<br>><br>>> >> > /gate/physics/SetMinKineticEnergyInRegion world 1 eV<br>>> >> > /gate/physics/SetMinKineticEnergyInRegion cell 1 eV<br>>> >> > /gate/physics/ActivateSpecialCuts gamma<br>><br>>> >> > BQ_END<br>><br>><br>>> >> > source.mac<br>><br>>> >> > BQ_BEGIN<br>><br>><br>>> >> > /gate/source/addSource mybeam gps<br>>> >> > /gate/source/mybeam/gps/particle gamma<br>>> >> > /gate/source/mybeam/gps/pos/type Beam<br>>> >> > /gate/source/mybeam/gps/ene/mono 5 keV<br>>> >> > /gate/source/mybeam/gps/ene/type Gauss<br>>> >> > /gate/source/mybeam/gps/ene/sigma 1.0 keV<br>>> >> > /gate/source/mybeam/gps/direction 0 0 -1<br>><br>>> >> > /gate/source/mybeam/gps/position 0 0 15 um<br>>> >> > /gate/source/mybeam/gps/pos/type Volume<br>>> >> > /gate/source/mybeam/gps/pos/shape Cylinder<br>>> >> > /gate/source/mybeam/gps/pos/inner_radius 0 mm<br>>> >> > /gate/source/mybeam/gps/pos/radius 10 um<br>>> >> > /gate/source/mybeam/gps/pos/halfz 0.01 um<br>>> >> > /gate/source/mybeam/gps/ang/type beam2d<br>><br>><br>><br>><br>><br>>> >> > BQ_END<br>><br>><br>><br>>> >> > _______________________________________________<br>>> >> > Gate-users mailing list<br>>> >> > Gate-users@lists.opengatecollaboration.org<br>>> >> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users<br>><br>>> > --<br>>> > Sarah Blind<br>>> > Ingénieure de recherche - CNRS<br>>> > Centre de Recherche en Automatique de Nancy (CRAN)<br>>> > Département Biologie, Signaux et Systèmes en Cancérologie et<br>>> Neurosciences<br>>> > (BioSiS)<br>>> > Site de la faculté de médecine<br>>> > 9, Avenue de la Forêt de Haye<br>>> > 54505 Vandoeuvre les Nancy<br>>> > Tél : 03.72.74.61.13<br>><br>><br>> --<br>> Sarah Blind<br>> Ingénieure de recherche - CNRS<br>> Centre de Recherche en Automatique de Nancy (CRAN)<br>> Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences<br>> (BioSiS)<br>> Site de la faculté de médecine<br>> 9, Avenue de la Forêt de Haye<br>> 54505 Vandoeuvre les Nancy<br>> Tél : 03.72.74.61.13<br>><br></blockquote></div><div><br></div><div data-marker="__SIG_POST__">-- <br></div><div>Sarah Blind<br>Ingénieure de recherche - CNRS<br>Centre de Recherche en Automatique de Nancy (CRAN) <br>Département Biologie, Signaux et Systèmes en Cancérologie et Neurosciences (BioSiS)<br>Site de la faculté de médecine <br>9, Avenue de la Forêt de Haye <br>54505 Vandoeuvre les Nancy <br>Tél : 03.72.74.61.13</div></div></body></html>