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Hi Xinjie,</div>
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<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="margin:0px;font-size:12pt">Correction, nothing can be water without this crash happening, unless water is removed from the Materials.xml.</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="margin:0px;font-size:12pt">I guess it's trying to delete the property table for water twice in the destructor? I'm not sure why the water materials properties are hard coded here:</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<span style="margin:0px;font-size:12pt"><a href="https://github.com/OpenGATE/Gate/blob/develop/source/geometry/src/GateMaterialDatabase.cc#L184" id="LPlnk935944">https://github.com/OpenGATE/Gate/blob/develop/source/geometry/src/GateMaterialDatabase.cc#L184</a><br>
</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
So if water is then duplicated in the Materials.xml it crashes. <span style="color: rgb(0, 0, 0); font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt;">Will need Gate authors to clarify.</span></div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
In the meantime I guess there are 2 options:</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
1) Accept the hard coded default for Water</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
2) Rename water (myWater ?) in Materials.xml and GateMaterials.db and use that in the macro.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
That's all I can think of for now...</div>
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<br>
</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Cheers,<br>
Lana</div>
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<span style="margin:0px;font-size:12pt"><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Gate-users <gate-users-bounces@lists.opengatecollaboration.org> on behalf of gate-users-request@lists.opengatecollaboration.org <gate-users-request@lists.opengatecollaboration.org><br>
<b>Sent:</b> 20 January 2021 19:22<br>
<b>To:</b> gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
<b>Subject:</b> Gate-users Digest, Vol 176, Issue 30</font>
<div> </div>
</div>
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<div class="PlainText">Send Gate-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Gate-users Digest, Vol 176, Issue 29 (Lana Beck)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 20 Jan 2021 19:50:42 +0000<br>
From: Lana Beck <lana.beck@bristol.ac.uk><br>
To: "gate-users@lists.opengatecollaboration.org"<br>
<gate-users@lists.opengatecollaboration.org><br>
Subject: Re: [Gate-users] Gate-users Digest, Vol 176, Issue 29<br>
Message-ID:<br>
<AM7PR06MB6566A5F3259D5191BFBF81B5B8A20@AM7PR06MB6566.eurprd06.prod.outlook.com><br>
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Content-Type: text/plain; charset="utf-8"<br>
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Hi Xinjie,<br>
<br>
I have been able to replicate your error (in Gate 8.2 on my mac). I made a short script with a beam and actor just to test. Phantom2 can be anything but water and it will work. Phantom1 can be water and it will work (as long as Phantom2 is something else).
It will also work if Materials.xml is not accessible to the script.<br>
<br>
As the error is in the destructor of GateMaterialDatabase and it refers to water_MPT, I think this part will be the cause:<br>
<a href="https://github.com/OpenGATE/Gate/blob/4389aa4e5230e56cc8afa4309c18786cc1e77fbf/source/geometry/src/GateMaterialDatabase.cc#L184">https://github.com/OpenGATE/Gate/blob/4389aa4e5230e56cc8afa4309c18786cc1e77fbf/source/geometry/src/GateMaterialDatabase.cc#L184</a><br>
as it requires: if ((materialName == "Water") ...<br>
<br>
That is as far as I've got, and I've only had time to have a quick look for now. Sorry I don't work on PET or I might understand it better. Script below to replicate the error when the Materials.xml is in the current dir.<br>
<br>
Cheers,<br>
Lana<br>
<br>
/gate/geometry/setMaterialDatabase GateMaterials.db<br>
<br>
/gate/world/setMaterial Air<br>
/gate/world/geometry/setXLength 1 m<br>
/gate/world/geometry/setYLength 1 m<br>
/gate/world/geometry/setZLength 2.5 m<br>
<br>
/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Air<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setRmin 2.4 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Water<br>
/gate/phantom2/attachPhantomSD<br>
<br>
#Physics<br>
/gate/physics/addPhysicsList emstandard_opt4<br>
<br>
#Actor<br>
/gate/actor/addActor DoseActor doseDistribution<br>
/gate/actor/doseDistribution/save PetDose.root<br>
/gate/actor/doseDistribution/attachTo phantom1<br>
/gate/actor/doseDistribution/stepHitType random<br>
/gate/actor/doseDistribution/setPosition 0 0 0 cm<br>
/gate/actor/doseDistribution/setSize 100 100 100 mm<br>
/gate/actor/doseDistribution/setResolution 20 20 20<br>
/gate/actor/doseDistribution/enableNumberOfHits false<br>
/gate/actor/doseDistribution/enableEdep true<br>
/gate/actor/doseDistribution/enableUncertaintyEdep false<br>
/gate/actor/doseDistribution/enableSquaredEdep false<br>
/gate/actor/doseDistribution/enableDose false<br>
/gate/actor/doseDistribution/enableUncertaintyDose false<br>
<br>
#=====================================================<br>
# INITIALISATION<br>
#=====================================================<br>
<br>
/gate/run/initialize<br>
<br>
#====================================================<br>
# BEAMS<br>
#=====================================================<br>
<br>
/gate/source/addSource PBS PencilBeam<br>
/gate/source/PBS/setParticleType proton<br>
/gate/source/PBS/setEnergy 188.0 MeV<br>
/gate/source/PBS/setSigmaEnergy 1.0 MeV<br>
/gate/source/PBS/setPosition 0 0 0 mm<br>
/gate/source/PBS/setSigmaX 2 mm<br>
/gate/source/PBS/setSigmaY 4 mm<br>
/gate/source/PBS/setSigmaTheta 3.3 mrad<br>
/gate/source/PBS/setSigmaPhi 3.8 mrad<br>
/gate/source/PBS/setEllipseXThetaEmittance 15 mm*mrad<br>
/gate/source/PBS/setEllipseXThetaRotationNorm negative<br>
/gate/source/PBS/setEllipseYPhiEmittance 20 mm*mrad<br>
/gate/source/PBS/setEllipseYPhiRotationNorm negative<br>
/gate/source/PBS/setRotationAxis 1 0 0<br>
/gate/source/PBS/setRotationAngle 90 deg<br>
<br>
#=====================================================<br>
# START BEAMS<br>
#=====================================================<br>
<br>
/gate/random/setEngineName MersenneTwister<br>
/gate/random/setEngineSeed 123456<br>
/gate/application/noGlobalOutput<br>
<br>
/gate/application/setTotalNumberOfPrimaries 10<br>
/gate/application/start<br>
<br>
<br>
<br>
-------------------<br>
Dr Lana Beck<br>
<br>
Research Associate<br>
<br>
Particle Physics Group<br>
<br>
University of Bristol<br>
<br>
<br>
________________________________<br>
From: Gate-users <gate-users-bounces@lists.opengatecollaboration.org> on behalf of gate-users-request@lists.opengatecollaboration.org <gate-users-request@lists.opengatecollaboration.org><br>
Sent: 20 January 2021 15:37<br>
To: gate-users@lists.opengatecollaboration.org <gate-users@lists.opengatecollaboration.org><br>
Subject: Gate-users Digest, Vol 176, Issue 29<br>
<br>
Send Gate-users mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: Weird Phantom Warning (Matthew Strugari)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 20 Jan 2021 16:05:49 +0000<br>
From: Matthew Strugari <matthew.strugari@dal.ca><br>
To: Xinjie Cao <xinjie.cao@stonybrook.edu><br>
Cc: "gate-users@lists.opengatecollaboration.org"<br>
<gate-users@lists.opengatecollaboration.org><br>
Subject: Re: [Gate-users] Weird Phantom Warning<br>
Message-ID: <10B1107C-243B-477E-830A-65C6EEADC144@dal.ca><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Xinjie,<br>
<br>
I’m not sure what could be causing your issue at this point. It appears to be a problem with your install. Hopefully somebody else might have an idea and can provide their insight.<br>
<br>
My next best suggestion would be to try vGATE and see if your issue occurs there. You could also try setting your material as G4_WATER instead. A more involved approach to determining the issue would involve recompiling GATE with your build type set to RelWithDebIbfo,
then run your code in a debugger such as gdb.<br>
<br>
Regards,<br>
Matthew<br>
<br>
On Jan 20, 2021, at 11:35 AM, Xinjie Cao <xinjie.cao@stonybrook.edu> wrote:<br>
<br>
<br>
CAUTION: The Sender of this email is not from within Dalhousie.<br>
Hi Matthew,<br>
<br>
I am using GATE v8.2 and geant4.10.05.p01. Our cluster workstations are with CentOS 7 operating system.<br>
<br>
Best,<br>
Xinjie<br>
<br>
On Tue, Jan 19, 2021 at 12:35 PM Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>> wrote:<br>
Hi Xinjie,<br>
<br>
What version of GATE and Geant4 are you using and what is your operating system? I find no relevant errors when running the simulation with phantom1 as Water.<br>
<br>
Aside from that, your code could be updated to use the new physics list mechanism<<a href="https://opengate.readthedocs.io/en/latest/setting_up_the_physics.html?highlight=physics%20list#new-physics-list-mechanism">https://opengate.readthedocs.io/en/latest/setting_up_the_physics.html?highlight=physics%20list#new-physics-list-mechanism</a>>
by replacing your physics section with “/gate/physics/addPhysicsList emstandard_opt4”. Your source definition also contains a few deprecation warnings.<br>
<br>
Cheers,<br>
Matthew<br>
<br>
From: Xinjie Cao <xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu>><br>
Date: Tuesday, January 19, 2021 at 11:41<br>
To: Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>><br>
Subject: Re: [Gate-users] Weird Phantom Warning<br>
CAUTION: The Sender of this email is not from within Dalhousie.<br>
Hi Matthew,<br>
<br>
I did the test as you recommended, there is still an error/warning with only phantom1 as water (no daughter). Also, I checked my GATE material database and I didn't find anything wrong. Here is the database file and a simplified macro, feel free to try it and
let me know if you have any questions or insight. Thank you for you kindly help!<br>
<br>
Best,<br>
Xinjie<br>
<br>
On Tue, Jan 19, 2021 at 10:11 AM Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>> wrote:<br>
Hi Xenjie,<br>
<br>
What happens when you define only phantom1 as water with no daughters? Check the definition of water in your materials database to make sure it’s not a problem there. If that doesn’t give any insight, could you send a simplified macro with the minimum lines
that reproduce your error?<br>
Matthew<br>
<br>
<br>
On Jan 19, 2021, at 11:01 AM, Xinjie Cao <xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu>> wrote:<br>
<br>
CAUTION: The Sender of this email is not from within Dalhousie.<br>
Hi Matthew,<br>
<br>
Same error, the error/warning disappears only when I change the phantom 3 material from water to air.<br>
<br>
Best,<br>
Xinjie<br>
<br>
On Tue, Jan 19, 2021 at 7:18 AM Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>> wrote:<br>
What happens when you define phantom 3 as the daughter of phantom 2? It’s still defined as the daughter of phantom 1.<br>
Matthew<br>
<br>
<br>
On Jan 19, 2021, at 12:14 AM, Xinjie Cao <xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu>> wrote:<br>
<br>
CAUTION: The Sender of this email is not from within Dalhousie.<br>
Hi Matthew,<br>
<br>
I tested another phantom configuration with some modification based on the before version. While the same error/warning showed again once I changed the phantom 3 material from the air to water, is there any rule about the material setting?<br>
<br>
/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Polyethylene<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setRmin 2.4 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Air<br>
/gate/phantom2/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom3<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom3/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom3/geometry/setRmax 1.6 mm<br>
/gate/phantom3/geometry/setHeight 700 mm<br>
/gate/phantom3/setMaterial Air<br>
/gate/phantom3/attachPhantomSD<br>
<br>
Best,<br>
Xinjie<br>
<br>
On Mon, Jan 18, 2021 at 3:16 PM Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>> wrote:<br>
You should always set the model dimensions to be exactly equal to the physical dimensions for accurate modelling. From there, check to make sure you do not have any overlapping geometries with the command “/geometry/test/run” in your macro following “/gate/run/initialize”.
If you do have overlapping geometries, GATE will tell you what is overlapping, where it’s overlapping, and by how much.<br>
<br>
In some cases of exact dimensions, I found that abutting geometries required trimming by 1um to avoid overlap warnings, but they are just warnings and should not restrict the simulation from running. I trimmed them for peace of mind.<br>
<br>
Best,<br>
Matthew<br>
<br>
From: Xinjie Cao <xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu>><br>
Date: Monday, January 18, 2021 at 15:40<br>
To: Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>><br>
Cc: gate-users@lists.opengatecollaboration.org<mailto:gate-users@lists.opengatecollaboration.org> <gate-users@lists.opengatecollaboration.org<mailto:gate-users@lists.opengatecollaboration.org>><br>
Subject: Re: [Gate-users] Weird Phantom Warning<br>
CAUTION: The Sender of this email is not from within Dalhousie.<br>
Hi Matthew,<br>
<br>
Thanks! I think I get your point now. One more question about the detailed size of the daughter volume. As for the example you presented in the last email, If the mother cylinder is with a 3.2 mm radius, what is the actual radius should I define for the following
daughter cylinder? Rmax is 3.2 or 3.199 (some number that is very close to 3.2) considering the overlap? Or it doesn't matter?<br>
<br>
Best,<br>
Xinjie<br>
<br>
On Mon, Jan 18, 2021 at 1:59 PM Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>> wrote:<br>
Hi Xinjie,<br>
<br>
In any geometry definition, it is important to follow these three rules when building a volume<<a href="https://opengate.readthedocs.io/en/latest/defining_a_geometry.html?highlight=daughter#building-a-volume">https://opengate.readthedocs.io/en/latest/defining_a_geometry.html?highlight=daughter#building-a-volume</a>>:<br>
<br>
* A volume which is located inside another must be its daughter<br>
* A daughter must be fully included in its mother<br>
* Volumes must not overlap.<br>
This may require you to get creative with daughter definitions in order to obtain a final geometry representing your physical setup.<br>
<br>
Your geometry does not satisfy these points based on the issues that I previously outlined. If part of your geometry requires polyethylene with a height of 800mm, I would start by defining that size as your mother volume. You can add on a daughter volume if
you need a specific 100 mm region to be replaced with air.<br>
<br>
Consider, for example, that you define a mother polyethylene cylinder with a radius of 3.2 mm. Next, you define a daughter cylinder of air with a radius r of 2.4 <= r(mm) < 3.2 and within that daughter, you define a daughter cylinder of water with a radius
of 0 <= r(mm) < 1.6. The remaining volume between 1.6 <= r(mm) < 2.4 will remain as polyethylene (i.e. there’s no need to redefine a daughter of polyethylene with those dimensions). Try to use that approach when defining your nested phantoms.<br>
<br>
Hth,<br>
Matthew<br>
<br>
<br>
From: Xinjie Cao <xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu>><br>
Date: Monday, January 18, 2021 at 13:08<br>
To: Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>><br>
Cc: gate-users@lists.opengatecollaboration.org<mailto:gate-users@lists.opengatecollaboration.org> <gate-users@lists.opengatecollaboration.org<mailto:gate-users@lists.opengatecollaboration.org>><br>
Subject: Re: [Gate-users] Weird Phantom Warning<br>
CAUTION: The Sender of this email is not from within Dalhousie.<br>
Hi Matthew,<br>
<br>
Thanks for your remind, how about setting the phantom 3 as the world daughter too to avoid that violation? Because that 800 mm length is according to the NEMA standard, so I am guessing better keep it if it could be solved.<br>
<br>
For the phantom 3 configuration, I think it is necessary. There is actually an air gap between the inner plastic tube and the outer 200 mm diameter plastic shell according to the standard I believe.<br>
<br>
Best,<br>
Xinjie<br>
<br>
On Mon, Jan 18, 2021 at 11:58 AM Matthew Strugari <matthew.strugari@dal.ca<mailto:matthew.strugari@dal.ca>> wrote:<br>
Hi Xinjie,<br>
<br>
It looks like you have issues with overlapping geometries. You could try nesting phantom4 within phantom3 and nest phantom3 within phantom2. Also, is the height of phantom3 correct at 800mm? This does not fit within your parent volume of phantom1.<br>
<br>
Alternatively, is phantom3 even required? It looks like you’re reinserting polystyrene after voiding the region with air in phantom2. This could be avoided by setting Rmin to 2.4mm in phantom2.<br>
<br>
Regards,<br>
Matthew<br>
<br>
From: Gate-users <gate-users-bounces@lists.opengatecollaboration.org<mailto:gate-users-bounces@lists.opengatecollaboration.org>> on behalf of Xinjie Cao <xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu>><br>
Date: Monday, January 18, 2021 at 12:38<br>
To: gate-users@lists.opengatecollaboration.org<mailto:gate-users@lists.opengatecollaboration.org> <gate-users@lists.opengatecollaboration.org<mailto:gate-users@lists.opengatecollaboration.org>><br>
Subject: [Gate-users] Weird Phantom Warning<br>
CAUTION: The Sender of this email is not from within Dalhousie.<br>
Dear GATE users,<br>
<br>
I am simulating the count rate performance of some PET scanners, while I found an interesting warning/error when I made a change to the phantom configuration.<br>
<br>
With the following simplified phantom configuration, both single thread or cluster tool can run the macro well:<br>
#==========================<br>
# P H A N T O M<br>
#==========================<br>
<br>
/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Polyethylene<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Air<br>
/gate/phantom2/attachPhantomSD<br>
<br>
While when I added two more daughter phantoms inside the previous outer shell volume as followed,<br>
<br>
#===========================<br>
# P H A N T O M<br>
#===========================<br>
<br>
/gate/world/daughters/name phantom1<br>
/gate/world/daughters/insert cylinder<br>
/gate/phantom1/placement/setTranslation 0.0 0.0 0.0 mm<br>
/gate/phantom1/geometry/setRmax 101.5 mm<br>
/gate/phantom1/geometry/setHeight 700 mm<br>
/gate/phantom1/setMaterial Polyethylene<br>
/gate/phantom1/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom2<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom2/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom2/geometry/setRmax 3.2 mm<br>
/gate/phantom2/geometry/setHeight 700 mm<br>
/gate/phantom2/setMaterial Air<br>
/gate/phantom2/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom3<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom3/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom3/geometry/setRmax 2.4 mm<br>
/gate/phantom3/geometry/setRmin 1.6 mm<br>
/gate/phantom3/geometry/setHeight 800 mm<br>
/gate/phantom3/setMaterial Polyethylene<br>
/gate/phantom3/attachPhantomSD<br>
<br>
/gate/phantom1/daughters/name phantom4<br>
/gate/phantom1/daughters/insert cylinder<br>
/gate/phantom4/placement/setTranslation 0.0 -45.0 0.0 mm<br>
/gate/phantom4/geometry/setRmax 1.6 mm<br>
/gate/phantom4/geometry/setHeight 700 mm<br>
/gate/phantom4/setMaterial Water<br>
/gate/phantom4/attachPhantomSD<br>
<br>
the GATE feedbacked a warning/error like this,<br>
<br>
*** Break *** segmentation violation<br>
<br>
===========================================================<br>
There was a crash.<br>
This is the entire stack trace of all threads:<br>
===========================================================<br>
#0 0x00007f563c6d146c in waitpid () at /lib64/libc.so.6<br>
#1 0x00007f563c64ef62 in do_system () at /lib64/libc.so.6<br>
#2 0x00007f564b4c70c4 in TUnixSystem::StackTrace() () at /home/goldan/GATE/root/lib/libCore.so.6.18<br>
#3 0x00007f564b4c97fc in TUnixSystem::DispatchSignals(ESignals) () at /home/goldan/GATE/root/lib/libCore.so.6.18<br>
#4 0x00007f56471f4630 in <signal handler called> () at /lib64/libpthread.so.0<br>
#5 0x0000000000000040 in ()<br>
#6 0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()<br>
#7 0x000000000087a8e6 in GateDetectorConstruction::~GateDetectorConstruction() ()<br>
#8 0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations() (this=this<br>
entry=0x32997c0) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236<br>
#9 0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0, __in_chrg=<optimized out>) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211<br>
#10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()<br>
#11 0x000000000050198f in main ()<br>
===========================================================<br>
<br>
<br>
The lines below might hint at the cause of the crash.<br>
You may get help by asking at the ROOT forum <a href="http://root.cern.ch/forum">
http://root.cern.ch/forum</a><br>
Only if you are really convinced it is a bug in ROOT then please submit a<br>
report at <a href="http://root.cern.ch/bugs">http://root.cern.ch/bugs</a> Please post the ENTIRE stack trace<br>
from above as an attachment in addition to anything else<br>
that might help us fixing this issue.<br>
===========================================================<br>
#5 0x0000000000000040 in ()<br>
#6 0x00000000008e2658 in GateMaterialDatabase::~GateMaterialDatabase() ()<br>
#7 0x000000000087a8e6 in GateDetectorConstruction::~GateDetectorConstruction() ()<br>
#8 0x00007f564423a1e6 in G4RunManager::DeleteUserInitializations() (this=this<br>
entry=0x32997c0) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:236<br>
#9 0x00007f564423ae75 in G4RunManager::~G4RunManager() (this=0x32997c0, __in_chrg=<optimized out>) at /home/goldan/GATE/geant4.10.05.p01/source/run/src/G4RunManager.cc:211<br>
#10 0x0000000000830e19 in GateRunManager::~GateRunManager() ()<br>
#11 0x000000000050198f in main ()<br>
===========================================================<br>
<br>
<br>
WARNING - Attempt to delete the physical volume store while geometry closed !<br>
WARNING - Attempt to delete the logical volume store while geometry closed !<br>
WARNING - Attempt to delete the solid store while geometry closed !<br>
WARNING - Attempt to delete the region store while geometry closed !<br>
<br>
The cluster tool could run the macro with added phantom configuration well with no warning/error, so I am not sure where the wrong with it or whether it has an influence on the simulation result. I probably have seen a similar issue when I used CASToR for reconstruction
so I am guessing it is related to ROOT?<br>
<br>
Did anyone ever meet this issue before? Any reply will be highly appreciated! Thanks!<br>
<br>
Best,<br>
Xinjie<br>
<br>
<br>
<br>
--<br>
....................................................<br>
Xinjie Cao<br>
M.E. / Ph.D. Candidate<br>
Research Project Assistant<br>
Department of Electrical and Computer Engineering & Radiology<br>
Novel Medical Imaging Technologies Lab<br>
Health Science Center Level 8<br>
Stony Brook, NY 11794-8460<br>
Tel: +1 (631)202-9445<br>
you.stonybrook.edu/goldan/people/<https://you.stonybrook.edu/goldan/people/><br>
email: xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu><br>
<br>
[<a href="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ">https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ</a>]
[<a href="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download">https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download</a>]<br>
....................................................<br>
It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<br>
<br>
<br>
--<br>
....................................................<br>
Xinjie Cao<br>
M.E. / Ph.D. Candidate<br>
Research Project Assistant<br>
Department of Electrical and Computer Engineering & Radiology<br>
Novel Medical Imaging Technologies Lab<br>
Health Science Center Level 8<br>
Stony Brook, NY 11794-8460<br>
Tel: +1 (631)202-9445<br>
you.stonybrook.edu/goldan/people/<https://you.stonybrook.edu/goldan/people/><br>
email: xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu><br>
<br>
[<a href="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ">https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ</a>]
[<a href="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download">https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download</a>]<br>
....................................................<br>
It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<br>
<br>
<br>
--<br>
....................................................<br>
Xinjie Cao<br>
M.E. / Ph.D. Candidate<br>
Research Project Assistant<br>
Department of Electrical and Computer Engineering & Radiology<br>
Novel Medical Imaging Technologies Lab<br>
Health Science Center Level 8<br>
Stony Brook, NY 11794-8460<br>
Tel: +1 (631)202-9445<br>
you.stonybrook.edu/goldan/people/<https://you.stonybrook.edu/goldan/people/><br>
email: xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu><br>
<br>
[<a href="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ">https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ</a>]
[<a href="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download">https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download</a>]<br>
....................................................<br>
It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<br>
<br>
<br>
--<br>
....................................................<br>
Xinjie Cao<br>
M.E. / Ph.D. Candidate<br>
Research Project Assistant<br>
Department of Electrical and Computer Engineering & Radiology<br>
Novel Medical Imaging Technologies Lab<br>
Health Science Center Level 8<br>
Stony Brook, NY 11794-8460<br>
Tel: +1 (631)202-9445<br>
you.stonybrook.edu/goldan/people/<https://you.stonybrook.edu/goldan/people/><br>
email: xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu><br>
<br>
[<a href="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ">https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ</a>]
[<a href="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download">https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download</a>]<br>
....................................................<br>
It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<br>
<br>
<br>
--<br>
....................................................<br>
Xinjie Cao<br>
M.E. / Ph.D. Candidate<br>
Research Project Assistant<br>
Department of Electrical and Computer Engineering & Radiology<br>
Novel Medical Imaging Technologies Lab<br>
Health Science Center Level 8<br>
Stony Brook, NY 11794-8460<br>
Tel: +1 (631)202-9445<br>
you.stonybrook.edu/goldan/people/<https://you.stonybrook.edu/goldan/people/><br>
email: xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu><br>
<br>
[<a href="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ">https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ</a>]
[<a href="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download">https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download</a>]<br>
....................................................<br>
It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<br>
<br>
<br>
--<br>
....................................................<br>
Xinjie Cao<br>
M.E. / Ph.D. Candidate<br>
Research Project Assistant<br>
Department of Electrical and Computer Engineering & Radiology<br>
Novel Medical Imaging Technologies Lab<br>
Health Science Center Level 8<br>
Stony Brook, NY 11794-8460<br>
Tel: +1 (631)202-9445<br>
you.stonybrook.edu/goldan/people/<https://you.stonybrook.edu/goldan/people/><br>
email: xinjie.cao@stonybrook.edu<mailto:xinjie.cao@stonybrook.edu><br>
<br>
[<a href="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ">https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ</a>]
[<a href="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download">https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download</a>]<br>
....................................................<br>
It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.<br>
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