[Gate-users] GATE on Raspberry Pi

Mon Jan 7 14:40:05 CET 2019

Thanks for the quick response

I'm using a release version of Gate downloaded directly from opengatecollaboration.org, gate --version gives me 8.1.p01.

While perhaps not the simplest macro, the below demonstrates what I'm doing:

#############################################################################
###  CHEMISTRY
/gate/geometry/setMaterialDatabase GateMaterials.db

###  WORLD
/gate/world/geometry/setXLength   1000. mm
/gate/world/geometry/setYLength   1000. mm
/gate/world/geometry/setZLength   1000. mm

#    SCREEN
/gate/world/daughters/name   screen
/gate/world/daughters/insert   box
/gate/screen/geometry/setXLength   300. mm
/gate/screen/geometry/setYLength   300. mm
/gate/screen/geometry/setZLength   0.1 mm
/gate/screen/setMaterial   Air

#    PROFILE
/gate/actor/addActor   DoseActor prof
/gate/actor/prof/attachTo   screen
/gate/actor/prof/save   profile.txt
/gate/actor/prof/stepHitType   random
/gate/actor/prof/setPosition   0. 0. 0. mm
/gate/actor/prof/setResolution   1 3000 1
/gate/actor/prof/enableDose   true
/gate/actor/prof/normaliseDoseToMax   true

#    RUN w NO OUTPUT
#/gate/output/allowNoOutput

###  PHYSICS
/gate/physics/addPhysicsList   QGSP_BIC_EMZ
/gate/physics/Gamma/SetCutInRegion   world 1. mm
/gate/physics/Electron/SetCutInRegion   world 1. mm
/gate/physics/Positron/SetCutInRegion   world 1. mm
/gate/physics/SetMaxStepSizeInRegion   world 1. mm
/gate/physics/ActivateStepLimiter   proton
/gate/physics/displayCuts

/gate/run/initialize

###  BEAM
/gate/source/addSource   pncBm PencilBeam
/gate/source/pncBm/setParticleType   proton
/gate/source/pncBm/setPosition   0. 0. -450. mm
/gate/source/pncBm/setEnergy   160.95 MeV
/gate/source/pncBm/setSigmaEnergy   1.52 MeV
/gate/source/pncBm/setSigmaX   1. mm
/gate/source/pncBm/setSigmaY   1. mm
/gate/source/pncBm/setSigmaTheta   1. mrad
/gate/source/pncBm/setSigmaPhi   1. mrad
/gate/source/pncBm/setEllipseXThetaEmittance   0.01 mm*mrad
/gate/source/pncBm/setEllipseYPhiEmittance   0.01 mm*mrad
/gate/source/pncBm/setEllipseXThetaRotationNorm   negative
/gate/source/pncBm/setEllipseYPhiRotationNorm   negative

###  SIMULATE !!!
/gate/random/setEngineName   MersenneTwister
/gate/random/setEngineSeed   auto

/gate/application/setTotalNumberOfPrimaries   1e3

/gate/application/start

exit
#############################################################################

If I remove the dose actor part of the macro (section below '#   PROFILE') and enable allowNoOutput then the simulation completes successfully, however if I include the dose actor I receive the error message in my first post.
I have been able to run the same macro on both my home Mac and a Linux box at work, so suspect it may be a library issue with the Pi, but any direction you may be able to give me would be hugely appreciated.

Thank you
Andrew

Andrew Gosling (DPhil)     |     Clinical Scientist (Proton Beam Physics)
UCLH Radiotherapy Physics, 1st Floor East, 250 Euston Road, London, NW1 2PG
andrew.gosling at nhs.net     |     +44 (0) 203 44 72490

-----Original Message-----
From: David Boersma [mailto:david.boersma at acmit.at]
Sent: 07 January 2019 12:42
To: GOSLING, Andrew (UNIVERSITY COLLEGE LONDON HOSPITALS NHS FOUNDATION TRUST); gate-users at lists.opengatecollaboration.org
Subject: AW: GATE on Raspberry Pi

Hi Andrew,

How cool, that you were able to install Gate on a Raspberry Pi!

In order to address your issue, we need to be able to reproduce your error. I am suspecting that this crash is not due to the hardware that it runs on, but due to incorrect usage. Ideally, incorrect use should result in informative error messages, but unfortunately Gate does not always check all its inputs, which especially for new users can easily result in such crashes. We hope to gradually improve on this, but it will take time.

(1) which version did you install (a release, or develop branch from git)?
(2) could you create a short Gate macro that we can use to reproduce this crash?

Thanks!
David

________________________________________
Von: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> im Auftrag von GOSLING, Andrew (UNIVERSITY COLLEGE LONDON HOSPITALS NHS FOUNDATION TRUST) <andrew.gosling at nhs.net>
Gesendet: Montag, 7. Jänner 2019 11:42:51
An: gate-users at lists.opengatecollaboration.org
Betreff: [Gate-users] GATE on Raspberry Pi

Dear Gate-ers

I'm trying to get GATE running on a Pi, all seems to run OK until I try to read out data from the simulation using an Actor.  I then get the error message:

*** Break *** segmentation violation

===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x72ce4c90 in __GI___waitpid (pid=pid
entry=888, stat_loc=stat_loc
entry=0x7e81f2d4, options=options
entry=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
#1  0x72c7fc60 in do_system (line=<optimized out>) at ../sysdeps/posix/system.c:148
#2  0x766f57e4 in TUnixSystem::Exec (shellcmd=<optimized out>, this=0x0) at /usr/local/root/root-6.12.06/core/unix/src/TUnixSystem.cxx:2118
#3  TUnixSystem::StackTrace (this=0x0) at /usr/local/root/root-6.12.06/core/unix/src/TUnixSystem.cxx:2412
#4  0x766f7c38 in TUnixSystem::DispatchSignals (this=0x250a168, sig=kSigSegmentationViolation) at /usr/local/root/root-6.12.06/core/unix/src/TUnixSystem.cxx:3643
#5  <signal handler called>
#6  0x002fb52c in GateImageWithStatistic::SaveData(int, bool) ()
#7  0x7e821660 in ?? ()
===========================================================

The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum http://root.cern.ch/forum.
Only if you are really convinced it is a bug in ROOT then please submit a
report at http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#6  0x002fb52c in GateImageWithStatistic::SaveData(int, bool) ()
#7  0x7e821660 in ?? ()
===========================================================

I have Gate 8.1, Geant4 10.3.03, and Root 6.12/06 running on a Pi 3 B+
Has anyone seen something similar before, or can point me towards a way to solve this issue?

Thanks
Andrew

Andrew Gosling (DPhil)     |     Clinical Scientist (Proton Beam Physics)
UCLH Radiotherapy Physics, 1st Floor East, 250 Euston Road, London, NW1 2PG
andrew.gosling at nhs.net<mailto:andrew.gosling at nhs.net>     |     +44 (0) 203 44 72490

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