[Gate-users] Gate-users Digest, Vol 167, Issue 23

Somayeh Asadi somayeh.asadi at polimi.it
Wed Apr 15 12:18:06 CEST 2020 

Dear David
Thank you very much for your explanation. I should say that an empty folder with the name of output was created and defined in the same path where the program is saved.
However, I changed the path written in the program and delete the output, so it is expected that output is created in the same folder where the program is saved. But there is still nothing. Statistic. txt is not created.
Another point is that, even if you make a mistake to define a correct path for output the program should run up to the end of that but you can not see the output in the folder. But here the core dumped occurs and I don't know the reason of  that.  I put the screenshot of the final error in the terminal here.
The full program may be would be helpful to understand what the problem is so below you can find the complete written program. May be the problem is because of the program in some part that I don't know.
#################################################################
#
# Example of hyperthermia therapy induced by gold nanoparticles
# irradiated by photons
#
##################################################################
 #=================================================================
# VISUALISATION
#=================================================================
/vis/open    VRML2FILE
/vis/drawVolume
/vis/viewer/set/viewpointThetaPhi   90 0
/vis/viewer/zoom                    1
/vis/drawVolume
/vis/viewer/flush
/vis/drawVolume
/tracking/storeTrajectory           1
/vis/scene/add/trajectories
/vis/scene/endOfEventAction         accumulate  10
#=================================================================
# VERBOSE
#=================================================================
/gate/verbose Physic    1
/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/output/verbose    1
#=================================================================
# W O R L D
#=================================================================
/gate/geometry/setMaterialDatabase    GateMaterials.db
/gate/world/geometry/setXLength       20. cm
/gate/world/geometry/setYLength       20. cm
/gate/world/geometry/setZLength       20. cm
/gate/world/setMaterial               Air
/gate/geometry/rebuild
#=================================================================
# P H A N T O M : M O B Y
#=================================================================
/gate/world/daughters/name                              Mouse
/gate/world/daughters/insert                            compressedMatrix
/gate/Mouse/geometry/insertReader                       interfile
/gate/Mouse/interfileReader/insertTranslator            range
/gate/Mouse/interfileReader/rangeTranslator/readTable   ./attenuation.dat
/gate/Mouse/interfileReader/rangeTranslator/describe    1
/gate/Mouse/interfileReader/readFile                    ./MOBY1cmTumor.h33
/gate/Mouse/placement/setTranslation                    0. 0. 0. cm
/gate/Mouse/placement/setRotationAxis                   1 0 0
/gate/Mouse/placement/setRotationAngle                  90 deg
/gate/Mouse/vis/forceWireframe
/gate/geometry/rebuild
#=================================================================
# P H Y S I C S
#=================================================================
/gate/physics/addProcess OpticalAbsorption
/gate/physics/addProcess OpticalRayleigh
/gate/physics/addProcess OpticalMie
/gate/physics/addProcess OpticalBoundary
/gate/physics/addProcess NanoAbsorption
/gate/physics/processList Enabled
/gate/physics/processList Initialized
#=================================================================
# T H E R M A L   A C T O R
#=================================================================
/gate/actor/addActor ThermalActor        nano
/gate/actor/nano/save                    Mobydose.mhd
/gate/actor/nano/attachTo                Mouse
/gate/actor/nano/stepHitType             random
/gate/actor/nano/setPosition             0. 0. 0. cm
/gate/actor/nano/setVoxelSize            0.25 0.25 0.25 mm
/gate/actor/nano/setDiffusionTime               2 s
/gate/actor/nano/setThermalDiffusivity         0.190 mm2/s
/gate/actor/nano/setBloodPerfusionRate 0.004
/gate/actor/nano/setBloodDensity           1.06E-6
/gate/actor/nano/setBloodHeatCapacity     3.6E6
/gate/actor/nano/setTissueDensity         1.04E-6
/gate/actor/nano/setTissueHeatCapacity     3.65E6
/gate/actor/nano/setSimulationScale         1E10
/gate/actor/nano/setNumberOfTimeFrames          60
/gate/actor/addActor SimulationStatisticActor Myactor
/gate/actor/Myactor/save                      Statistics.txt
/gate/actor/Myactor/attachTo                Mouse
/gate/actor/Myactor/save     EveryNSeconds              0.5
#=================================================================
# INITIALISATION
#=================================================================
/gate/run/initialize
#=================================================================
# S O U R C E
#=================================================================
/gate/source/addSource                           Mysource gps
/gate/source/Mysource/gps/particle               opticalphoton
/gate/source/Mysource/gps/energytype             Mono
/gate/source/Mysource/setActivity                20000 becquerel
/gate/source/Mysource/gps/polarization           1 0 0
/gate/source/Mysource/gps/monoenergy             1.51 eV
/gate/source/Mysource/gps/type Beam
/gate/source/Mysource/gps/pos/centre             0. 0.45 -1.3 cm
/gate/source/Mysource/gps/direction              0. 0. 1.
/gate/source/Mysource/gps/pos/shape Circle
/gate/source/Mysource/gps/pos/radius 2.5 mm
/gate/source/Mysource/gps/mintheta -30. deg
/gate/source/Mysource/gps/maxtheta  30. deg
/gate/source/Mysource/gps/minphi   0. deg
/gate/source/Mysource/gps/maxphi 360. deg
#=================================================================
# R A N D O M
#=================================================================
/gate/random/setEngineName MersenneTwister
/gate/random/setEngineSeed auto
#/gate/random/setEngineSeed 666677
/gate/random/verbose 1
#=================================================================
# A C Q U I S I T I O N
#=================================================================
/gate/application/setTimeSlice   60 s
/gate/application/setTimeStart   0 s
/gate/application/setTimeStop    60 s
/gate/application/startDAQ

[cid:ae5d4b04-f1a8-4e80-bf4d-2e06fdf9a7b7]

If you do me a favor and guide me in this regard I would be so grateful.

Respectfully


Somayeh Asadi (PhD)
Postdoctoral Researcher
Department of Mechanical Engineering
Politecnico di Milano, Italy

Via Giuseppe La Masa,1
20156 - Milano - Italy
phone: +39 0223998572

somayeh.asadi at polimi.it

________________________________
From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> on behalf of gate-users-request at lists.opengatecollaboration.org <gate-users-request at lists.opengatecollaboration.org>
Sent: Tuesday, April 14, 2020 11:17 PM
To: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: Gate-users Digest, Vol 167, Issue 23

Send Gate-users mailing list submissions to
        gate-users at lists.opengatecollaboration.org

To subscribe or unsubscribe via the World Wide Web, visit
        http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
or, via email, send a message with subject or body 'help' to
        gate-users-request at lists.opengatecollaboration.org

You can reach the person managing the list at
        gate-users-owner at lists.opengatecollaboration.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Gate-users digest..."


Today's Topics:

   1. error while loading shared libraries: libG4global.so
      (Mohammed REZZOUG)
   2. Re: Core dumped, Error, Failed to create output (David Boersma)


----------------------------------------------------------------------

Message: 1
Date: Tue, 14 Apr 2020 20:54:33 +0100
From: Mohammed REZZOUG <nmedrezz at gmail.com>
To: gate-users at lists.opengatecollaboration.org
Subject: [Gate-users] error while loading shared libraries:
        libG4global.so
Message-ID:
        <CAOGFTHAM-babgiyS72cKX_CBz61FeNwOoRQzLuMqzdwzT=f0qg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Gate users
I’m getting the following error:
---
med at med-SATELLITE-C855-2CE:~$ sudo condor_master
[sudo] Mot de passe de med :
med at med-SATELLITE-C855-2CE:~$ export GC_DOT_GATE_DIR=/home/med/linac2/main
med at med-SATELLITE-C855-2CE:~$ export
GC_GATE_EXE_DIR=/usr/local/GATE/Gate-9.0-install/bin
med at med-SATELLITE-C855-2CE:~$
/usr/local/GATE/Gate-9.0/cluster_tools/jobsplitter/gjs  -numberofsplits 50
-clusterplatform condor -condorscript
/usr/local/GATE/Gate-9.0/cluster_tools/jobsplitter/script/condor.script
/home/med/linac2/main/main.mac
/usr/local/GATE/Gate-9.0/cluster_tools/jobsplitter/gjs:* error while
loading shared libraries: libG4global.so: cannot open shared object file:
No such file or directory*

*----*
Thank you very much for your reading and any suggestion.
Sincere wishes,

Rezzoug
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200414/dbbd07e3/attachment-0001.html>

------------------------------

Message: 2
Date: Tue, 14 Apr 2020 21:35:24 +0000
From: David Boersma <david.boersma at acmit.at>
To: "gate-users at lists.opengatecollaboration.org"
        <gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Core dumped, Error, Failed to create output
Message-ID: <e96b05dc542644f2a9028782cdc5c2e1 at acmit.at>
Content-Type: text/plain; charset="iso-8859-1"

Dear Somayeh Asadi,

The error message basically says that it is not able to create the output file.
I think that one quite commonly occurring way to get this error is if the directory in which you run Gate does not yet have an "output" subdirectory. You request that the output is written to "output/Mobydose.mhd"; the "output/" folder is *not* automatically created if does not exist yet. (Or maybe it does exist, but you don't have writing permissions for it. Or maybe the disk is full.)

Could you please let us know if this is the case, before we try fancier explanations?

(Maybe someone should create a GitHub #issue about this. Inability to write the output to the configured filepath should not result in an ugly crash, it should either exit gracefully with a friendly informative error message, or it should kindly try to fix it, if all it takes is creating a subdirectory automagically.)


HTH,

David

________________________________
Von: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> im Auftrag von Somayeh Asadi <somayeh.asadi at polimi.it>
Gesendet: Dienstag, 14. April 2020 14:18:45
An: gate-users at lists.opengatecollaboration.org
Betreff: [Gate-users] Core dumped, Error, Failed to create output

Dear Gate User

I want to run the ready program in Gate with the name of Thermal being in the folder of Imaging/Thermal in the subfolder of GateContrib-master. In the program, It was asked for the two outputs name: Mobydose.mhd   and  Statistics.txt  written in the part related to Actor.

/vis/open    VRML2FILE
/vis/drawVolume
/vis/viewer/set/viewpointThetaPhi   90 0
/vis/viewer/zoom                    1
/vis/drawVolume
/vis/viewer/flush
/vis/drawVolume
/tracking/storeTrajectory           1
/vis/scene/add/trajectories
/vis/scene/endOfEventAction         accumulate  10
#################################################
/gate/actor/addActor ThermalActor        nano
/gate/actor/nano/save                    output/Mobydose.mhd
/gate/actor/nano/attachTo                Mouse
/gate/actor/nano/stepHitType             random
/gate/actor/nano/setPosition             0. 0. 0. cm
/gate/actor/nano/setVoxelSize            0.25 0.25 0.25 mm
/gate/actor/nano/setDiffusionTime               2 s
/gate/actor/nano/setThermalDiffusivity         0.190 mm2/s
/gate/actor/nano/setBloodPerfusionRate 0.004
/gate/actor/nano/setBloodDensity           1.06E-6
/gate/actor/nano/setBloodHeatCapacity     3.6E6
/gate/actor/nano/setTissueDensity         1.04E-6
/gate/actor/nano/setTissueHeatCapacity     3.65E6
/gate/actor/nano/setSimulationScale         1E10
/gate/actor/nano/setNumberOfTimeFrames          60
/gate/actor/addActor SimulationStatisticActor Myactor
/gate/actor/Myactor/save    output/Statistics.txt
/gate/actor/Myactor/attachTo                Mouse
/gate/actor/Myactor/save     EveryNSeconds              0.5



When the program is running, core dumped accrues, n output created and the error in below is received:
----------------------------------------------------------------------------------------------------------------
terminate called after throwing an instance of 'itk::ImageFileReaderException'
  what():  /home/BuildFiles/ITK/InsightToolkit-5.0.0-Source/Modules/IO/ImageBase/include/itkImageFileReader.hxx:136:
 Could not create IO object for reading file output/Mobydose-AbsorptionMap.mhd
  Tried to create one of the following:
    GDCMImageIO
  You probably failed to set a file suffix, or
    set the suffix to an unsupported type.

Aborted (core dumped)
----------------------------------------------------------------------------------------------------------------

 Has any person had the same problem and know about the meaning of this error?
"I have installed ITK and put the part related to the optical photon in ON".
Thank you very much for your reading and any suggestion.

Sincere Wishes,




Somayeh Asadi (PhD)
Postdoctoral Researcher
Department of Mechanical Engineering
Politecnico di Milano, Italy

Via Giuseppe La Masa,1
20156 - Milano - Italy
phone: +39 0223998572

somayeh.asadi at polimi.it

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200414/1fbadad3/attachment.html>

------------------------------

Subject: Digest Footer

_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

------------------------------

End of Gate-users Digest, Vol 167, Issue 23
*******************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200415/9465cab4/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 305555 bytes
Desc: image.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200415/9465cab4/attachment-0001.png>

More information about the Gate-users mailing list