[Gate-users] Core dumped, Error, Failed to create output

[David Boersma]

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

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