[Run issue]: Problem running demos

[jonahpeter]

Contact Details

No response

What was the issue?

Hi all, I get the following error when running source rundemos.sh from the /Applications/TOPAS-nBio directory

(base) dhcp-10-250-246-187:Scoring jonahpeter$ cd /Applications/TOPAS-nBio/
(base) dhcp-10-250-246-187:TOPAS-nBio jonahpeter$ source rundemos.sh
Topas quitting, unable to open parameter file:../../scorers/DNAScorerStepByStep.txt
--failed -- dna/CharltonDNA.txt
Topas quitting, unable to open parameter file:../../scorers/DNAScorerStepByStep.txt
--failed -- dna/LinearDNA.txt
Topas quitting, unable to open parameter file:../../scorers/DNAScorerStepByStep.txt
--failed -- dna/CircularPlasmid.txt
^C

best,
Jonah

TOPAS-nBio category

Example

Version

3.0

What Operative System (OS) are you running on?

MacOS

Relevant log output

No response

Code of Conduct

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[icmeyer]

Hi again Jonah,
So it looks like there are two different example scripts. One in the source code directory (wherever you cloned nBio to) one in the build and install directories (/Applications/TOPAS/OpenTOPAS-build from the current README`). Trying the one in the source code directory gives me the same output that you got (aka it's broken!), but the one in the installation directory looks something like this

#!/bin/csh -f
#
cd examples/TimeFeature
../../bin/topas BoxWithinBox.txt
../../bin/topas CameraRotateAndZoom.txt
../../bin/topas CylinderGrowingInPhi.txt
cd ../UCSFETF
../../bin/topas User_SOBP24_Viewer.txt
../../bin/topas User_Beamline_WC_Viewer.txt
cd ../SpecialComponents
../../bin/topas QuadAndDipoleMagnets.txt
../../bin/topas PurgingMagnet_move.txt
../../bin/topas MultiLeafCollimator_sequence.txt
../../bin/topas RangeModulator_CurrentModulatedBeam.txt
cd ../Nozzle
../../bin/topas ScatteringNozzle_run.txt
../../bin/topas ScanningTargetMovingHorizontal.txt
cd ../Patient
unzip Abdomen.zip
../../bin/topas ViewAbdomen.txt
rm -rf Abdomen
tar -zxf synthetic_lung.tar.bz2
../../bin/topas DoseTo4DCT.txt
rm -rf synthetic_lung
unzip DICOM_Box
../../bin/topas Implant.txt
rm -rf DICOM_Box
cd ../TimeFeature
../../bin/topas Darkening.txt
rm *.csv
../../bin/topas Logo.txt
cd ../..
rm examples/*/NbParticlesInTime.txt

It should have the file extension .csh. You can try running that one for now while rundemos.sh is broken

[JoseRamosMendez]

The issue with the topas-nbio's rundemos.sh is the hierarchy of the subdirectories. That is, the script calls (e.g.,)

topas dna/CharltonDNA.txt

But that parameter file calls for ../../DNAScorerStepByStep.txt without entering the directory examples/dna/. But we recently moved to a continuous integration suite that you can download here. It does the same thing than rundemos.sh but in a more structured way.

Note

Put attention while installing nrtest so you don't affect your current python installation

[jonahpeter]

Great, thank you both for the help!