[Gate-users] Running Gate on a Cluster using GateTools 'gate_split_and_run.py' Script

Mijat Paunovic paunovicjata at gmail.com
Sat Feb 26 16:21:50 CET 2022


Dear Gate Community,
I am trying to run my Gate script with Python script
'gate_split_and_run.py' from GateTools but I get an error message that says
that my script was not able to be found. A detailed explanation follows.

I am running a Python script with the following command:
*python3
/home/vgate/Desktop/GateTools-master/clustertools/gate_split_and_run.py
/home/vgate/Desktop/master/mac/main.mac -o
/home/vgate/Desktop/master/cluster*

This is what I get in the terminal (complete terminal output is in the
*troubleshooting.txt* attachment):




*[Core-0] Starting macro
/home/vgate/Desktop/master/cluster/mac/main.mac[G4-cerr] ERROR: Can not
open a macro file </home/vgate/Desktop/master/cluster/mac/main.mac>. Set
macro path with "/control/macroPath" if needed.[Gate] Sorry, error in a
macro command : abort.ERROR: gate failed*

This looks to me like a *path* problem so I changed all the paths in my
Gate script to absolute paths. The problem remained the same.

Note: At the moment, I am just trying to run Gate on the 4 CPUs that I
provided to VirtualBox but I plan on using it on a Unix cluster soon.

Kind regards,
Mijat Paunovic
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(base) vgate at vgate:~/Desktop/master$ python3 /home/vgate/Desktop/GateTools-master/clustertools/gate_split_and_run.py /home/vgate/Desktop/master/mac/main.mac -o /home/vgate/Desktop/master

/home/vgate/Desktop/master/mac/main.mac
Found Gate in folder: /home/vgate/Software/Gate/bin/Gate
ERROR: The data folder does not exist: /home/vgate/Desktop/master/data
(base) vgate at vgate:~/Desktop/master$ python3 /home/vgate/Desktop/GateTools-master/clustertools/gate_split_and_run.py /home/vgate/Desktop/master/mac/main.mac -o /home/vgate/Desktop/master/cluster
/home/vgate/Desktop/master/mac/main.mac
Found Gate in folder: /home/vgate/Software/Gate/bin/Gate
WARNING: The output folder already exist: /home/vgate/Desktop/master/cluster
Evereything will be overwritten
Run Id is: cluster
No qsub, run Gate on multiple cores.
/home/vgate/Desktop/master/cluster
Sourcing bashrc
Checking
Linux vgate 5.13.0-28-generic #31~20.04.1-Ubuntu SMP Wed Jan 19 14:08:10 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux
MACRODIR=/home/vgate/Desktop/master/cluster
MACROFILE=/home/vgate/Desktop/master/cluster/mac/main.mac
RELEASEDIR=NONE
OUTPUTDIR=/home/vgate/Desktop/master/cluster
ENVCOMMAND=NONE
PBS_JOBID=local_0
INDEX=0
INDEXMAX=0
PARAM=  -a [JOB_ID,0][JOB_ID,0]
General environment
Using /home/vgate/Software/Gate/bin/Gate
	linux-vdso.so.1 (0x00007ffcea5c0000)
	libG4Tree.so => /home/vgate/Software/Geant4/install/lib/libG4Tree.so (0x00007f5c58ce2000)
	libG4FR.so => /home/vgate/Software/Geant4/install/lib/libG4FR.so (0x00007f5c58cca000)
	libG4GMocren.so => /home/vgate/Software/Geant4/install/lib/libG4GMocren.so (0x00007f5c58c7e000)
	libG4visHepRep.so => /home/vgate/Software/Geant4/install/lib/libG4visHepRep.so (0x00007f5c58be2000)
	libG4RayTracer.so => /home/vgate/Software/Geant4/install/lib/libG4RayTracer.so (0x00007f5c58bb5000)
	libG4VRML.so => /home/vgate/Software/Geant4/install/lib/libG4VRML.so (0x00007f5c58b96000)
	libG4OpenGL.so => /home/vgate/Software/Geant4/install/lib/libG4OpenGL.so (0x00007f5c58afb000)
	libGL.so.1 => /lib/x86_64-linux-gnu/libGL.so.1 (0x00007f5c58a60000)
	libG4vis_management.so => /home/vgate/Software/Geant4/install/lib/libG4vis_management.so (0x00007f5c58946000)
	libG4modeling.so => /home/vgate/Software/Geant4/install/lib/libG4modeling.so (0x00007f5c58842000)
	libG4interfaces.so => /home/vgate/Software/Geant4/install/lib/libG4interfaces.so (0x00007f5c587b0000)
	libQt5Core.so.5 => /lib/x86_64-linux-gnu/libQt5Core.so.5 (0x00007f5c58265000)
	libG4readout.so => /home/vgate/Software/Geant4/install/lib/libG4readout.so (0x00007f5c58259000)
	libG4physicslists.so => /home/vgate/Software/Geant4/install/lib/libG4physicslists.so (0x00007f5c580a2000)
	libG4run.so => /home/vgate/Software/Geant4/install/lib/libG4run.so (0x00007f5c58010000)
	libG4event.so => /home/vgate/Software/Geant4/install/lib/libG4event.so (0x00007f5c57f93000)
	libG4tracking.so => /home/vgate/Software/Geant4/install/lib/libG4tracking.so (0x00007f5c57f43000)
	libG4processes.so => /home/vgate/Software/Geant4/install/lib/libG4processes.so (0x00007f5c56302000)
	libG4digits_hits.so => /home/vgate/Software/Geant4/install/lib/libG4digits_hits.so (0x00007f5c56228000)
	libG4track.so => /home/vgate/Software/Geant4/install/lib/libG4track.so (0x00007f5c56207000)
	libG4particles.so => /home/vgate/Software/Geant4/install/lib/libG4particles.so (0x00007f5c560e0000)
	libG4geometry.so => /home/vgate/Software/Geant4/install/lib/libG4geometry.so (0x00007f5c55de0000)
	libG4materials.so => /home/vgate/Software/Geant4/install/lib/libG4materials.so (0x00007f5c55cfc000)
	libG4graphics_reps.so => /home/vgate/Software/Geant4/install/lib/libG4graphics_reps.so (0x00007f5c55cae000)
	libG4intercoms.so => /home/vgate/Software/Geant4/install/lib/libG4intercoms.so (0x00007f5c55c38000)
	libG4global.so => /home/vgate/Software/Geant4/install/lib/libG4global.so (0x00007f5c55bc1000)
	libG4clhep.so => /home/vgate/Software/Geant4/install/lib/libG4clhep.so (0x00007f5c55b1e000)
	libCore.so => /home/vgate/Software/root/bin/lib/libCore.so (0x00007f5c5557c000)
	libRIO.so => /home/vgate/Software/root/bin/lib/libRIO.so (0x00007f5c551a9000)
	libHist.so => /home/vgate/Software/root/bin/lib/libHist.so (0x00007f5c54d86000)
	libGpad.so => /home/vgate/Software/root/bin/lib/libGpad.so (0x00007f5c54ca8000)
	libTree.so => /home/vgate/Software/root/bin/lib/libTree.so (0x00007f5c54b1a000)
	libPhysics.so => /home/vgate/Software/root/bin/lib/libPhysics.so (0x00007f5c54ac9000)
	libMathCore.so => /home/vgate/Software/root/bin/lib/libMathCore.so (0x00007f5c548a8000)
	libtorch_cpu.so => /home/vgate/Software/libtorch/lib/libtorch_cpu.so (0x00007f5c43eef000)
	libc10.so => /home/vgate/Software/libtorch/lib/libc10.so (0x00007f5c43c6f000)
	libtorch.so => /home/vgate/Software/libtorch/lib/libtorch.so (0x00007f5c43a6d000)
	libfftw3_threads.so.3 => /lib/x86_64-linux-gnu/libfftw3_threads.so.3 (0x00007f5c43a63000)
	libfftw3.so.3 => /lib/x86_64-linux-gnu/libfftw3.so.3 (0x00007f5c4385d000)
	libfftw3f_threads.so.3 => /lib/x86_64-linux-gnu/libfftw3f_threads.so.3 (0x00007f5c43853000)
	libfftw3f.so.3 => /lib/x86_64-linux-gnu/libfftw3f.so.3 (0x00007f5c43643000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f5c434f2000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f5c434cf000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f5c434c9000)
	libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f5c432e7000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f5c432cc000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f5c430da000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f5c5a3da000)
	libG4zlib.so => /home/vgate/Software/Geant4/install/lib/libG4zlib.so (0x00007f5c430ba000)
	libG4tasking.so => /home/vgate/Software/Geant4/install/lib/libG4tasking.so (0x00007f5c4305a000)
	libG4ptl.so.0 => /home/vgate/Software/Geant4/install/lib/libG4ptl.so.0 (0x00007f5c4302e000)
	libG4gl2ps.so => /home/vgate/Software/Geant4/install/lib/libG4gl2ps.so (0x00007f5c43010000)
	libQt5OpenGL.so.5 => /lib/x86_64-linux-gnu/libQt5OpenGL.so.5 (0x00007f5c42fb4000)
	libQt5Widgets.so.5 => /lib/x86_64-linux-gnu/libQt5Widgets.so.5 (0x00007f5c42917000)
	libX11.so.6 => /lib/x86_64-linux-gnu/libX11.so.6 (0x00007f5c427da000)
	libXmu.so.6 => /lib/x86_64-linux-gnu/libXmu.so.6 (0x00007f5c427be000)
	libQt5Gui.so.5 => /lib/x86_64-linux-gnu/libQt5Gui.so.5 (0x00007f5c421d3000)
	libGLdispatch.so.0 => /lib/x86_64-linux-gnu/libGLdispatch.so.0 (0x00007f5c4211b000)
	libGLX.so.0 => /lib/x86_64-linux-gnu/libGLX.so.0 (0x00007f5c420e7000)
	libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f5c420c9000)
	libicui18n.so.66 => /lib/x86_64-linux-gnu/libicui18n.so.66 (0x00007f5c41dca000)
	libicuuc.so.66 => /lib/x86_64-linux-gnu/libicuuc.so.66 (0x00007f5c41be4000)
	libpcre2-16.so.0 => /lib/x86_64-linux-gnu/libpcre2-16.so.0 (0x00007f5c41b61000)
	libdouble-conversion.so.3 => /lib/x86_64-linux-gnu/libdouble-conversion.so.3 (0x00007f5c41b4b000)
	libglib-2.0.so.0 => /lib/x86_64-linux-gnu/libglib-2.0.so.0 (0x00007f5c41a20000)
	libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f5c419f2000)
	libG4analysis.so => /home/vgate/Software/Geant4/install/lib/libG4analysis.so (0x00007f5c4147a000)
	libThread.so => /home/vgate/Software/root/bin/lib/libThread.so (0x00007f5c41420000)
	libMatrix.so => /home/vgate/Software/root/bin/lib/libMatrix.so (0x00007f5c4129b000)
	libGraf.so => /home/vgate/Software/root/bin/lib/libGraf.so (0x00007f5c41095000)
	libImt.so => /home/vgate/Software/root/bin/lib/libImt.so (0x00007f5c41084000)
	libNet.so => /home/vgate/Software/root/bin/lib/libNet.so (0x00007f5c40d3f000)
	libgomp-75eea7e8.so.1 => /home/vgate/Software/libtorch/lib/libgomp-75eea7e8.so.1 (0x00007f5c40b18000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f5c40b0d000)
	libxcb.so.1 => /lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f5c40ae3000)
	libXt.so.6 => /lib/x86_64-linux-gnu/libXt.so.6 (0x00007f5c4087a000)
	libXext.so.6 => /lib/x86_64-linux-gnu/libXext.so.6 (0x00007f5c40863000)
	libpng16.so.16 => /lib/x86_64-linux-gnu/libpng16.so.16 (0x00007f5c4082b000)
	libharfbuzz.so.0 => /lib/x86_64-linux-gnu/libharfbuzz.so.0 (0x00007f5c40726000)
	libicudata.so.66 => /lib/x86_64-linux-gnu/libicudata.so.66 (0x00007f5c3ec65000)
	libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00007f5c3ebf2000)
	libtbb.so.2 => /home/vgate/Software/root/bin/lib/libtbb.so.2 (0x00007f5c3ebad000)
	libXau.so.6 => /lib/x86_64-linux-gnu/libXau.so.6 (0x00007f5c3eba7000)
	libXdmcp.so.6 => /lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f5c3eb9f000)
	libSM.so.6 => /lib/x86_64-linux-gnu/libSM.so.6 (0x00007f5c3eb94000)
	libICE.so.6 => /lib/x86_64-linux-gnu/libICE.so.6 (0x00007f5c3eb76000)
	libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f5c3eab5000)
	libgraphite2.so.3 => /lib/x86_64-linux-gnu/libgraphite2.so.3 (0x00007f5c3ea88000)
	libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007f5c3ea6e000)
	libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007f5c3ea65000)
Copying inputs
Lauching macro
jeu. 24 févr. 2022 23:57:50 CET
Gate -a [JOB_ID,0][JOB_ID,0] /home/vgate/Desktop/master/cluster/mac/main.mac
1 jobs running
Run folder is: /home/vgate/Desktop/master/cluster
(base) vgate at vgate:~/Desktop/master$ [G4] 
[G4] **************************************************************
[G4]  Geant4 version Name: geant4-10-07    (4-December-2020)
[G4]                        Copyright : Geant4 Collaboration
[G4]                       References : NIM A 506 (2003), 250-303
[G4]                                  : IEEE-TNS 53 (2006), 270-278
[G4]                                  : NIM A 835 (2016), 186-225
[G4]                              WWW : http://geant4.org/
[G4] **************************************************************
[G4] 
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Core-0] Initialization of actors
[Core-0] 
[Core-0] *************************************************
[Core-0]  GATE version 9.1 (2021)
[Core-0]  Copyright : OpenGATE Collaboration
[Core-0]  Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0]  Reference : Phys. Med. Biol. 56 (2011) 881-901
[Core-0]  Reference : Med. Phys. 41(6)    (2014)
[Core-0]  http://www.opengatecollaboration.org        
[Core-0] *************************************************
[Core-0] 
[Core-0] You are using Geant4 version 10.7.0
/control/alias JOB_ID 0
/control/alias JOB_ID 0
[Core-0] Starting macro /home/vgate/Desktop/master/cluster/mac/main.mac
[G4-cerr] ERROR: Can not open a macro file </home/vgate/Desktop/master/cluster/mac/main.mac>. Set macro path with "/control/macroPath" if needed.
[Gate] Sorry, error in a macro command : abort.
ERROR: gate failed



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