[gate-users] benchmark runtime problems

[Stevens, Paul]

in the GATE 1.0 distribution

The gateSingles.dat output from the SPECT benchmark contains more columns
than the C analysis programs expect. By modifying the file reading code I
managed to get the results to agree to my satisfaction.
The projction analysis will require the same changes.

I had to abandon the PET benchmark due to thrashing when the working memory
reached 1.1GB. I suspect that that there is a memory leak in this example,
although it might well run to completion on a machine with suficient memory.

Paul Stevens

Bristol Haematology and Oncology Centre.

-----Original Message-----
From: M A Lewis [mailto:Matthew.Lewis at utsouthwestern.edu]
Sent: 26 May 2004 00:26
To: GATE feedback and helpline for Users;
christopher.c.heath at vanderbilt.edu
Subject: Re: [gate-users] benchmark runtime problems


for some reason the Digitizer modules are dependent upon the Ascii
output modules. I had the same errors you have below until I set
G4ANALYSIS_USE_FILE=1
The Root output can also be enabled by setting the environmental
variable G4ANALYSIS_USE_ROOT=1.
Once I got everything compiled correctly, benchmarkPET worked perfectly
as described in the documentation.
Unfortunately, I still can't get benchmarkSPECT to work. The docs
mention a Root .C file which was missing from my source. When I run
benchmark_projections gateSingles.dat
I get all scattered photons, 0 primary photons, and the file Primary is
all 0x00.
Can someone confirm that benchmarkSPECT is working?

although I have compiled Gate with Ascii output under Cygwin/Win XP/VS
.NET 2003, I am still trying to get Root output working.

Matthew Lewis, Ph.D.
UT Southwestern Medical Center at Dallas





Heath, Christopher Charles wrote:
> After installing Gate, I attempted to run one the SPECT benchmark to
ensure it
> was installed correctly.  The following error came up:
> 
> **********************************************
>  Geant4 version $Name:  $
>                                 (3-October-2003)
>              Copyright : Geant4 Collaboration
> **********************************************
> macro file <visOGL.mac> could not open.
> ***** COMMAND NOT FOUND </vis/viewer/zoom 1.25> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </vis/viewer/zoom 0.5> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </vis/viewer/set/viewpointThetaPhi 120 60 deg>
*****
> ***** Command ignored *****
> [GateSystemListManager::CheckScannerAutoCreation:
>         Creating new system based on volume inserter 'SPECThead'
> ***** COMMAND NOT FOUND </gate/SPECThead/ring/setAngularPitch 90. deg>
*****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert adder> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert blurring> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/blurring/setResolution
0.10> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND
</gate/digitizer/Singles/blurring/setEnergyOfReference
> 140. keV> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert spblurring> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND
</gate/digitizer/Singles/spblurring/setSpresolution 2.0
> mm> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/spblurring/verbose 1>
*****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert thresholder> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/thresholder/setThreshold
20.
> keV> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/insert upholder> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/digitizer/Singles/upholder/setUphold 190.
keV> *****
> ***** Command ignored *****
>  
> GATE object:        'systems/SPECThead'
> Components:
>  
> GATE object:        'systems/SPECThead/base'
> Attached to volume: SPECThead
> Nb of children:       1
>  
>         GATE object:        'systems/SPECThead/crystal'
>         Attached to volume: crystal
>         Nb of children:       1
>  
>                 GATE object:        'systems/SPECThead/pixel'
>                 Attached to volume: ---
>                 Nb of children:       0
> Selected processes for gamma physics:
>         Rayleigh effect:      lowenergy
>         Photoelectric effect: lowenergy
>         Compton scattering:   lowenergy
>         Gamma conversion:     inactive
>  
> WARNING !
>  SetCutValueForOthers became obsolete.
>  It is harmless to remove this invokation without any side effects.
>  This dummy method implementation will be removed soon.
> Confirming confinement to volume 'movsource_P'...
>  Confinement to volume 'movsource_P' confirmed
> ***** COMMAND NOT FOUND </gate/output/root/setSaveRndmFlag 1> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/root/setFileName benchSPECT> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/root/setRootSinglesAdderFlag 1>
*****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/root/setRootSinglesBlurringFlag 1 >
*****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/root/setRootSinglesSpblurringFlag 1>
> ********** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/root/setRootSinglesThresholderFlag
1> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/root/setRootSinglesUpholderFlag 1>
*****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/ascii/setOutFileSinglesAdderFlag 0>
*****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND
</gate/output/ascii/setOutFileSinglesSpblurringFlag 0> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/ascii/setOutFileSinglesBlurringFlag
0> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND
</gate/output/ascii/setOutFileSinglesThresholderFlag 0>
> *****
> ***** Command ignored *****
> ***** COMMAND NOT FOUND </gate/output/ascii/setOutFileSinglesUpholderFlag
0> *****
> ***** Command ignored *****
> 
> Neither the /gate/output nor /gate/digitizer directories seem to be
present. 
> However everything else seems to work fine
> 
> Thanks
> Christopher
> -----------------------------------------------------------------
> Heath, Christopher Charles
> Vanderbilt University
> Email: christopher.c.heath at Vanderbilt.Edu
> _______________________________________________
> gate-users mailing list
> gate-users at lphe1pet1.epfl.ch
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> 



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