[Gate-users] Problems with Gate7.0 on MacOS

[Paola Solevi]

Hi David,
thanks for your help!

>From sudo port  no way to make it works:
gate @7.0_1+geant496+qt4 (active)
geant4.9.6 @4.9.6.p03_0+gdml+qt (active)
geant4.9.6-data @4.9.6_0 (active)
geant4_select @1.0_0 (active)
root5
@5.34.22_0+cocoa+gcc48+graphviz+gsl+http+minuit2+opengl+roofit+soversion+ssl+tmva+xml
(active)

Even commenting the verbose line of random generator as you suggested, it
doesn't work.
I made a quick test then:
1) commented the "execute physics.mac" line and simulation went fine (of
course, empty leaves in the root output)
2) added the line /gate/physics/addPhysicsList emstandard_opt3 to use built
physics list and again I got a similar error:
"...
....
### === G4UAtomicDeexcitation::InitialiseForNewRun()
### ===  PIXE model for hadrons: Empirical  1
### ===  PIXE model for e+-:     Livermore  1
/opt/local/bin/Gate: line 12: 59691 Segmentation fault: 11
 /opt/local/libexec/gate/Gate $@
"

I eventually went for virtualization , as you suggested, and everything
went fine!

Thanks a lot again,
cheers
p.





On Wed, Oct 22, 2014 at 2:48 PM, Dávid Völgyes <david.volgyes at gmail.com>
wrote:

> Hi Paola,
>
> Try to disable the verbose output of the random events.
> There is a bug in the Geant4 (actually, in the embedded CLHEP) inside
> the Mersenne Twister random number generator. Depending on actual
> compilation differences, sometimes it does not cause any problem, like
> in the vGATE, and sometimes it does. The code tries to read 625
> elements from a 624 long array. If there is another data after this
> array, then it's fine. If there is code there, then you get a
> segfault.
>
> So first, try to remove this line from the benchPET.mac:
> /gate/random/verbose 1
> if you still get segfault, then it is another bug, and please, report it.
>
> Mac compilation: don't have Macs, but in worst case you can run the
> vGate in a virtual machine on Mac, or a dockerized version of Gate.
> (Which also runs in kind of a virtual machine.)
> https://docs.docker.com/installation/mac/
>
> Cheers from Oslo!
>
> David
>
>
> On Wed, Oct 22, 2014 at 2:18 PM, Paola Solevi <paola.solevi at gmail.com>
> wrote:
> > Dear Gate Users,
> > I have to go back to an issue open in March (Mojca et al) but I can't
> find a
> > solution to my problem.
> >
> > I'm trying to install Gate on my Mac (10.9.3).
> > I made two different attempts:
> > 1) following the port strategy, everything went smooth but when I type
> Gate
> > benchPET.mac (to test the benchmark) I got:
> > "....
> > .....
> > annihil:   for  e+, applyCuts: 1     SubType= 5
> >       ===== EM models for the G4Region  DefaultRegionForTheWorld ======
> >             eplus2gg :  Emin=        0 eV    Emax=       10 TeV
> >
> > /opt/local/bin/Gate: line 12: 25102 Segmentation fault: 11
> > /opt/local/libexec/gate/Gate $@
> > "
> >
> > 2) I try to manually install everything from source using cmake (even
> with
> > system clhep or g4 internal clhep, to be sure it was not clhep error).
> > Geant4 installation went fine, then I go to Gate -I guess I correctly
> > configured by ccmake- but after make command it builds CXX object down to
> > 100% but then I get a long list of printouts and error at the very end:
> > ".......
> > .........
> >   "_gROOT", referenced from:
> >       _main in Gate.cc.o
> >       GateToRoot::RecordBeginOfAcquisition() in GateToRoot.cc.o
> >   "_gRandom", referenced from:
> >       GateRandomEngine::Initialize() in GateRandomEngine.cc.o
> > ld: symbol(s) not found for architecture x86_64
> > clang: error: linker command failed with exit code 1 (use -v to see
> > invocation)
> > make[2]: *** [Gate] Error 1
> > make[1]: *** [CMakeFiles/Gate.dir/all] Error 2
> > make: *** [all] Error 2
> > "
> > ROOT path is correctly set (5.34/14), geant4 path too. Can be a problem
> with
> > the compiler?
> >
> > I have:
> > /usr/bin/c++ -v
> > Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
> > Target: x86_64-apple-darwin13.2.0
> > Thread model: posix
> >
> >  /usr/bin/gcc -v
> > Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr
> > --with-gxx-include-dir=/usr/include/c++/4.2.1
> > Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
> > Target: x86_64-apple-darwin13.2.0
> > Thread model: posix
> > Paolas-MacBook-Air-2:geant4.9.6.p03 psolevi$
> >
> > I attach the configuration shell screenshot of Gate, if it can help.
> >
> > Any help will be precious!
> >
> > Thanks a lot,
> > p.
> >
> >
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
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