[gate-users] Re: gate-users Digest, Vol 20, Issue 3

[patrice descourt]

gate-users-request at lphe1pet1.epfl.ch wrote:

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>Today's Topics:
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>   1. Re: Installation without OpenGL (Sebastien JAN)
>   2. Re: Re: gate-users Digest, Vol 20, Issue 1 (Vandana Kohli)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 02 Nov 2005 12:05:29 +0100
>From: Sebastien JAN <jan at shfj.cea.fr>
>Subject: Re: [gate-users] Installation without OpenGL
>To: GATE feedback and helpline for Users
>	<gate-users at lphe1pet1.epfl.ch>
>Message-ID: <43689D79.7060300 at shfj.cea.fr>
>Content-Type: text/plain; charset=us-ascii; format=flowed
>
>
>
>Hi Mikhail,
>
>Probably you need to comment the following lines in your GNUmakefile:
>
>##########
>LDFLAGS += -L/usr/X11R6/lib -lXt
>ifdef G4VIS_USE_OPENGLXM
>LDFLAGS += -lXm
>endif
>##########
>
>Seb
>
>Mikhail Shilov wrote:
>  
>
>>Dear All,
>>
>>I was just wondering if there is a way to compile Gate without OpenGL visualization module. When I disable the visualization in Geant4 compilation and then try to compile Gate it gives me an error that G4OpenGL library is not found....
>>
>>Mikhail A. Shilov
>>The Johns Hopkins University
>>Department of Radiology
>>Division of Medical Imaging Physics
>>Tel:  443-287-7315
>>Fax:  410-614-1977
>>mailto: mshilov1 at jhmi.edu
>>
>>_______________________________________________
>>gate-users mailing list
>>gate-users at lphe1pet1.epfl.ch
>>http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>>
>>
>>    
>>
>
>------------------------------
>
>Message: 2
>Date: Wed, 2 Nov 2005 12:57:56 -1000
>From: Vandana Kohli <kohli.vandana at gmail.com>
>Subject: Re: [gate-users] Re: gate-users Digest, Vol 20, Issue 1
>To: GATE feedback and helpline for Users
>	<gate-users at lphe1pet1.epfl.ch>
>Message-ID:
>	<298e9e170511021457h5f16c8adm2177cf69f82cbd59 at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
>Thanks Patrice. I will be trying it out hopefully nextweek. Also, If we are
>writing ECAT7 output along with the root where else would I need to make
>changes??
>Just one more question, see below
>
>On 11/1/05, patrice descourt <patrice.descourt at univ-brest.fr> wrote:
>  
>
>>Dear Vandana
>>
>>you do not have to bother about installing geant or gate on each node,
>>MPI logs on each node via rsh or ssh depending on your parameterization.
>>
>>Below are outlines along which you can get parallel jobs
>>
>>
>>I will be pleased to give the final codes in a directory when I have
>>written those because for now I only focus on the second implementation
>>which is far more cumbersome.
>>
>>The first one should not present any problems :
>>
>>You just have to install MPI and compile Geant and Gate with mpicc which
>>replaces gcc
>>
>>and run Gate via mpirun :
>>
>>mpirun -np #number of nodes your_compiled_code.exe
>>
>>you have to include
>>
>>#include "mpi.h" in each file using MPI library e.g Gate.cc and
>>G4RunManager.hh >>>Are these the only two files where we have to include "
>>mpi.h" ???
>>
>>
>>
>>
>>In Gate.cc you need at the beginning of main()
>>
>>to add
>>
>>MPI::Init(argc,argv); : this is to initialize MPI
>>
>>at the end of Gate.cc main()
>>
>>you put
>>
>>MPI::Finalize();
>>
>>
>>in G4RunManager::DoEventLoop()
>>
>>you put
>>
>>G4int proc_number = MPI::COMM_WORLD.Get_size();
>>G4int proc_ID = MPI::COMM_WORLD.Get_rank();
>>
>>before the for loop
>>
>>which you replace with
>>
>>for(i_event = proc_ID; i_event<n_event; i_event += proc_number)
>>
>>now for the output, I review the ROOT one but the scheme is the same
>>for any GateVOutputModule :
>>
>>in GateToRoot.hh you put #include "mpi.h"
>>
>>and put at the beginning of GateToRoot:RecordBeginOfAcquisition
>>
>>G4int proc_ID = MPI::COMM_WORLD.Get_rank();
>>
>>and replace each GetFilePath() by GetFilePath()+"proc_"+proc_ID
>>
>>I will give all the codes when this is all implemented
>>
>>Cheers
>>P.Descourt
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>>
>>    
>>
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>End of gate-users Digest, Vol 20, Issue 3
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>  
>
Dear Vandana

have a look in GateSinoToEcat7.cc


of course at the end of the GATE job you need to merge all output files 
in a single one

Cheers
Patrice
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