[Gate-users] Re : Re : !! Gate v6.0.0 on Mac OS X >>still not OK
Samuel BURG
samuel_burg at yahoo.fr
Sat Jan 29 18:25:21 CET 2011
ok,
it seam there is some flags missing for GCC during compilation of LMF.
your log outputs here says that the system doesn't found a specific function
inside LMF dynamic lib, because it has not been referenced.
so your compilation is ok but for this specific flag, maybe -fpic or something
like that.
I don't know the exact flag to enable the "symbol" for each function to be saved
inside the lib.
you should check gcc syntax in the other libs (makefiles, logs ...) your are
using with gate, and you should be able to found the good flags this way.
regards,
-----------------------------------------------------------
Samuel Burg
Mail : <samuel_burg at yahoo.fr>
-----------------------------------------------------------
"Aw, come on, who would be so stupid as to insert a cast
to make an error go away without actually fixing the error?"
Apparently everyone.
-- Raymond Chen --
-----------------------------------------------------------
________________________________
De : Sergio Furuie <sergio.furuie at leb.usp.br>
À : Samuel BURG <samuel_burg at yahoo.fr>
Cc : gate-users at lists.opengatecollaboration.org
Envoyé le : Ven 28 janvier 2011, 1h 25min 35s
Objet : Re: Re : [Gate-users] !! Gate v6.0.0 on Mac OS X >>still not OK
Hi Samuel,
I had the same problem reported by Uwe Pietrzyk in (2010-03-02 à 14:26)
Compilations of gate v6 and lmf3.0 are ok, but when we run benchPET, we get:
Symbol not found: _fillEHforGATE
-----------------------
[G4]
[G4] *************************************************************
[G4] Geant4 version Name: geant4-09-02-patch-04 (16-September-2010)
[G4] Copyright : Geant4 Collaboration
[G4] Reference : NIM A 506 (2003), 250-303
[G4] WWW : http://cern.ch/geant4
[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 name: gate_v6.0_p01
[Core-0] Copyright : OpenGATE Collaboration
[Core-0] Reference : Phys. Med. Biol. 49 (2004) 4543-4561
[Core-0] WWW : http://www.opengatecollaboration.org/
[Core-0] **********************************************************************
[Core-0]
[Core-0] Starting macro benchPET.mac
[G4] Got standard cmap
[G4] Window name: viewer-0 (OpenGLStoredX)
[G4] /tracking/storeTrajectory 1
dyld: lazy symbol binding failed: Symbol not found: _fillEHforGATE
Referenced from:
/Users/furuie/projetos/gate_v6.0_p01/tmp/Darwin-g++/Gate/libGate.dylib
Expected in: flat namespace
----------------------
I also followed your suggestion of (Tue Jun 1 19:54:34 CEST 2010, [Gate-users]
Re : Re : Request Assistance with LMF to GATE) :
but with same error.
Some guys are disabling LMF for gate compilation because of this problem
as reported by Uwe and Marc (below) and it seems to be specific to Mac OS.
However, I need to use LMF...
Should we give up using Mac OS X, if we intend to use LMF?
Best regards,
Sergio.
-----------------------------------
On 03.03.2010, at 00:01, Pietrzyk, Uwe wrote:>
> Hi Marc, hi Didier,
>
> omitting the lmf-library was the key! On 64-bit-systems, I found the lmf
> not working anymore and you are right to disable it, in case you are not
> interested in.
> According to Didier, I will not start any production on my Mac until the
> bugs are fixed.
>
> Many thanks and kind regards,
>
> Uwe
>
> -----
> On 02.03.2010, at 20:55, Didier Benoit wrote:
>
>> Hi Uwe and Marc,
>>
>> Yes, the problem is in the physical processes. It' a bug in the "GateVProcess"
>>and "GatePhysicsList" classes. I hope I could fix this bug the next week, and
>>surely there will be a new patch (gate_v6.0.1).
>>
>> Kind Regards,
>> Didier
>>
>> Le 02/03/2010 20:41, Marc Chamberland a écrit :
>>>
>>> Hi Uwe,
>>>
>>> I had the same problem as you, but disabling the LMF libraries (which I don't
>>>expect to use for now) solved it.
>>>
>>>
>>> However, Didier pointed out that there are problems with certain processes on
>>>Mac OS X. Indeed, when I tried running the benchmark for PET, Gate didn't
>>>recognize any of the physical processes. I'll wait for the coming fix in the
>>>meantime.
>>>
>>> Cheers!
>>> Marc
>>>
-----------------------------------
2011/1/27 Samuel BURG <samuel_burg at yahoo.fr>
Hi,
>
>I don't know what is your issue with LMF3, but with Alexandre Dupas we manage to
>run GATE v5 on MacOS-X (don't remeber if it was with or without LMF but I think
>it was running)
>For now we stop to run any simulation on MacOS-X because of a bug with Condor
>(clustering system) not alowing us to use full power of the 2x4 cores CPU we
>have.
>... we have intalled Linux over it ... ok ok don't shout me, thanks.
>
>If you explain exactly your issue with LMF we should be able to help you.
>Before that try to use the bug-fixed versionof LMF we have send a few weeks ago
>on the list.
>
>regards,
>
>Samuel
>
>
>
-----------------------------------------------------------
>Samuel Burg
>
>
>Mail : <samuel_burg at yahoo.fr>
>-----------------------------------------------------------
>"Aw, come on, who would be so stupid as to insert a cast
>to make an error go away without actually fixing the error?"
>Apparently everyone.
>-- Raymond Chen --
>-----------------------------------------------------------
>
>
>
>
>
________________________________
De : Sergio Furuie <sergio.furuie at leb.usp.br>
>À : gate-users at lists.opengatecollaboration.org
>Envoyé le : Jeu 27 janvier 2011, 16h 52min 17s
>Objet : [Gate-users] !! Gate v6.0.0 on Mac OS X >>still not OK
>
>
>Hi Didier,
>
>Regarding to the use of Gate v6.0.1 with LMFv3 on Mac OS X, is there any
>news?
>I looked into Gate Users Archive, but I couldn't find any further
>information.
>Should we give up using Mac OS X (10.6.6) ?
>
>Thanks in advance.
>Sergio.
>
>--
>*Didier Benoit* benoit at cppm.in2p3.fr
><gate-users%40lists.opengatecollaboration.org?Subject=Re%3A%20%5BGate-users%5D%20%21%21%20Gate%20v6.0.0%20on%20Mac%20OS%20X%20%3E%3Estill%20not%20OK&In-Reply-To=%3C4B8D9F21.9080304%40cppm.in2p3.fr%3E>
>
>*Wed Mar 3 00:28:33 CET 2010*
>
>
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>------------------------------
>
>
>Hi Uwe,
>
>Yes it's the "normal" bug :), the processes are not loaded in GATE6 on
>Mac Os X.
>
>Kind regards,
>Didier
>
>Le 03/03/2010 00:25, Uwe Pietrzyk a écrit :
>>**>* Hi,*>**>* I briefly tested the benchPET. I could start GATE, but there is
>>nothing*>* written to the root-file after 20 min. Also, the visualisation does
>>*>* not work*>* and crashes the X11-environment ...*>**>* So I will wait until
>>bugs are solved. Let me know, when I can continue*>* testing Gate6 on Mac Os X
>>...*>**>* Kind regards,*>**>* Uwe*>* -----*>* On 03.03.2010, at 00:01,
>>Pietrzyk, Uwe wrote:*>**>>**>>* Hi Marc, hi Didier,*>>**>>* omitting the
>>lmf-library was the key! On 64-bit-systems, I found the lmf*>>* not working
>>anymore and you are right to disable it, in case you are not*>>* interested
>>in.*>>* According to Didier, I will not start any production on my Mac until
>>the*>>* bugs are fixed.*>>**>>* Many thanks and kind regards,*>>**>>* Uwe*>>
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--
Prof.Dr. Sergio S Furuie
Laboratório de Engenharia Biomédica
Departamento de Engenharia de Telecomunicações e Controle - Escola Politécnica
da USP
Av Prof Luciano Gualberto, Travessa 3, 158 - sala D2-06 CEP 05508-970 São Paulo
- SP
Tel.: 11-3091-5130 Fax:11-3091-5718 E-mail: sergio.furuie at Leb.usp.br Web:
http://www.Leb.usp.br
[Professor Titular da EPUSP, orientador da Pós-graduação da Eng.Elétrica e da
FMUSP/Cardiologia]
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