[Gate-users] Σχετ: Gate-users Digest, Vol 129, Issue 39 [SEC=UNCLASSIFIED]

Andrew Nixon Andrew.Nixon at uhb.nhs.uk
Fri Feb 24 17:27:36 CET 2017 

Just to contribute to this thread, I have successfully built gate against Root 6.08 by ensuring that it's compiled without the C++14 extensions. Maybe this is hiding an unknown problem for the future but it certainly completes the build and runs simulations output to Root files.

In Fedora 25, the .rpm build of Root is incompatible, I think, because of the C++14 extensions.

Andrew.

Andrew Nixon
Medical Physics - Clinical Scientist
 
 
 
Internal: 15068     
Email: Andrew.Nixon at uhb.nhs.uk 
Web: http://www.uhb.nhs.uk  


Medical Physics - University Hospitals Birmingham NHS Foundation Trust

Birmingham, B15 2TH



-----Original Message-----
From: Gate-users [mailto:gate-users-bounces at lists.opengatecollaboration.org] On Behalf Of David Boersma
Sent: 24 February 2017 16:20
To: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Σχετ: Gate-users Digest, Vol 129, Issue 39 [SEC=UNCLASSIFIED]

Ahem. Oops. I wrote:

 > I just tried it on my own machine and I can  > compile gate 7.2 just fine with geant4 10.03.

That is not correct.

The cmake stage goes fine and the compile happily proceeds through about 70% of the build but then actually fails for multiple reasons (CLHEP namespace for units, and 'theParticleIterator' is no longer #defined).

You can *not* compile Gate v7.2 with geant4 version 10.03.

My apologies for any confusion that my wrong statement may have caused, David Boersma

Den 24/02/2017 kl. 12:36, skrev David Boersma:
> Hi Farshid,
>
> Konstantinos is partly right about the incompatible geant4 versions.
>
> ROOT 6.* will not compile with Gate 7.2 (for a silly simple reason 
> that is fixed on github, so in the upcoming release you'll be able to 
> use ROOT6).
>
> Geant4 10.03 has not been *validated* for gate 7.2 (because geant4 
> 10.03 was released long after gate 7.2 was released), but it should 
> not give you this build error. I just tried it on my own machine and I 
> can compile gate 7.2 just fine with geant4 10.03. So I strongly 
> suspect that after you'll install (the latest patch version of) geant4 
> 10.02 you will run into the same build error.
>
> (The rest of this mail I wrote already before Konstantinos wrote to 
> the
> list...)
>
> From those regex errors we can conclude that for some reason cmake 
> does not manage to define the Geant4_VERSION variable. That is 
> strange, because in the first line of the quoted output you show that 
> it does find the installation prefix and it even quotes the version in 
> parentheses. We need to collect more diagnostics, hopefully that will 
> give us a clue.
>
> (1) multiple installs?
>
> Do you have other geant4 installations on your system besides the one 
> you intend to use, and could you check the output of
>
> printenv | grep -i geant4
>
> to see if maybe your shell environment somehow has a mixture of 
> multiple versions?
>
> (2) install method
>
> How did you install geant4? Build from source or unpack a binary tarball?
>
> (3) check cmake and geant4-config
>
> Could you cd to the *build* directory where you most recently tried to 
> run cmake, and then copy-paste the following commands into you shell, 
> and then copy-paste the resulting output into a mail to the list?
>
> echo $SHELL
> type cmake
> cmake --version
> grep Geant4_DIR CMakeCache.txt
> type geant4-config
> geant4-config --version
> geant4-config --prefix
>
> Maybe this helps to get a clue to what's going on on your system. If 
> it doesn't then I can try to come up with some more diagnostic tests...
>
> Good luck,
> David
>
>
> Den 24/02/2017 kl. 11:40, skrev Konstantinos P. Chatzipapas, MSc:
>> Hello,
>>
>> I see that you have install Geant4 V10.3.0 and Root V6.08/02 that 
>> doesn't work for GATE V7.2.
>> You must install Geant4 V10.02.p03 and Root V5.34/36, so that GATE 
>> V7.2 would work.
>>
>> Kind Regards,
>> Konstantinos
>>
>> -----------------------------------------------------
>>  Konstantinos Chatzipapas
>>     Medical Physicist, MSc
>>        University of Patras
>>
>>    web page: Physics Magazine <http://www.physicsmag.com/>
>>
>>
>> Στις 7:19 π.μ. Παρασκευή, 24 Φεβρουαρίου 2017, ο/η "Salehzahi, 
>> Farshid (Health)" <Farshid.Salehzahi at act.gov.au> έγραψε:
>>
>>
>> Hi Konstantinos
>>
>> Thanks for taking the time to support.
>> I can confirm that source geant4.sh is in our bashrc.
>> I can also confirm that we ran GEANT4 example, which was completed 
>> smoothly indicating the GEANT4 us running trouble-free. :)
>>
>> I have copied the text below from the terminal, which shows the 
>> errors we are facing for your further analysis and possible advice please.
>>
>> Below is the output from CMake specifying the errors encountered.
>>
>> Found Geant4: /home/cneeley/apps/Geant4/geant4.10.3-install/bin/..
>> (10.3.0)
>> CMake Error at CMakeLists.txt:67 (STRING):
>>   string sub-command REGEX, mode REPLACE needs at least 6 arguments 
>> total to
>>   command.
>>
>>
>> CMake Error at CMakeLists.txt:68 (STRING):
>>   string sub-command REGEX, mode REPLACE needs at least 6 arguments 
>> total to
>>   command.
>>
>>
>> CMake Error at CMakeLists.txt:69 (STRING):
>>   string sub-command REGEX, mode REPLACE needs at least 6 arguments 
>> total to
>>   command.
>>
>>
>> Warning! GATE version 7.2 is not validated for Geant4 . distribution.
>> Please use Geant4 10.1 or 10.2 distribution instead.
>> Found ROOT 6.08/02 in /home/cneeley/apps/Root/root6.08 CMake Error at 
>> CMakeLists.txt:173 (INCLUDE):
>>   include called with wrong number of arguments.  include() only 
>> takes one
>>   file.
>>
>>
>> CMake Error at CMakeLists.txt:175 (INCLUDE):
>>   include could not find load file:
>>
>>     /home/cneeley/apps/GATE/gate_v7.2/source/general/include
>>
>> Yours Sincerely
>> Farshid
>>
>> Farshid Salehzahi (CSci, MIPEM, Clinical Scientist, MACPSEM) Head of 
>> Molecular and Nuclear Medicine Physics Section Medical Physics and 
>> Radiation Engineering ANU Visiting Fellow Research School of Physics 
>> and Engineering, ANU College of Physical and Mathematical Sciences
>>
>> TCH Phone: 6244 4091 | Fax: 6244 2977
>> |mailto:Farshid.Salehzahi at act.gov.au
>> <mailto:Farshid.Salehzahi at act.gov.au>
>> Clinical Support Services
>> Canberra Hospital and Health Services
>>
>>
>> -----Original Message-----
>> From: Gate-users
>> [mailto:gate-users-bounces at lists.opengatecollaboration.org
>> <mailto:gate-users-bounces at lists.opengatecollaboration.org>] On 
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>> <mailto:gate-users-request at lists.opengatecollaboration.org>
>> Sent: Thursday, 23 February 2017 7:53 PM
>> To: gate-users at lists.opengatecollaboration.org
>> <mailto:gate-users at lists.opengatecollaboration.org>
>> Subject: Gate-users Digest, Vol 129, Issue 39
>>
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>> Today's Topics:
>>
>>   1. Σχετ:  GATE Installation Problem [SEC=UNCLASSIFIED]
>>       (Konstantinos P. Chatzipapas, MSc)
>>
>>
>> ---------------------------------------------------------------------
>> -
>>
>> Message: 1
>> Date: Thu, 23 Feb 2017 08:52:40 +0000 (UTC)
>> From: "Konstantinos P. Chatzipapas, MSc" <konhat88 at yahoo.gr 
>> <mailto:konhat88 at yahoo.gr>>
>> To: "Salehzahi, Farshid (Health)" <Farshid.Salehzahi at act.gov.au 
>> <mailto:Farshid.Salehzahi at act.gov.au>>,
>>     "gate-users at lists.opengatecollaboration.org
>> <mailto:gate-users at lists.opengatecollaboration.org>"
>>     <gate-users at lists.opengatecollaboration.org
>> <mailto:gate-users at lists.opengatecollaboration.org>>
>> Subject: [Gate-users] Σχετ:  GATE Installation Problem
>>     [SEC=UNCLASSIFIED]
>> Message-ID: <1484310233.5675768.1487839960381 at mail.yahoo.com
>> <mailto:1484310233.5675768.1487839960381 at mail.yahoo.com>>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hello,
>> Have source your geant4.sh in your bashrc??
>> Best Regards,Konstantinos
>>  ----------------------------------------------------- Konstantinos 
>> Chatzipapas
>>     Medical Physicist, MSc
>>        University of Patras
>>    web page: Physics Magazine
>>
>>     Στις 5:44 π.μ. Παρασκευή, 17 Φεβρουαρίου 2017, ο/η "Salehzahi, 
>> Farshid (Health)" <Farshid.Salehzahi at act.gov.au 
>> <mailto:Farshid.Salehzahi at act.gov.au>> έγραψε:
>>
>>
>>   <!--#yiv8120087482 _filtered #yiv8120087482 {font-family:"Cambria
>> Math";panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv8120087482
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>> 1
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>> #yiv8120087482 li.yiv8120087482MsoNormal, #yiv8120087482 
>> div.yiv8120087482MsoNormal 
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>> ri",
>> "sans-serif";}#yiv8120087482
>> a:link, #yiv8120087482 span.yiv8120087482MsoHyperlink
>> {color:blue;text-decoration:underline;}#yiv8120087482 a:visited,
>> #yiv8120087482 span.yiv8120087482MsoHyperlinkFollowed
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>> p.yiv8120087482MsoAcetate, #yiv8120087482 li.yiv8120087482MsoAcetate,
>> #yiv8120087482 div.yiv8120087482MsoAcetate 
>> {margin:0cm;margin-bottom:.0001pt;font-size:8.0pt;font-family:"Tahoma
>> ",
>> "sans-serif";}#yiv8120087482 span.yiv8120087482EmailStyle17 
>> {font-family:"Garamond", "serif";color:windowtext;}#yiv8120087482
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>> "sans-serif";}#yiv8120087482 .yiv8120087482MsoChpDefault {} _filtered
>> #yiv8120087482 {margin:72.0pt 72.0pt 72.0pt 72.0pt;}#yiv8120087482
>> div.yiv8120087482WordSection1 {}-->Hello GATE-Users,    One of my
>> colleagues is trying to set up GATE_v7.2 (Geant4-10.2.3, Qt5.8) on an 
>> Ubuntu server. The Geant4 built successfully. The problem is that the 
>> GATE CMakeList.txt file tries to initiailise the Geant4_USE_FILE 
>> parameter. The Geant4_USE_FILE is not set correctly and he would like to
>> know what file/variable etc this is trying to point to?    I would
>> really appreciate your prompt response to this matter as we are looking
>> forward to using GATE’s applications.       Yours Sincerely, Farshid
>> Farshid Salehzahi (CSci, MIPEM, Clinical Scientist, MACPSEM) Head of 
>> Molecular and Nuclear Medicine Physics Section Medical Physics and 
>> Radiation Engineering ANU Visiting Fellow Research School of Physics 
>> and Engineering, ANU College of Physical and Mathematical Sciences 
>> TCH
>> Phone: 6244 4091 | Fax: 6244 2977 
>> |mailto:Farshid.Salehzahi at act.gov.au
>> <mailto:Farshid.Salehzahi at act.gov.au> Clinical Support Services 
>> Canberra Hospital and Health Services  We acknowledge the traditional 
>> custodians of the ACT, the Ngunnawal people. We acknowledge and 
>> respect their continuing culture and the contribution they make to 
>> the life of this city and this region.
>>
>> ---------------------------------------------------------------------
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