[Gate-users] Unable to make connecting path between Gate and Root
Robert Wilson
rkwilson at mail.sdsu.edu
Fri Dec 2 00:08:44 CET 2016
Thank you so much. I will give this a whirl and see what happens. You're
the best.
Cheers,
*R. Kevin Wilson*
San Diego State University | *2017*
Department of Physics | *M.S Medical Physics*
Radiation Detection Measuring & Modeling Laboratory
*PET/SPECT Modeling - vGate & GEANT4*
Clemson University | *2015*
College of Engineering & Science
Department of Physics & Astronomy | *B.S. Applied Physics*
CU EBIT & Atomic Physics Laboratory *|* *Intern Recipient and Student
Researcher*
rkwilson at mail.sdsu.edu
rkwilso at g.clemson.edu
(828) 216-5310
On Thu, Dec 1, 2016 at 2:18 AM, David Boersma <david.boersma at physics.uu.se>
wrote:
> Hi Robert,
>
> In the first figures you showed that you were trying to tell the build
> system to use a ROOT 6 installation. GATE release 7.2 needs version 5 (it's
> a small fix in the GATE source code to make it work with ROOT 6, you'll
> find that described in other messages here on the list, but for now I
> recommend that you stick with ROOT 5).
>
> Then in the later figures you show that you tried to tell cmake that a
> ROOT 5 install (good!) should be found in a system directory, specifically
> in figure 10 you give the ROOTCINT location as
> /usr/local/lib/root_v5.34.36c/root/bin/rootcint, but you do not show that
> ROOT is indeed installed in that directory. You do show (in figure 8) the
> "ls" output for a ROOT install in ~/Downloads/Root/root_v5.34.36. This is
> in your home directory, instead of the system directory, and the version is
> 5.34.36 instead of 5.34.36c. For GATE it does not matter whether ROOT is
> installed in system directories or your home directories, the only thing is
> that the path that you give root ROOTCINT indeed points to the rootcint
> executable of an existing ROOT 5 installation.
>
> (I suspect that you *may* have the same problems with Geant4. The steps
> for solving those problems will be very similar. For now I assume that your
> geant4 install is OK.)
>
> If you *do* indeed have a ROOT 5 install under /usr/local, the please
> double check that you got the rootcint path correctly. Any typo (e.g. maybe
> the "c" is spurious"?) would result in the error message that you are
> getting. Please check the output of
>
> ls -ld /usr/local/lib/root*
> ls -l /usr/local/lib/root_v5.34.36c/root
> source thisroot.sh
> ldd /usr/local/lib/root_v5.34.36c/root/bin/root.exe
>
> If you do *not* have ROOT installed in your system directories, then I
> recommend that you try the ROOT 5 install that you do seem to have in your
> home directory, under ~/Downloads. Try the following sequence:
>
> cd /home/wilson/Downloads/Root/root_v5.34.36/bin
> source ./thisroot.sh
> ldd ./root.exe
>
> (That "ldd" command just serves to test your ROOT installation. It should
> result in a long list of libraries that the linker wants to use if you
> would run ROOT as a standalone program. If any of the libraries is listed
> as "not found", then something is wrong with your ROOT installation.)
>
> If neither your system directories nor your home directories seem to have
> a working ROOT installation, then you should first work on fixing that. If
> one of them is OK, then let's proceed with that.
>
> I see that you set "GATE_USE_RTK" to ON in ccmake, and that you are
> getting errors for that. If you know what RTK is and you are convinced that
> you will need it, then you should first install it. Otherwise you probably
> do not need it. Then you should set that option to OFF.
>
> I hope that this helps to at least *change* the error messages. :-)
> The build will probably get stuck somewhere else now. Please let us know
> how far you get, and provide us with the output and error messages.
>
> Instead of (or in addition to) ccmake screenshots, it would be helpful for
> us if you could attach the CMakeCache.txt and CMakeFiles/CMakeOutput.log
> text files that you have in your build directory. This would provide us
> with some possibly useful extra diagnostics, and it also may reduce the
> number of typos in commands that we are going to suggest. :-)
>
> Good luck!
> David B.
>
>
>
> Den 01/12/2016 kl. 03:48, skrev Robert Wilson:
>
>> Okay. Awesome. First let me say thanks getting back to me so quickly.
>> Getting this program to be fully functional as soon as possible is
>> really super important.
>> So first off the only thing that jumps out at me as not EXACTLY like the
>> instructions is the version of CLHEP I'm using is a little different. It
>> says to use 2.3.1.1, and I'm using 2.3.3.2. I didn't think it would make
>> that big of a difference, but if you think that may be the culprit, I
>> can go back and do it that way.
>> If you don't think that is probably the problem, I am including several
>> screen shots of my command screen to show the process I'm attempting to
>> use. So if you see any fatal errors I'm making, do please let me know.
>> Thank you again so much for all of your help, and I look forward to
>> hearing from you again soon.
>>
>> Best regards,
>>
>> *R. Kevin Wilson*
>>
>> San Diego State University | /2017/
>> Department of Physics | /M.S Medical Physics/
>> Radiation Detection Measuring & Modeling Laboratory
>> /PET/SPECT Modeling - vGate & GEANT4/
>>
>>
>>
>> Clemson University | /2015/
>> College of Engineering & Science
>> Department of Physics & Astronomy | /B.S. Applied Physics/
>> CU EBIT & Atomic Physics Laboratory *|* /Intern Recipient and Student
>> Researcher/
>>
>> ///
>> /
>> rkwilson at mail.sdsu.edu <mailto:rkwilson at mail.sdsu.edu>
>> rkwilso at g.clemson.edu <mailto:rkwilso at g.clemson.edu>
>> (828) 216-5310
>>
>> On Wed, Nov 30, 2016 at 2:12 PM, Robert Wilson <rkwilson at mail.sdsu.edu
>> <mailto:rkwilson at mail.sdsu.edu>> wrote:
>>
>> Okay. Awesome. First let me say thanks getting back to me so
>> quickly. Getting this program to be fully functional as soon as
>> possible is really super important.
>> So first off the only thing that jumps out at me as not EXACTLY like
>> the instructions is the version of CLHEP I'm using is a little
>> different. It says to use 2.3.1.1, and I'm using 2.3.3.2. I didn't
>> think it would make that big of a difference, but if you think that
>> may be the culprit, I can go back and do it that way.
>> If you don't think that is probably the problem, I am including
>> several screen shots of my command screen to show the process I'm
>> attempting to use. So if you see any fatal errors I'm making, do
>> please let me know.
>> Thank you again so much for all of your help, and I look forward to
>> hearing from you again soon.
>>
>> Best regards,
>>
>> *R. Kevin Wilson*
>>
>> San Diego State University | /2017/
>> Department of Physics | /M.S Medical Physics/
>> Radiation Detection Measuring & Modeling Laboratory
>> /PET/SPECT Modeling - vGate & GEANT4/
>>
>>
>>
>> Clemson University | /2015/
>> College of Engineering & Science
>> Department of Physics & Astronomy | /B.S. Applied Physics/
>> CU EBIT & Atomic Physics Laboratory *|* /Intern Recipient
>> and Student Researcher/
>>
>> ///
>> /
>> rkwilson at mail.sdsu.edu <mailto:rkwilson at mail.sdsu.edu>
>> rkwilso at g.clemson.edu <mailto:rkwilso at g.clemson.edu>
>> (828) 216-5310 <tel:%28828%29%20216-5310>
>>
>> On Tue, Nov 29, 2016 at 1:47 AM, David Boersma
>> <david.boersma at physics.uu.se <mailto:david.boersma at physics.uu.se>>
>>
>> wrote:
>>
>> Hi Robert,
>>
>> (Please disregard the mail I sent erroneously only to you, and
>> reply to this one, to the whole mailing list...)
>>
>> Some basics that may help us to reproduce your problem and/or
>> give you hints for a solution:
>>
>> 1. what operating system are you on (if linux: which distro,
>> which release)?
>>
>> 2. which version of Gate are you trying to compile/install?
>>
>> Den 28/11/2016 kl. 21:07, skrev Robert Wilson:
>>
>> I have been following the procedure extremely closely, but
>> when I
>> attempt to make a path to rootcint with cmake it is unable
>> to create it.
>>
>>
>> The compilation steps are described in this wiki page:
>>
>> http://wiki.opengatecollaboration.org/index.php/Compilation_
>> Instructions_V7.2
>> <http://wiki.opengatecollaboration.org/index.php/
>> Compilation_Instructions_V7.2>
>>
>> Is this indeed "the procedure" that you have followed extremely
>> closely?
>> If no: what *did* you use?
>>
>> If yes: could you specify where exactly you get stuck, and what
>> you mean by "make a path to rootcint"? Can you quote the error
>> messages? It is better to quote to much than too little.
>>
>> Random guess (sorry if I'm completely off): did you run "source
>> /PATH/TO/ROOT/bin/thisroot.sh" (or .csh, if you are a csh user)
>> in the same shell as where you are running ccmake? To test this,
>> just *before* starting the cmake step, issue this command (in
>> the shell):
>>
>> which root-config
>>
>> If this gives the correct path, then the shell is configured
>> with your favorite ROOT version and cmake should be able to find
>> it. If the answer is empty (or an error) then maybe you should
>> try to source root (again?) before running the cmake step.
>>
>>
>> All files and directories show that they are in the proper
>> places, and I
>> am quite confident that the command I am using is correct,
>> but if anyone
>> else has had this problem I would really appreciate any
>> input on how to
>> resolve it. This is the final step in having a fully
>> functional Gate
>> running computer, and I really need it in order to move
>> forward in my
>> research.
>>
>>
>> Unfortunately, I need to warn you here. You *never* really know
>> if a specific compiling problem (or to some bug) is the "final
>> one" until you have explicitly confirmed that fixing that one
>> problem resulted in a correctly running program. Behind the
>> current roadblock many others may still be hiding.
>>
>> Hope that helps,
>> David Boersma
>>
>> PS: You have quite an illustrious name! (I work in proton
>> therapy.)
>>
>>
>>
>> Many thanks in advance,
>>
>> *R. Kevin Wilson*
>>
>> San Diego State University | /2017/
>> Department of Physics | /M.S Medical Physics/
>> Radiation Detection Measuring & Modeling Laboratory
>> /PET/SPECT Modeling - vGate & GEANT4/
>>
>>
>>
>> Clemson University | /2015/
>> College of Engineering & Science
>> Department of Physics & Astronomy | /B.S. Applied Physics/
>> CU EBIT & Atomic Physics Laboratory *|* /Intern Recipient
>> and Student
>> Researcher/
>>
>> ///
>> /
>> rkwilson at mail.sdsu.edu <mailto:rkwilson at mail.sdsu.edu>
>> <mailto:rkwilson at mail.sdsu.edu <mailto:rkwilson at mail.sdsu.edu
>> >>
>> rkwilso at g.clemson.edu <mailto:rkwilso at g.clemson.edu>
>> <mailto:rkwilso at g.clemson.edu <mailto:rkwilso at g.clemson.edu>>
>> (828) 216-5310 <tel:%28828%29%20216-5310>
>>
>>
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