[Gate-users] Unable to make connecting path between Gate and Root
David Boersma
david.boersma at physics.uu.se
Thu Dec 1 11:18:05 CET 2016
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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