[Rtk-users] IRTK compiling problems

Wed Oct 17 10:18:11 EDT 2012

The other linux compile errors have been fixed, they were caused by
the recent gcc that you seem to be using. Sorry for this hassle, we do
not have tested all possible combinations of gccs yet...

>From your CMakeCache.txt, it seems that you have gengetopt installed here:
C:/Program Files (x86)/GnuWin32/bin/gengetopt.exe
A way to solve this would be to remove it from the Windows path so
that cmake doesn't use it because gengetopt code has been copied in
RTK and will be compiled automatically if it's not in the path. In the
future, we should check on gengetopt version and compile it
automatically if the system version is too old. I have opened a bug:
http://kingkong.grid.creatis.insa-lyon.fr:9002/issues/1707
This should fix the gengetopt enum errors but I still have to figure
out the linking problem if it's still here. It's strange that it does
not show up on my windows box...

Simon

On Wed, Oct 17, 2012 at 3:08 PM, Marta Peroni
<marta.peroni at mail.polimi.it> wrote:
> Hi Simon!
> that fixed the error thanks :) But I am afraid I have another one....
> (log_linux attached hed).
> I also send you the CMakeCache.txt, but I am afraid your intuition might be
> right...
> For windows, where do you get the gengeopt? just to make sure we are
> up-to-date
> thanks a lot
> Marta
>
>
> On 17 October 2012 14:56, Simon Rit <simon.rit at creatis.insa-lyon.fr> wrote:
>>
>> Hi Marta,
>>
>> Yes still ITK 3.20, see instructions here:
>> http://wiki.openrtk.org/index.php/RTK/Users.
>> I fixed the linux error, a commit of 2 days ago was causing it.
>> I don't, however, understand some of your windows errors. It seems
>> that it does not understand the ggo files with enum variables although
>> this has been working on Windows and Linux so far. A potential
>> explanation would be that you have installed an old version of
>> gengetopt on your computer? Maybe you can send me your CMakeCache.txt
>> to help me fixing it? You mentioned a problem with getopt.h in your
>> first email but I did not see it in the log.
>> There is also a linking problem with Cuda that your CMakeCache.txt
>> might help me to understand.
>> Thanks,
>> Simon
>>
>> On Wed, Oct 17, 2012 at 9:53 AM, Marta Peroni
>>
>> <marta.peroni at mail.polimi.it> wrote:
>> > Hi!
>> > sorry that it took soo long to answer.
>> > For windows:
>> > compiler is Visual Studio Express 2008 and we are using Windows 7  (see
>> > log_windows attached)
>> >
>> > For Linux:
>> > I downloaded the latest version from here:
>> > https://github.com/SimonRit/RTK
>> > and tried to compile against ITK 3.20 (should I try with ITK4?)
>> > Got over the usual nvcc error, but still could not compile unfortunately
>> > (see log_linux attached)
>> >
>> > thanks a lot
>> > Marta
>> >
>> > On 12 October 2012 11:19, Simon Rit <simon.rit at creatis.insa-lyon.fr>
>> > wrote:
>> >>
>> >> Hi Marta,
>> >> Thanks for the feedback. Yes, we would be interested in knowing what
>> >> are the problems with getopt.h. Could you send us more information
>> >> (logs, Windows version, compiler, ...)?
>> >> Regarding Cuda, this is a bit of a weird problem. I have tried to
>> >> merge the latest version of Plastimatch cmake files with rtk. Could
>> >> you update your RTK repository and give it another try?
>> >> A simple Shepp Logan reconstruction example is available here
>> >> http://wiki.openrtk.org/index.php/RTK/Scripts/FDK, code examples are
>> >> available here http://wiki.openrtk.org/index.php/RTK/Users.
>> >> Good luck,
>> >> Simon
>> >>
>> >> On Fri, Oct 12, 2012 at 1:42 AM, Marta Peroni
>> >> <marta.peroni at mail.polimi.it> wrote:
>> >> > Dear Simon and David,
>> >> > was a pleasure to meet you at MICCAI. As I mentioned, we are looking
>> >> > into
>> >> > acquiring CBCT on robotic C-arm at CNAO and as you suggested, we had
>> >> > a
>> >> > look
>> >> > at IRTK.
>> >> >
>> >> > Now, problem is that we were not able to compile it neither on
>> >> > windows
>> >> > nor
>> >> > linux (arch distrib).
>> >> >
>> >> > For windows, main issues were related to the windows version of
>> >> > getopt
>> >> > which
>> >> > generate syntax error (Marco can provide you a log file, if you'd
>> >> > like).
>> >> >
>> >> > For linux, I had cuda problem. In particular, although correctly
>> >> > configured,
>> >> > I am stuck with this:
>> >> > [  7%] Building NVCC (Device) object
>> >> >
>> >> >
>> >> > code/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_rtkCudaFFTRampImageFilter.cu.o
>> >> > /usr/include/surface_functions.h: In function 'void surf1Dread(T*,
>> >> > surface<void, 1>, int, int, cudaSurfaceBoundaryMode)':
>> >> > /usr/include/surface_functions.h:100: error: there are no arguments
>> >> > to
>> >> > '__surf1Dreadc1' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf1Dreadc1' must be available
>> >> > /usr/include/surface_functions.h:100: error: (if you use
>> >> > '-fpermissive',
>> >> > G++
>> >> > will accept your code, but allowing the use of an undeclared name is
>> >> > deprecated)
>> >> > /usr/include/surface_functions.h:101: error: there are no arguments
>> >> > to
>> >> > '__surf1Dreads1' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf1Dreads1' must be available
>> >> > /usr/include/surface_functions.h:102: error: there are no arguments
>> >> > to
>> >> > '__surf1Dreadu1' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf1Dreadu1' must be available
>> >> > /usr/include/surface_functions.h:103: error: there are no arguments
>> >> > to
>> >> > '__surf1Dreadu2' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf1Dreadu2' must be available
>> >> > /usr/include/surface_functions.h:104: error: there are no arguments
>> >> > to
>> >> > '__surf1Dreadu4' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf1Dreadu4' must be available
>> >> > /usr/include/surface_functions.h: In function 'void surf2Dread(T*,
>> >> > surface<void, 2>, int, int, int, cudaSurfaceBoundaryMode)':
>> >> > /usr/include/surface_functions.h:460: error: there are no arguments
>> >> > to
>> >> > '__surf2Dreadc1' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf2Dreadc1' must be available
>> >> > /usr/include/surface_functions.h:461: error: there are no arguments
>> >> > to
>> >> > '__surf2Dreads1' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf2Dreads1' must be available
>> >> > /usr/include/surface_functions.h:462: error: there are no arguments
>> >> > to
>> >> > '__surf2Dreadu1' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf2Dreadu1' must be available
>> >> > /usr/include/surface_functions.h:463: error: there are no arguments
>> >> > to
>> >> > '__surf2Dreadu2' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf2Dreadu2' must be available
>> >> > /usr/include/surface_functions.h:464: error: there are no arguments
>> >> > to
>> >> > '__surf2Dreadu4' that depend on a template parameter, so a
>> >> > declaration
>> >> > of
>> >> > '__surf2Dreadu4' must be available
>> >> > CMake Error at
>> >> > cuda_compile_generated_rtkCudaFFTRampImageFilter.cu.o.cmake:252
>> >> > (message):
>> >> >   Error generating file
>> >> >
>> >> >
>> >> >
>> >> > /home/marta/provaIRTK/build/code/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_rtkCudaFFTRampImageFilter.cu.o
>> >> >
>> >> >
>> >> > make[2]: ***
>> >> >
>> >> >
>> >> > [code/CMakeFiles/cuda_compile.dir/./cuda_compile_generated_rtkCudaFFTRampImageFilter.cu.o]
>> >> > Error 1
>> >> > make[1]: *** [code/CMakeFiles/rtkcuda.dir/all] Error 2
>> >> > make: *** [all] Error 2
>> >> >
>> >> > I remember having the same issue in plastimatch some time ago (it is
>> >> > due
>> >> > to
>> >> > cuda version) and James added some -fpermissive to fix the issue.
>> >> >
>> >> > But anyhow, can you please guide us through a compilation to make it
>> >> > work
>> >> > and test it on the new projections?
>> >> >
>> >> > thanks a lot
>> >> > Best Regards,
>> >> > Marta Peroni
>> >> >
>> >> >
>> >> > --
>> >> > *******************************************************************
>> >> > Marta Peroni, PhD
>> >> > Bioengineering department - Politecnico di Milano (IT)
>> >> >
>> >> > contacts:
>> >> > mail: marta.peroni at mail.polimi.it , m.peroni at gmail.com
>> >> > mobile: +393488202136 (IT)
>> >> > office: +39 02 2399 9022
>> >> >
>> >> > ********************************************************************
>> >> >
>> >>
>> >>
>> >
>> >
>> >
>> > --
>> > *******************************************************************
>> > Marta Peroni, PhD
>> > Bioengineering department - Politecnico di Milano (IT)
>> >
>> > contacts:
>> > mail: marta.peroni at mail.polimi.it , m.peroni at gmail.com
>> > mobile: +393488202136 (IT)
>> > office: +39 02 2399 9022
>> >
>> > ********************************************************************
>> >
>>
>>
>
>
>
> --
> *******************************************************************
> Marta Peroni, PhD
> Bioengineering department - Politecnico di Milano (IT)
>
> contacts:
> mail: marta.peroni at mail.polimi.it , m.peroni at gmail.com
> mobile: +393488202136 (IT)
> office: +39 02 2399 9022
>
> ********************************************************************
>