[Insight-developers] [Insight-users] Problems with ITK
Cory Quammen
cquammen at cs.unc.edu
Wed Oct 24 14:55:26 EDT 2012
Gabriel,
Please keep the discussion on the list so that others with similar
questions may benefit from our discussion.
I suspect your error message is longer. Can you please post the full
error message?
Thank you,
Cory
On Wed, Oct 24, 2012 at 7:27 AM, Gabriel Santiago
<santiago.eletrica at gmail.com> wrote:
> Cory,
>
> Here they are! My .cu, .h, cpp and my CMakeLists.txt.
>
> Thank you very much for your help!
>
>
> On 23 October 2012 17:17, Cory Quammen <cquammen at cs.unc.edu> wrote:
>>
>> To help you further, I'll need to see your CMakeLists.txt and source
>> files.
>>
>> Cory
>>
>> On Tue, Oct 23, 2012 at 2:28 PM, Gabriel Santiago
>> <santiago.eletrica at gmail.com> wrote:
>> > By the way, I don't know if this is relevant, but I am actually using
>> > Cuda
>> > 5.0 with Nsight as editor/ debugger.
>> >
>> > Even if I use pure C++, I get the very same error message as if I use
>> > some
>> > Cuda code.
>> >
>> > Regards,
>> >
>> > On 23 October 2012 15:49, Gabriel Santiago <santiago.eletrica at gmail.com>
>> > wrote:
>> >>
>> >> Still not working... The problem happens when CMake/ ITK comes into
>> >> scene...
>> >>
>> >> I get this error message:
>> >>
>> >> CMake Error at Proj_generated_loadVar_Cuda.cu.o.cmake:256 (message):
>> >> Error generating file
>> >>
>> >>
>> >> /home/gabriel/cuda-workspace/Proj/CMakeFiles/teste6.dir//./Proj_generated_loadVar_Cuda.cu.o
>> >>
>> >> My CMakeLists.txt is the same as the example. Also, I've found this
>> >> page:
>> >>
>> >>
>> >>
>> >> https://gforge.sci.utah.edu/gf/project/findcuda/scmsvn/?action=browse&path=%2F*checkout*%2Ftrunk%2FFindCuda.html
>> >>
>> >> But nothing...
>> >>
>> >> On 23 October 2012 14:01, Cory Quammen <cquammen at cs.unc.edu> wrote:
>> >>>
>> >>> By including your .cuh and .cu files like that, your standard C++
>> >>> compiler is going to try to compile the CUDA code in those source
>> >>> files. Since it doesn't know anything about CUDA, you are getting
>> >>> errors.
>> >>>
>> >>> This is off the top of my head, and I haven't tried to compile it, but
>> >>> your source files will look something like this:
>> >>>
>> >>> In my_cuda.h:
>> >>>
>> >>> extern "C"
>> >>> void someCudaFunction();
>> >>>
>> >>> In my_cuda.cu:
>> >>>
>> >>> __global__ void someCudaFunction()
>> >>> {
>> >>> }
>> >>>
>> >>> In my_main.cpp:
>> >>>
>> >>> #include "my_cuda.h"
>> >>> #include <itkMyFavoriteFilter.h>
>> >>>
>> >>> int main(int argc, char*argv[])
>> >>> {
>> >>> // Do some ITK stuff here
>> >>>
>> >>> // Do some CUDA stuff here.
>> >>> someCudaFunction<<<block,grid>>>();
>> >>> }
>> >>>
>> >>> In CMakeLists.txt:
>> >>>
>> >>> PROJECT( PROJECT_NAME )
>> >>> CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
>> >>> FIND_PACKAGE ( ITK REQUIRED )
>> >>> FIND_PACKAGE(CUDA)
>> >>> INCLUDE(FindCUDA)
>> >>> IF ( ITK_FOUND )
>> >>> INCLUDE( ${ITK_USE_FILE} )
>> >>> ENDIF( ITK_FOUND )
>> >>> CUDA_ADD_EXECUTABLE( PROJECT_NAME my_cuda.cu my_main.cpp )
>> >>> TARGET_LINK_LIBRARIES ( PROJECT_NAME ITKCommon ITKIO)
>> >>>
>> >>> Hope that helps,
>> >>> Cory
>> >>>
>> >>> On Tue, Oct 23, 2012 at 11:19 AM, Gabriel Santiago
>> >>> <santiago.eletrica at gmail.com> wrote:
>> >>> > Thank you for your attention, Cory. But this can sound very stupid,
>> >>> > but
>> >>> > *how* exactly do I do that?
>> >>> >
>> >>> > I packed everything in a .cuh and a .cu file and than included then
>> >>> > in
>> >>> > my
>> >>> > main.cpp file, but the compiler complains about my cuda functions,
>> >>> > saying
>> >>> > that the qualifier __global__ does not name a type.
>> >>> >
>> >>> > Could you please, give me a quick example on how my files should
>> >>> > look
>> >>> > like?
>> >>> > I would be very grateful.
>> >>> >
>> >>> >
>> >>> > On 23 October 2012 11:56, Cory Quammen <cquammen at cs.unc.edu> wrote:
>> >>> >>
>> >>> >> Gabriel,
>> >>> >>
>> >>> >> You must be trying to use CUDA in your project. I wouldn't be
>> >>> >> surprised if the CUDA compiler has trouble with all the features of
>> >>> >> C++ that ITK uses.
>> >>> >>
>> >>> >> The good news is that you don't need to define your main function
>> >>> >> inside a CUDA source file. You can instead compile only your CUDA
>> >>> >> source with the CUDA compiler, and all your regular C++ code as C++
>> >>> >> files. Just put the CUDA code in a .cu file, put your main C++ code
>> >>> >> in
>> >>> >> a .cpp file, then add all the source files to your call to
>> >>> >> CUDA_ADD_EXECUTABLE. CMake should figure out how to compile them
>> >>> >> automatically.
>> >>> >>
>> >>> >> Hope that helps,
>> >>> >> Cory
>> >>> >>
>> >>> >> On Tue, Oct 23, 2012 at 9:45 AM, Bill Lorensen
>> >>> >> <bill.lorensen at gmail.com>
>> >>> >> wrote:
>> >>> >> > Why are you using .cu?
>> >>> >> >
>> >>> >> > On Tue, Oct 23, 2012 at 9:37 AM, Gabriel Santiago
>> >>> >> > <santiago.eletrica at gmail.com> wrote:
>> >>> >> >>
>> >>> >> >> I am using 3.20.1 version.
>> >>> >> >>
>> >>> >> >> If I change to .cpp instead of .cu everything works fine.
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> On 23 October 2012 11:34, Bill Lorensen
>> >>> >> >> <bill.lorensen at gmail.com>
>> >>> >> >> wrote:
>> >>> >> >>>
>> >>> >> >>> Please keep on list....
>> >>> >> >>>
>> >>> >> >>> What version of ITK? And what happens if you define it as a
>> >>> >> >>> .cxx
>> >>> >> >>> rather
>> >>> >> >>> than .cu?
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>> On Tue, Oct 23, 2012 at 9:17 AM, Gabriel Santiago
>> >>> >> >>> <santiago.eletrica at gmail.com> wrote:
>> >>> >> >>>>
>> >>> >> >>>> Sure!
>> >>> >> >>>>
>> >>> >> >>>> In my main.cu file:
>> >>> >> >>>>
>> >>> >> >>>> #include <iostream>
>> >>> >> >>>> #include <string>
>> >>> >> >>>> #include "itkImageFileReader.h"
>> >>> >> >>>>
>> >>> >> >>>> using std::cout;
>> >>> >> >>>> using std::string;
>> >>> >> >>>>
>> >>> >> >>>> int main(void){
>> >>> >> >>>>
>> >>> >> >>>> string filename = "dicom_file.dcm";
>> >>> >> >>>>
>> >>> >> >>>> typedef signed int InputPixelType;
>> >>> >> >>>> typedef itk::Image<InputPixelType, 3> InputImageType;
>> >>> >> >>>> typedef itk::ImageFileReader<InputImageType> ReaderType;
>> >>> >> >>>> ReaderType::Pointer reader = ReaderType::New();
>> >>> >> >>>> reader->SetFileName(filename.c_str());
>> >>> >> >>>>
>> >>> >> >>>> return 0;
>> >>> >> >>>>
>> >>> >> >>>> }
>> >>> >> >>>>
>> >>> >> >>>> My CMakeLists.txt file conatins:
>> >>> >> >>>>
>> >>> >> >>>> PROJECT( PROJECT_NAME )
>> >>> >> >>>> CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
>> >>> >> >>>> FIND_PACKAGE ( ITK REQUIRED )
>> >>> >> >>>> FIND_PACKAGE(CUDA)
>> >>> >> >>>> INCLUDE(FindCUDA)
>> >>> >> >>>> IF ( ITK_FOUND )
>> >>> >> >>>> INCLUDE( ${ITK_USE_FILE} )
>> >>> >> >>>> ENDIF( ITK_FOUND )
>> >>> >> >>>> CUDA_ADD_EXECUTABLE( PROJECT_NAME main.cu )
>> >>> >> >>>> TARGET_LINK_LIBRARIES ( PROJECT_NAME ITKCommon ITKIO)
>> >>> >> >>>>
>> >>> >> >>>> Thank you for your reply,
>> >>> >> >>>>
>> >>> >> >>>> On 23 October 2012 11:08, Bill Lorensen
>> >>> >> >>>> <bill.lorensen at gmail.com>
>> >>> >> >>>> wrote:
>> >>> >> >>>>>
>> >>> >> >>>>> Gabriel,
>> >>> >> >>>>>
>> >>> >> >>>>> Can you provide a small compilable example to illustrate your
>> >>> >> >>>>> problem?
>> >>> >> >>>>>
>> >>> >> >>>>> Bill
>> >>> >> >>>>>
>> >>> >> >>>>> On Mon, Oct 22, 2012 at 7:35 AM, Gabriel Santiago
>> >>> >> >>>>> <santiago.eletrica at gmail.com> wrote:
>> >>> >> >>>>>>
>> >>> >> >>>>>> Hi guys,
>> >>> >> >>>>>>
>> >>> >> >>>>>> I am trying to read a DICOM file using ITK. I am doing
>> >>> >> >>>>>> exactly
>> >>> >> >>>>>> what
>> >>> >> >>>>>> is
>> >>> >> >>>>>> described in the ITK User Guide but I am getting some weird
>> >>> >> >>>>>> error
>> >>> >> >>>>>> messages.
>> >>> >> >>>>>> Here they are:
>> >>> >> >>>>>>
>> >>> >> >>>>>> overriding ‘itk::ImageBase<VImageDimension>::Pointer
>> >>> >> >>>>>> itk::ImageBase<VImageDimension>::CreateAnother() const [with
>> >>> >> >>>>>> unsigned int
>> >>> >> >>>>>> VImageDimension = 3u,
>> >>> >> >>>>>> itk::ImageBase<VImageDimension>::Pointer
>> >>> >> >>>>>> =
>> >>> >> >>>>>> itk::SmartPointer<itk::ImageBase<3u> >]’
>> >>> >> >>>>>>
>> >>> >> >>>>>> overriding ‘virtual itk::LightObject::Pointer
>> >>> >> >>>>>> itk::Object::CreateAnother() const’
>> >>> >> >>>>>>
>> >>> >> >>>>>> invalid covariant return type for
>> >>> >> >>>>>> ‘itk::ImageBase<VImageDimension>::Pointer
>> >>> >> >>>>>> itk::ImageBase<VImageDimension>::CreateAnother() const [with
>> >>> >> >>>>>> unsigned int
>> >>> >> >>>>>> VImageDimension = 3u,
>> >>> >> >>>>>> itk::ImageBase<VImageDimension>::Pointer
>> >>> >> >>>>>> =
>> >>> >> >>>>>> itk::SmartPointer<itk::ImageBase<3u> >]’
>> >>> >> >>>>>>
>> >>> >> >>>>>> invalid covariant return type for ‘itk::LightObject::Pointer
>> >>> >> >>>>>> itk::Image<TPixel, VImageDimension>::CreateAnother() const
>> >>> >> >>>>>> [with
>> >>> >> >>>>>> TPixel =
>> >>> >> >>>>>> int, unsigned int VImageDimension = 3u,
>> >>> >> >>>>>> itk::LightObject::Pointer =
>> >>> >> >>>>>> itk::SmartPointer<itk::LightObject>]’
>> >>> >> >>>>>>
>> >>> >> >>>>>> All of them are not in my code. Can anyone here, please tell
>> >>> >> >>>>>> me
>> >>> >> >>>>>> what
>> >>> >> >>>>>> is going on?
>> >>> >> >>>>>>
>> >>> >> >>>>>> Thank you all,
>> >>> >> >>>>>>
>> >>> >> >>>>>> --
>> >>> >> >>>>>> Gabriel Santiago
>> >>> >> >>>>>>
>> >>> >> >>>>>> ~"As long as I live so long do I learn"~
>> >>> >> >>>>>> Ramakhrishna
>> >>> >> >>>>>>
>> >>> >> >>>>>>
>> >>> >> >>>>>> _____________________________________
>> >>> >> >>>>>> Powered by www.kitware.com
>> >>> >> >>>>>>
>> >>> >> >>>>>> Visit other Kitware open-source projects at
>> >>> >> >>>>>> http://www.kitware.com/opensource/opensource.html
>> >>> >> >>>>>>
>> >>> >> >>>>>> Kitware offers ITK Training Courses, for more information
>> >>> >> >>>>>> visit:
>> >>> >> >>>>>> http://www.kitware.com/products/protraining.php
>> >>> >> >>>>>>
>> >>> >> >>>>>> Please keep messages on-topic and check the ITK FAQ at:
>> >>> >> >>>>>> http://www.itk.org/Wiki/ITK_FAQ
>> >>> >> >>>>>>
>> >>> >> >>>>>> Follow this link to subscribe/unsubscribe:
>> >>> >> >>>>>> http://www.itk.org/mailman/listinfo/insight-users
>> >>> >> >>>>>>
>> >>> >> >>>>>
>> >>> >> >>>>>
>> >>> >> >>>>>
>> >>> >> >>>>> --
>> >>> >> >>>>> Unpaid intern in BillsBasement at noware dot com
>> >>> >> >>>>>
>> >>> >> >>>>
>> >>> >> >>>>
>> >>> >> >>>>
>> >>> >> >>>> --
>> >>> >> >>>> Gabriel Santiago
>> >>> >> >>>>
>> >>> >> >>>>
>> >>> >> >>>> ~"As long as I live so long do I learn"~
>> >>> >> >>>> Ramakhrishna
>> >>> >> >>>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>>
>> >>> >> >>> --
>> >>> >> >>> Unpaid intern in BillsBasement at noware dot com
>> >>> >> >>>
>> >>> >> >>
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> --
>> >>> >> >> Gabriel Santiago
>> >>> >> >>
>> >>> >> >> ~"As long as I live so long do I learn"~
>> >>> >> >> Ramakhrishna
>> >>> >> >>
>> >>> >> >
>> >>> >> >
>> >>> >> >
>> >>> >> > --
>> >>> >> > Unpaid intern in BillsBasement at noware dot com
>> >>> >> >
>> >>> >> >
>> >>> >> > _______________________________________________
>> >>> >> > Powered by www.kitware.com
>> >>> >> >
>> >>> >> > Visit other Kitware open-source projects at
>> >>> >> > http://www.kitware.com/opensource/opensource.html
>> >>> >> >
>> >>> >> > Kitware offers ITK Training Courses, for more information visit:
>> >>> >> > http://kitware.com/products/protraining.php
>> >>> >> >
>> >>> >> > Please keep messages on-topic and check the ITK FAQ at:
>> >>> >> > http://www.itk.org/Wiki/ITK_FAQ
>> >>> >> >
>> >>> >> > Follow this link to subscribe/unsubscribe:
>> >>> >> > http://www.itk.org/mailman/listinfo/insight-developers
>> >>> >> >
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> --
>> >>> >> Cory Quammen
>> >>> >> Research Associate
>> >>> >> Department of Computer Science
>> >>> >> The University of North Carolina at Chapel Hill
>> >>> >
>> >>> >
>> >>> >
>> >>> >
>> >>> > --
>> >>> > Gabriel Santiago
>> >>> >
>> >>> > ~"As long as I live so long do I learn"~
>> >>> > Ramakhrishna
>> >>> >
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Cory Quammen
>> >>> Research Associate
>> >>> Department of Computer Science
>> >>> The University of North Carolina at Chapel Hill
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Gabriel Santiago
>> >>
>> >> ~"As long as I live so long do I learn"~
>> >> Ramakhrishna
>> >>
>> >
>> >
>> >
>> > --
>> > Gabriel Santiago
>> >
>> > ~"As long as I live so long do I learn"~
>> > Ramakhrishna
>> >
>>
>>
>>
>> --
>> Cory Quammen
>> Research Associate
>> Department of Computer Science
>> The University of North Carolina at Chapel Hill
>
>
>
>
> --
> Gabriel Santiago
>
> ~"As long as I live so long do I learn"~
> Ramakhrishna
>
--
Cory Quammen
Research Associate
Department of Computer Science
The University of North Carolina at Chapel Hill
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