dchansen / gt-tomography Goto Github PK

CMake Error at xray/CMakeLists.txt:71 (add_executable):
Cannot find source file:

convolveTest.cpp

Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
.hxx .in .txx

wow~ ⊙o⊙，what a grate job !

cmake -D GADGETRON_HOME=$GADGETRON_HOME -DCMAKE_INSTALL_PREFIX=/software/opt/trusty/x86_64/gt-tomography_build/git20151127 -D HDF5_DIR=/usr

results in an error:
Compiling with -gencode arch=compute_52,code=sm_52
-- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_MAIN_LIBRARY)
GTest src package found. Compiling as part of Gadgetron.
-- Configuring done
CMake Error at proton/CMakeLists.txt:26 (add_executable):
Cannot find source file:

FilteredProtonReconstruct.cpp

Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp
.hxx .in .txx

There is another error when I do make install:

CMake Error at solvers/cmake_install.cmake:36 (FILE):
file INSTALL cannot find
"/scratch-local/rauscher/gt-tomography/solvers/nonLinearCGSolver.h".
Call Stack (most recent call first):
cmake_install.cmake:38 (INCLUDE)

29%] Building CXX object proton/CMakeFiles/DROPProtonReconstruct.dir/DROPProtonReconstruct.cpp.o
In file included from /project/med/PROSTATE/CBCT_PROJECTIONS_TEST/4D/gt-tomography/gt-tomography_20160604/proton/DROPProtonReconstruct.cpp:16:0:
/project/med/PROSTATE/CBCT_PROJECTIONS_TEST/4D/gt-tomography/gt-tomography_20160604/proton/protonSubsetOperator.h:2:28: fatal error: subsetOperator.h: No such file or directory
#include "subsetOperator.h"
^
compilation terminated.
make[2]: *** [proton/CMakeFiles/DROPProtonReconstruct.dir/DROPProtonReconstruct.cpp.o] Error 1
make[1]: *** [proton/CMakeFiles/DROPProtonReconstruct.dir/all] Error 2
make: *** [all] Error 2

There is still a compile error at our site. I configure with cmake -D GADGETRON_HOME=/software/opt/trusty/x86_64/gadgetron/git20151112 -DCMAKE_INSTALL_PREFIX=/software/opt/trusty/x86_64/gt-tomography_build/git20151127 -D HDF5_DIR=/usr ../gt-tomography

The compilation (make VERBOSE=1) results in the following error:
Linking CXX shared library libproton_kernels.so
cd /scratch-local/rauscher/gt-tomography_build/proton && /usr/bin/cmake -E cmake_link_script CMakeFiles/proton_kernels.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -fopenmp -Wno-deprecated --std=c++11 -shared -Wl,-soname,libproton_kernels.so -o libproton_kernels.so CMakeFiles/proton_kernels.dir/./proton_kernels_generated_splineBackprojectionOperator.cu.o CMakeFiles/proton_kernels.dir/./proton_kernels_generated_proton_kernels.cu.o CMakeFiles/proton_kernels.dir/./proton_kernels_generated_histogram.cu.o CMakeFiles/proton_kernels.dir/./proton_kernels_generated_hoCuParallelProjection.cu.o CMakeFiles/proton_kernels.dir/./proton_kernels_generated_protonPreconditioner.cu.o CMakeFiles/proton_kernels.dir/./proton_kernels_generated_proton_utils.cu.o CMakeFiles/proton_kernels.dir/./proton_kernels_generated_protonDataset.cu.o -L/build/buildd/gdcm-2.2.4/obj-x86_64-linux-gnu/bin/. /usr/local/cuda/lib64/libcudart.so -lgadgetron_toolbox_gpucore -lgadgetron_toolbox_gpufft -lgadgetron_toolbox_gpunfft ../solvers/libtomography_solvers.so /usr/local/cuda/lib64/libcudart.so ../operators/libtomography_operators.so /usr/local/cuda/lib64/libcudart.so -Wl,-rpath,/build/buildd/gdcm-2.2.4/obj-x86_64-linux-gnu/bin/.:/usr/local/cuda/lib64:/scratch-local/rauscher/gt-tomography_build/solvers:/scratch-local/rauscher/gt-tomography_build/operators
/usr/bin/ld: cannot find -lgadgetron_toolbox_gpucore
/usr/bin/ld: cannot find -lgadgetron_toolbox_gpufft
/usr/bin/ld: cannot find -lgadgetron_toolbox_gpunfft

I notice, that there is no -L /software/opt/trusty/x86_64/gadgetron/git20151112/lib among the linker arguments.

Thanks for your help!

I get the following error when trying to make

$ make
[ 1%] Built target gtest
[ 3%] Built target gtest_main
[ 5%] Building NVCC (Device) object solvers/CMakeFiles/tomography_solvers.dir//./tomography_solvers_generated_solver_utils.cu.o
/usr/lib/gcc/x86_64-linux-gnu/4.8/include/stddef.h(432): error: identifier "nullptr" is undefined

/usr/lib/gcc/x86_64-linux-gnu/4.8/include/stddef.h(432): error: expected a ";"

/usr/include/x86_64-linux-gnu/c++/4.8/bits/c++config.h(190): error: expected a ";"

/usr/include/c++/4.8/exception(63): error: expected a ";"

/usr/include/c++/4.8/exception(68): error: expected a ";"

/usr/include/c++/4.8/exception(76): error: expected a ";"

/usr/include/c++/4.8/exception(83): error: expected a ";"

/usr/include/c++/4.8/exception(93): error: expected a "{"

/usr/include/c++/4.8/bits/exception_ptr.h(64): error: function "std::current_exception" returns incomplete type "std::__exception_ptr::exception_ptr"

/usr/include/c++/4.8/bits/exception_ptr.h(64): error: expected a "{"

/usr/include/c++/4.8/bits/exception_ptr.h(79): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(81): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(82): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(84): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(86): error: declaration is incompatible with previous "std::current_exception"
(64): here

/usr/include/c++/4.8/bits/exception_ptr.h(86): error: use of a local type to declare a function

/usr/include/c++/4.8/bits/exception_ptr.h(86): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(87): error: use of a local type to declare a function

/usr/include/c++/4.8/bits/exception_ptr.h(90): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(92): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(95): error: incomplete type is not allowed

/usr/include/c++/4.8/bits/exception_ptr.h(95): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(116): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(126): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(143): error: use of a local type to declare a function

/usr/include/c++/4.8/bits/exception_ptr.h(144): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(147): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(152): error: use of a local type to declare a function

/usr/include/c++/4.8/bits/exception_ptr.h(153): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(156): error: use of a local type to declare a function

/usr/include/c++/4.8/bits/exception_ptr.h(157): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(160): error: use of a local type to declare a function

/usr/include/c++/4.8/bits/exception_ptr.h(161): error: expected a ";"

/usr/include/c++/4.8/bits/exception_ptr.h(169): error: expected a ";"

/usr/include/c++/4.8/bits/nested_exception.h(57): error: incomplete type is not allowed

/usr/include/c++/4.8/bits/nested_exception.h(60): error: expected a ";"

/usr/include/c++/4.8/bits/nested_exception.h(66): error: expected a ";"

/usr/include/c++/4.8/bits/nested_exception.h(70): error: identifier "rethrow_exception" is undefined

/usr/include/c++/4.8/bits/nested_exception.h(73): error: function "std::nested_exception::nested_ptr" returns incomplete type "std::__exception_ptr::exception_ptr"

/usr/include/c++/4.8/new(95): error: expected a "{"

/usr/include/c++/4.8/new(110): error: identifier "__p" is undefined

/usr/include/c++/4.8/new(111): error: expected a "{"

/usr/include/c++/4.8/new(115): error: expected a "{"

/usr/include/c++/4.8/new(116): error: expected a "{"

/usr/local/cuda/include/common_functions.h(102): warning: exception specification is incompatible with that of previous function "operator new[](std::size_t, void *)"
/usr/include/c++/4.8/new(111): here

/usr/local/cuda/include/common_functions.h(103): warning: exception specification is incompatible with that of previous function "operator delete(void *, void *)"
/usr/include/c++/4.8/new(115): here

/usr/local/cuda/include/common_functions.h(104): warning: exception specification is incompatible with that of previous function "operator delete[](void *, void *)"
/usr/include/c++/4.8/new(116): here

/usr/include/c++/4.8/bits/cpp_type_traits.h(184): error: identifier "char16_t" is undefined

/usr/include/c++/4.8/bits/cpp_type_traits.h(191): error: identifier "char32_t" is undefined

/usr/include/c++/4.8/bits/cpp_type_traits.h(191): error: class "std::__is_integer<>" has already been defined

/usr/include/c++/4.8/bits/cpp_type_traits.h(314): error: namespace "std::__gnu_cxx" has no member "__normal_iterator"

/usr/include/c++/4.8/bits/cpp_type_traits.h(314): error: expected a ">"

/usr/include/c++/4.8/cmath(80): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(80): error: expected a ";"

/usr/include/c++/4.8/cmath(105): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(105): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(105): error: expected a ";"

/usr/include/c++/4.8/cmath(124): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(124): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(124): error: expected a ";"

/usr/include/c++/4.8/cmath(143): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(143): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(143): error: expected a ";"

/usr/include/c++/4.8/cmath(162): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(162): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(162): error: expected a ";"

/usr/include/c++/4.8/cmath(183): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(183): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(183): error: expected a ";"

/usr/include/c++/4.8/cmath(202): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(202): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(202): error: expected a ";"

/usr/include/c++/4.8/cmath(221): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(221): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(221): error: expected a ";"

/usr/include/c++/4.8/cmath(240): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(240): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(240): error: expected a ";"

/usr/include/c++/4.8/cmath(259): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(259): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(259): error: expected a ";"

/usr/include/c++/4.8/cmath(278): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(278): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(278): error: expected a ";"

/usr/include/c++/4.8/cmath(297): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(297): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(297): error: expected a ";"

/usr/include/c++/4.8/cmath(328): error: "constexpr" is not a function or static data member

/usr/include/c++/4.8/cmath(337): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(337): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(337): error: expected a ";"

/usr/include/c++/4.8/cmath(356): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(356): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(356): error: expected a ";"

/usr/include/c++/4.8/cmath(375): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(375): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(375): error: expected a ";"

/usr/include/c++/4.8/cmath(406): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(406): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(406): error: expected a ";"

/usr/include/c++/4.8/cmath(443): error: inline specifier allowed on function declarations only

/usr/include/c++/4.8/cmath(443): error: variable "std::constexpr" has already been defined

/usr/include/c++/4.8/cmath(443): error: expected a ";"

Error limit reached.
100 errors detected in the compilation of "/tmp/tmpxft_000039a1_00000000-7_solver_utils.cpp1.ii".
Compilation terminated.
CMake Error at tomography_solvers_generated_solver_utils.cu.o.cmake:264 (message):
Error generating file
/project/med/PROSTATE/CBCT_PROJECTIONS_TEST/4D/gt-tomography/gt-tomography_20160604_build/solvers/CMakeFiles/tomography_solvers.dir//./tomography_solvers_generated_solver_utils.cu.o

make[2]: *** [solvers/CMakeFiles/tomography_solvers.dir/./tomography_solvers_generated_solver_utils.cu.o] Error 1
make[1]: *** [solvers/CMakeFiles/tomography_solvers.dir/all] Error 2
make: *** [all] Error 2