Gadgetron / Discussion / General Discussion: question about installing GadgeTron on Windows 7 using VM player for Ubuntu

Yu Cai - 2014-03-18

Dear gadgetron expert

This is Yu Cai, a new user of gadgetron software. First, I appreciate Dr Hansen and his group provide us a useful but free open source recon software.

Here I have a questions to ask? I try to install Gadgetron on my Windows 7 PC. I used VM player and installed Ubuntu 12.04 on this Windows 7 PC. in Ubuntu, I used the instructions for linux installation http://sourceforge.net/p/gadgetron/home/Linux%20Installation/

Before the following steps , everything looks fine

cd gadgetron/
mkdir build
cd build
cmake ../

However, after cmake ../, the following error message show up. It looks CUDA, DCMTK missing. Anything to make a remedy? Is it allowed to use such instruction for Ubuntu on virtual machine on Windows 7?

Many thanks

Best Regards

Yu

-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
64bit system is found ...
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
OpenMP multithreading enabled
Build dynamic toolbox libray ...
-- Boost version: 1.46.1
-- Found the following Boost libraries:
-- system
-- thread
-- Found FFTW3: /usr/lib/libfftw3f.so
-- Found ACE library: /usr/lib/libACE.so
-- Found ACE include: /usr/include
ACE found, the streaming framework will be compiled.
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version "4.1")
-- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_MAIN_LIBRARY)
GTest src package found. Compiling as part of Gadgetron.
-- Found PythonInterp: /usr/bin/python (found version "2.7.3")
-- Looking for include files CMAKE_HAVE_PTHREAD_H
-- Looking for include files CMAKE_HAVE_PTHREAD_H - found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found Armadillo: /usr/lib/libarmadillo.so (found version "4.100.2")
Armadillo is found NOT to use long long for BLAS calls ...
Note the ARMADILLO_BLAS_LONG_LONG must be defined in the /usr/include/armadillo_bits/config.hpp to link against MKL ILP64 interface ...
MKL is found at /opt/intel/mkl
-- Found MKL libraries: libmkl_intel_lp64.a;libmkl_intel_thread.a;libmkl_core.a;iomp5
-- MKL_INCLUDE_DIR: /opt/intel/mkl/include
-- MKL_LIB_DIR: /opt/intel/mkl/lib/intel64
-- MKL_COMPILER_LIB_DIR: /opt/intel/compiler/lib/intel64;/opt/intel/lib/intel64
CUDA not found. CUDA components will not be compiled.
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found.
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found.
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found.
-- Found Qt4: /usr/bin/qmake (found suitable version "4.8.1", required is "4.6")
-- Found PythonLibs: /usr/lib/libpython2.7.so
-- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
GLEW FOUND
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so
-- Found HDF5: /usr/lib/libhdf5_cpp.so;/usr/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libm.so (Required is at least version "1.8")
-- Found Ismrmrd: /usr/local/ismrmrd/include
ISMRMRD found
-- Found XSD: /usr/include
-- Could NOT find Matlab (missing: MATLAB_ROOT MATLAB_INCLUDE_DIR MATLAB_LIBRARIES)
Compiling cpu based optical flow registration toolbox.
XSDS_SOURCES is /home/yucai/gadgetron/build/toolboxes/gadgettools/src/xsd/gadgetron.cxx/home/yucai/gadgetron/build/toolboxes/gadgettools/src/xsd/gadgetron.hxx
MKL Found for gtPlus ...
MATLAB NOT FOUND ...
MKL Found for gtPlus ...
Matlab not found. Matlab wrapper for registration toolbox will not be compiled.
MATLAB NOT FOUND: matlab wrapper for gtplus toolbox will not be compiled.
MKL Found for gtPlus ...
MKL Found, enabling MKL for mri_core gadgets.
Cuda NOT found, NOT compiling gpu accelerated gadgets
-- Boost version: 1.46.1
-- Found the following Boost libraries:
-- python
PYTHON_INCLUDE_DIRS: /usr/include/python2.7
PYTHON_LIBRARIES: /usr/lib/libpython2.7.so
NUMPY_INCLUDE_DIRS: /usr/lib/python2.7/dist-packages/numpy/core/include
Compiling Python Gadgets
-- Could NOT find DCMTK (missing: DCMTK_config_INCLUDE_DIR DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY DCMTK_oflog_INCLUDE_DIR DCMTK_oflog_LIBRARY DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR DCMTK_dcmimgle_LIBRARY)
DCMTK NOT found, not compiling DICOM gadget
-- Found Doxygen: /usr/bin/doxygen
Docbook tools found, building manual XSLTPROCEXE: /usr/bin/xsltproc
FOP found, Building PDF Manual, FOPEXE: /usr/bin/fop
CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
Please set them or make sure they are set and tested correctly in the CMake files:
CUDA_TOOLKIT_INCLUDE (ADVANCED)
used as include directory in directory /home/yucai/gadgetron/test

-- Configuring incomplete, errors occurred!

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- Souheil Inati - 2014-03-18
  
  You’ll need to follow the linux install instructions to get all the dependencies,
  https://sourceforge.net/p/gadgetron/home/Linux%20Installation/
  
  Souheil Inati, PhD
  Staff Scientist
  FMRI Facility
  NIMH/NIH/DHHS
  souheil.inati@nih.govsouheil.inati@nih.gov
  
  On Mar 18, 2014, at 11:09 AM, Yu Cai caiyu27@users.sf.netamp#99;amp#97;amp#105;amp#121;amp#117;amp#50;amp#55;amp#64;amp#117;amp#115;amp#101;amp#114;amp#115;amp#46;amp#115;amp#102;amp#46;amp#110;amp#101;amp#116; wrote:
  
  Dear gadgetron expert
  
  This is Yu Cai, a new user of gadgetron software. First, I appreciate Dr Hansen and his group provide us a useful but free open source recon software.
  
  Here I have a questions to ask? I try to install Gadgetron on my Windows 7 PC. I used VM player and installed Ubuntu 12.04 on this Windows 7 PC. in Ubuntu, I used the instructions for linux installation http://sourceforge.net/p/gadgetron/home/Linux%20Installation/
  
  Before the following steps , everything looks fine
  
  cd gadgetron/
  mkdir build
  cd build
  cmake ../
  
  However, after cmake ../, the following error message show up. It looks CUDA, DCMTK missing. Anything to make a remedy? Is it allowed to use such instruction for Ubuntu on virtual machine on Windows 7?
  
  Many thanks
  
  Best Regards
  
  Yu
  
  -- The C compiler identification is GNU
  -- The CXX compiler identification is GNU
  -- Check for working C compiler: /usr/bin/gcc
  -- Check for working C compiler: /usr/bin/gcc -- works
  -- Detecting C compiler ABI info
  -- Detecting C compiler ABI info - done
  -- Check for working CXX compiler: /usr/bin/c++
  -- Check for working CXX compiler: /usr/bin/c++ -- works
  -- Detecting CXX compiler ABI info
  -- Detecting CXX compiler ABI info - done
  64bit system is found ...
  -- Try OpenMP C flag = [-fopenmp]
  -- Performing Test OpenMP_FLAG_DETECTED
  -- Performing Test OpenMP_FLAG_DETECTED - Success
  -- Try OpenMP CXX flag = [-fopenmp]
  -- Performing Test OpenMP_FLAG_DETECTED
  -- Performing Test OpenMP_FLAG_DETECTED - Success
  -- Found OpenMP: -fopenmp
  OpenMP multithreading enabled
  Build dynamic toolbox libray ...
  -- Boost version: 1.46.1
  -- Found the following Boost libraries:
  -- system
  -- thread
  -- Found FFTW3: /usr/lib/libfftw3f.so
  -- Found ACE library: /usr/lib/libACE.so
  -- Found ACE include: /usr/include
  ACE found, the streaming framework will be compiled.
  CUDA_TOOLKIT_ROOT_DIR not found or specified
  -- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY) (Required is at least version "4.1")
  -- Could NOT find GTest (missing: GTEST_LIBRARY GTEST_MAIN_LIBRARY)
  GTest src package found. Compiling as part of Gadgetron.
  -- Found PythonInterp: /usr/bin/python (found version "2.7.3")
  -- Looking for include files CMAKE_HAVE_PTHREAD_H
  -- Looking for include files CMAKE_HAVE_PTHREAD_H - found
  -- Looking for pthread_create in pthreads
  -- Looking for pthread_create in pthreads - not found
  -- Looking for pthread_create in pthread
  -- Looking for pthread_create in pthread - found
  -- Found Threads: TRUE
  -- Found Armadillo: /usr/lib/libarmadillo.so (found version "4.100.2")
  Armadillo is found NOT to use long long for BLAS calls ...
  Note the ARMADILLO_BLAS_LONG_LONG must be defined in the /usr/include/armadillo_bits/config.hpp to link against MKL ILP64 interface ...
  MKL is found at /opt/intel/mkl
  -- Found MKL libraries: libmkl_intel_lp64.a;libmkl_intel_thread.a;libmkl_core.a;iomp5
  -- MKL_INCLUDE_DIR: /opt/intel/mkl/include
  -- MKL_LIB_DIR: /opt/intel/mkl/lib/intel64
  -- MKL_COMPILER_LIB_DIR: /opt/intel/compiler/lib/intel64;/opt/intel/lib/intel64
  CUDA not found. CUDA components will not be compiled.
  -- Looking for Q_WS_X11
  -- Looking for Q_WS_X11 - found
  -- Looking for Q_WS_WIN
  -- Looking for Q_WS_WIN - not found.
  -- Looking for Q_WS_QWS
  -- Looking for Q_WS_QWS - not found.
  -- Looking for Q_WS_MAC
  -- Looking for Q_WS_MAC - not found.
  -- Found Qt4: /usr/bin/qmake (found suitable version "4.8.1", required is "4.6")
  -- Found PythonLibs: /usr/lib/libpython2.7.so
  -- Found NumPy: version "1.6.1" /usr/lib/python2.7/dist-packages/numpy/core/include
  GLEW FOUND
  -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
  -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found
  -- Looking for gethostbyname
  -- Looking for gethostbyname - found
  -- Looking for connect
  -- Looking for connect - found
  -- Looking for remove
  -- Looking for remove - found
  -- Looking for shmat
  -- Looking for shmat - found
  -- Looking for IceConnectionNumber in ICE
  -- Looking for IceConnectionNumber in ICE - found
  -- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so
  -- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so
  -- Found HDF5: /usr/lib/libhdf5_cpp.so;/usr/lib/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libm.so (Required is at least version "1.8")
  -- Found Ismrmrd: /usr/local/ismrmrd/include
  ISMRMRD found
  -- Found XSD: /usr/include
  -- Could NOT find Matlab (missing: MATLAB_ROOT MATLAB_INCLUDE_DIR MATLAB_LIBRARIES)
  Compiling cpu based optical flow registration toolbox.
  XSDS_SOURCES is /home/yucai/gadgetron/build/toolboxes/gadgettools/src/xsd/gadgetron.cxx/home/yucai/gadgetron/build/toolboxes/gadgettools/src/xsd/gadgetron.hxx
  MKL Found for gtPlus ...
  MATLAB NOT FOUND ...
  MKL Found for gtPlus ...
  Matlab not found. Matlab wrapper for registration toolbox will not be compiled.
  MATLAB NOT FOUND: matlab wrapper for gtplus toolbox will not be compiled.
  MKL Found for gtPlus ...
  MKL Found, enabling MKL for mri_core gadgets.
  Cuda NOT found, NOT compiling gpu accelerated gadgets
  -- Boost version: 1.46.1
  -- Found the following Boost libraries:
  -- python
  PYTHON_INCLUDE_DIRS: /usr/include/python2.7
  PYTHON_LIBRARIES: /usr/lib/libpython2.7.so
  NUMPY_INCLUDE_DIRS: /usr/lib/python2.7/dist-packages/numpy/core/include
  Compiling Python Gadgets
  -- Could NOT find DCMTK (missing: DCMTK_config_INCLUDE_DIR DCMTK_ofstd_INCLUDE_DIR DCMTK_ofstd_LIBRARY DCMTK_oflog_INCLUDE_DIR DCMTK_oflog_LIBRARY DCMTK_dcmdata_INCLUDE_DIR DCMTK_dcmdata_LIBRARY DCMTK_dcmimgle_INCLUDE_DIR DCMTK_dcmimgle_LIBRARY)
  DCMTK NOT found, not compiling DICOM gadget
  -- Found Doxygen: /usr/bin/doxygen
  Docbook tools found, building manual XSLTPROCEXE: /usr/bin/xsltproc
  FOP found, Building PDF Manual, FOPEXE: /usr/bin/fop
  CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
  Please set them or make sure they are set and tested correctly in the CMake files:
  CUDA_TOOLKIT_INCLUDE (ADVANCED)
  used as include directory in directory /home/yucai/gadgetron/test
  
  -- Configuring incomplete, errors occurred!
  
  question about installing GadgeTron on Windows 7 using VM player for Ubuntu https://sourceforge.net/p/gadgetron/discussion/general/thread/bfc12c25/?limit=50#1843
  
  Sent from sourceforge.nethttp://sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

David Hansen - 2014-03-18

In addition, it is currently not possible to use CUDA in a virtual machine. All GPU code must run directly on a windows or linux machine.

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Yu Cai - 2014-03-20

Thank for both help. Indeed I followed the instruction https://sourceforge.net/p/gadgetron/home/Linux%20Installation/

Is it necessary for Gadgetron to use CUDA if I do not use GPU code?

If there is no way, I will try to install on Windows directly.

Thanks

Yu

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- Michael Hansen - 2014-03-20
  
  No need for CUDA if you don't use GPU code.
  
  And installing on Windows is not your way to easy installation. I would avoid that if I was you.
  
  Michael
  
  Sent from a mobile device - please excuse brevity and/or typos.
  
  On Mar 20, 2014, at 6:36 PM, "Yu Cai" caiyu27@users.sf.net wrote:
  
  Thank for both help. Indeed I followed the instruction https://sourceforge.net/p/gadgetron/home/Linux%20Installation/
  
  Is it necessary for Gadgetron to use CUDA if I do not use GPU code?
  If there is no way, I will try to install on Windows directly.
  
  Thanks
  
  Yu
  
  question about installing GadgeTron on Windows 7 using VM player for Ubuntu
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  alternate
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Yu Cai - 2014-04-07

Dear Dr Hansen

Still the question about the installation. using cmake ../ still failed. If CUDA code is unnecessary, the other error message is : MATLAB not found, is it the reason to cause the installation failure? I must install Matlab to make it work ? Thanks

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David Hansen - 2014-04-07

I took a look at the error message you're getting, and the problem seems to come from the fact that the code is trying to compile the CUDA tests for Gadgetron, even though you don't have CUDA. This is obviously a bug, but until we fix it, you can do a temporary fix by replacing

if (GTEST_FOUND AND ARMADILLO_FOUND)
add_subdirectory(test)
endif (GTEST_FOUND AND ARMADILLO_FOUND)

with

#if (GTEST_FOUND AND ARMADILLO_FOUND)
# add_subdirectory(test)
#endif (GTEST_FOUND AND ARMADILLO_FOUND)

in gadgetron/CMakeLists.txt

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Yu Cai - 2014-04-08
  
  Dear Dr Hansen
  
  Thank for help. After I comment these lines. cmake../ works. The proceed to run make, however, after 46% completion, it shows the error message.
  It seems that it still needs CUDA code to complete the installation.
  
  Thanks
  
  Yu
  
  /home/yucai/gadgetron/toolboxes/gtplus/workflow/gtPlusISMRMRDReconWorker3DTSPIRIT.h: In member function ‘bool Gadgetron::gtPlus::gtPlusReconWorker3DTSPIRIT<t>::autoReconParameter(Gadgetron::gtPlus::gtPlusReconWorkOrder<t>*) [with T = std::complex<float>]</float>’:
  /home/yucai/gadgetron/toolboxes/gtplus/ut/spirit_test.cpp:425:1: instantiated from here
  /home/yucai/gadgetron/toolboxes/gtplus/workflow/gtPlusISMRMRDReconWorker3DTSPIRIT.h:122:9: warning: comparison between ‘enum Gadgetron::gtPlus::ISMRMRDALGO’ and ‘enum Gadgetron::gtPlus::ISMRMRDCALIBMODE’ [-Wenum-compare]
  Linking CXX executable gtplus_ut_spirit
  [ 45%] Built target gtplus_ut_spirit
  Scanning dependencies of target gtplus_ut_util
  [ 46%] Building CXX object toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/gtplus_ut.cpp.o
  [ 48%] Building CXX object toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/util_test.cpp.o
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘virtual void gtPlus_IO_Test_recon2DCoilMapGPU_Test<gtest_typeparam_>::TestBody()’:
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:123:9: error: ‘GPUTimer’ was not declared in this scope
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:123:18: error: expected ‘;’ before ‘t’
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:5: error: ‘cuNDArray’ was not declared in this scope
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:29: error: expected primary-expression before ‘>’ token
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:52: error: there are no arguments to ‘device_data’ that depend on a template parameter, so a declaration of ‘device_data’ must be available [-fpermissive]
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:52: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:139:48: error: template argument 1 is invalid
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:139:50: error: expected unqualified-id before ‘>’ token
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:140:63: error: ‘csm’ was not declared in this scope
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:164:21: error: there are no arguments to ‘cudaDeviceReset’ that depend on a template parameter, so a declaration of ‘cudaDeviceReset’ must be available [-fpermissive]
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘virtual void gtPlus_IO_Test_recon3DCoilMapGPU_Test<gtest_typeparam_>::TestBody()’:
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:193:9: error: ‘GPUTimer’ was not declared in this scope
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:193:18: error: expected ‘;’ before ‘t’
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:222:21: error: there are no arguments to ‘cudaDeviceReset’ that depend on a template parameter, so a declaration of ‘cudaDeviceReset’ must be available [-fpermissive]
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘void gtPlus_IO_Test_recon3DCoilMapGPU_Test<gtest_typeparam_>::TestBody() [with gtest_TypeParam_ = std::complex<float>]</float>’:
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:222:5: error: ‘cudaDeviceReset’ was not declared in this scope
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘void gtPlus_IO_Test_recon2DCoilMapGPU_Test<gtest_typeparam_>::TestBody() [with gtest_TypeParam_ = std::complex<float>]</float>’:
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:5: error: ‘device_data’ was not declared in this scope
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
  /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:164:5: error: ‘cudaDeviceReset’ was not declared in this scope
  make[2]: *** [toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/util_test.cpp.o] Error 1
  make[1]: *** [toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/all] Error 2
  make: *** [all] Error 2</gtest_typeparam_></gtest_typeparam_></gtest_typeparam_></gtest_typeparam_></t></t>
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - Michael Hansen - 2014-04-08
    
    Did you delete your everything in your build folder before running cmake
    again?
    
    On Mon, Apr 7, 2014 at 10:52 PM, Yu Cai caiyu27@users.sf.net wrote:
    
    Dear Dr Hansen
    
    Thank for help. After I comment these lines. cmake../ works. The proceed
    to run make, however, after 46% completion, it shows the error message.
    It seems that it still needs CUDA code to complete the installation.
    
    Thanks
    
    Yu
    
    /home/yucai/gadgetron/toolboxes/gtplus/workflow/gtPlusISMRMRDReconWorker3DTSPIRIT.h:
    In member function 'bool
    Gadgetron::gtPlus::gtPlusReconWorker3DTSPIRIT::autoReconParameter(Gadgetron::gtPlus::gtPlusReconWorkOrder
    
    *) [with T = std::complex]':
    /home/yucai/gadgetron/toolboxes/gtplus/ut/spirit_test.cpp:425:1:
    instantiated from here
    /home/yucai/gadgetron/toolboxes/gtplus/workflow/gtPlusISMRMRDReconWorker3DTSPIRIT.h:122:9:
    warning: comparison between 'enum Gadgetron::gtPlus::ISMRMRDALGO' and 'enum
    Gadgetron::gtPlus::ISMRMRDCALIBMODE' [-Wenum-compare] Linking CXX
    executable gtplus_ut_spirit [ 45%] Built target gtplus_ut_spirit Scanning
    dependencies of target gtplus_ut_util [ 46%] Building CXX object
    toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/gtplus_ut.cpp.o [ 48%]
    Building CXX object
    toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/util_test.cpp.o
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function
    'virtual void gtPlus_IO_Test_recon2DCoilMapGPU_Test::TestBody()':
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:123:9: error:
    'GPUTimer' was not declared in this scope
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:123:18: error:
    expected ';' before 't'
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:5: error:
    'cuNDArray' was not declared in this scope
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:29: error:
    expected primary-expression before '>' token
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:52: error:
    there are no arguments to 'device_data' that depend on a template
    parameter, so a declaration of 'device_data' must be available
    [-fpermissive]
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:52: note: (if
    you use '-fpermissive', G++ will accept your code, but allowing the use of
    an undeclared name is deprecated)
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:139:48: error:
    template argument 1 is invalid
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:139:50: error:
    expected unqualified-id before '>' token
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:140:63: error:
    'csm' was not declared in this scope
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:164:21: error:
    there are no arguments to 'cudaDeviceReset' that depend on a template
    parameter, so a declaration of 'cudaDeviceReset' must be available
    [-fpermissive] /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In
    member function 'virtual void
    gtPlus_IO_Test_recon3DCoilMapGPU_Test::TestBody()':
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:193:9: error:
    'GPUTimer' was not declared in this scope
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:193:18: error:
    expected ';' before 't'
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:222:21: error:
    there are no arguments to 'cudaDeviceReset' that depend on a template
    parameter, so a declaration of 'cudaDeviceReset' must be available
    [-fpermissive] /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In
    member function 'void gtPlus_IO_Test_recon3DCoilMapGPU_Test::TestBody()
    [with gtest_TypeParam_ = std::complex]':
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated
    from here /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:222:5:
    error: 'cudaDeviceReset' was not declared in this scope
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function
    'void gtPlus_IO_Test_recon2DCoilMapGPU_Test::TestBody() [with
    gtest_TypeParam_ = std::complex]':
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated
    from here /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:5:
    error: 'device_data' was not declared in this scope
    /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated
    from here /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:164:5:
    error: 'cudaDeviceReset' was not declared in this scope make[2]: *
    * [toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/util_test.cpp.o]
    Error 1 make[1]: * [toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/all]Error 2
    make: ** [all] Error 2
    
    question about installing GadgeTron on Windows 7 using VM player for
    Ubuntu
    https://sourceforge.net/p/gadgetron/discussion/general/thread/bfc12c25/?limit=25#c65b/ab3b
    
    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/gadgetron/discussion/general/
    
    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/subscriptions/
    
    alternate
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
    - Yu Cai - 2014-04-08
      
      Dear Dr Hansen
      
      Thank you help. I deleted all content in build directory and try again. When run "make", still only 48% complete. Show such error.
      
      Any previous steps I did wrong? But no error report until this step.
      
      Thanks
      
      Best
      
      Yu
      
      [ 46%] Building CXX object toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/gtplus_ut.cpp.o
      [ 48%] Building CXX object toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/util_test.cpp.o
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘virtual void gtPlus_IO_Test_recon2DCoilMapGPU_Test<gtest_typeparam_>::TestBody()’:
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:123:9: error: ‘GPUTimer’ was not declared in this scope
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:123:18: error: expected ‘;’ before ‘t’
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:5: error: ‘cuNDArray’ was not declared in this scope
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:29: error: expected primary-expression before ‘>’ token
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:52: error: there are no arguments to ‘device_data’ that depend on a template parameter, so a declaration of ‘device_data’ must be available [-fpermissive]
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:52: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:139:48: error: template argument 1 is invalid
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:139:50: error: expected unqualified-id before ‘>’ token
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:140:63: error: ‘csm’ was not declared in this scope
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:164:21: error: there are no arguments to ‘cudaDeviceReset’ that depend on a template parameter, so a declaration of ‘cudaDeviceReset’ must be available [-fpermissive]
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘virtual void gtPlus_IO_Test_recon3DCoilMapGPU_Test<gtest_typeparam_>::TestBody()’:
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:193:9: error: ‘GPUTimer’ was not declared in this scope
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:193:18: error: expected ‘;’ before ‘t’
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:222:21: error: there are no arguments to ‘cudaDeviceReset’ that depend on a template parameter, so a declaration of ‘cudaDeviceReset’ must be available [-fpermissive]
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘void gtPlus_IO_Test_recon3DCoilMapGPU_Test<gtest_typeparam_>::TestBody() [with gtest_TypeParam_ = std::complex<float>]</float>’:
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:222:5: error: ‘cudaDeviceReset’ was not declared in this scope
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘void gtPlus_IO_Test_recon2DCoilMapGPU_Test<gtest_typeparam_>::TestBody() [with gtest_TypeParam_ = std::complex<float>]</float>’:
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:5: error: ‘device_data’ was not declared in this scope
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
      /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:164:5: error: ‘cudaDeviceReset’ was not declared in this scope
      make[2]: *** [toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/util_test.cpp.o] Error 1
      make[1]: *** [toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/all] Error 2
      make: *** [all] Error 2</gtest_typeparam_></gtest_typeparam_></gtest_typeparam_></gtest_typeparam_>
      
      If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
      - Hui Xue - 2014-04-09
        
        Hi Yu,
        
        I think one way to bypass this problem is to disable the gtest in your cmake.
        
        You can open the cmake and find the variables GTEST_INCLUDE_DIR and set this variable to be empty. Please do not delete this variable, otherwise cmake will set it automatically.
        
        Then you can run configure and generate the solution.
        
        Regards
        
        Hui Xue
        
        From: Yu Cai [caiyu27@users.sf.net]
        Sent: Tuesday, April 08, 2014 7:12 PM
        To: [gadgetron:discussion]
        Subject: [gadgetron:discussion] Re: question about installing GadgeTron on Windows 7 using VM player for Ubuntu
        
        Dear Dr Hansen
        
        Thank you help. I deleted all content in build directory and try again. When run "make", still only 48% complete. Show such error.
        
        Any previous steps I did wrong? But no error report until this step.
        
        Thanks
        
        Best
        
        Yu
        
        [ 46%] Building CXX object toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/gtplus_ut.cpp.o
        [ 48%] Building CXX object toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/util_test.cpp.o
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘virtual void gtPlus_IO_Test_recon2DCoilMapGPU_Test::TestBody()’:
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:123:9: error: ‘GPUTimer’ was not declared in this scope
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:123:18: error: expected ‘;’ before ‘t’
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:5: error: ‘cuNDArray’ was not declared in this scope
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:29: error: expected primary-expression before ‘>’ token
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:52: error: there are no arguments to ‘device_data’ that depend on a template parameter, so a declaration of ‘device_data’ must be available [-fpermissive]
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:52: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:139:48: error: template argument 1 is invalid
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:139:50: error: expected unqualified-id before ‘>’ token
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:140:63: error: ‘csm’ was not declared in this scope
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:164:21: error: there are no arguments to ‘cudaDeviceReset’ that depend on a template parameter, so a declaration of ‘cudaDeviceReset’ must be available [-fpermissive]
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘virtual void gtPlus_IO_Test_recon3DCoilMapGPU_Test::TestBody()’:
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:193:9: error: ‘GPUTimer’ was not declared in this scope
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:193:18: error: expected ‘;’ before ‘t’
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:222:21: error: there are no arguments to ‘cudaDeviceReset’ that depend on a template parameter, so a declaration of ‘cudaDeviceReset’ must be available [-fpermissive]
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘void gtPlus_IO_Test_recon3DCoilMapGPU_Test::TestBody() [with gtest_TypeParam_ = std::complex]’:
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:222:5: error: ‘cudaDeviceReset’ was not declared in this scope
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp: In member function ‘void gtPlus_IO_Test_recon2DCoilMapGPU_Test::TestBody() [with gtest_TypeParam_ = std::complex]’:
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:138:5: error: ‘device_data’ was not declared in this scope
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:223:1: instantiated from here
        /home/yucai/gadgetron/toolboxes/gtplus/ut/util_test.cpp:164:5: error: ‘cudaDeviceReset’ was not declared in this scope
        make[2]: [toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/util_test.cpp.o] Error 1
        make[1]: [toolboxes/gtplus/ut/CMakeFiles/gtplus_ut_util.dir/all] Error 2
        make: *** [all] Error 2
        
        question about installing GadgeTron on Windows 7 using VM player for Ubuntu https://sourceforge.net/p/gadgetron/discussion/general/thread/bfc12c25/?limit=25#c65b/ab3b/30fa/d3a9
        
        Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
        
        To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
        
        If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
        
        Yu Cai - 2014-04-09
        
        Dear Dr Xue
        
        Thank for help. Could you give more detail which file I should look for. In CMakeLists.txt, I try to find GTEST_INCLUDE_DIR but only found
        
        if (GTEST_SRC_DIR AND GTEST_INCLUDE_DIRS) // one is here
        MESSAGE("GTest src package found. Compiling as part of Gadgetron.")
        add_subdirectory(${GTEST_SRC_DIR} ${CMAKE_BINARY_DIR}/gtest )
        include_directories(${ GTEST_INCLUDE_DIRGTEST_INCLUDE_DIRS}) //one may be here
        set(GTEST_FOUND 1)
        set(GTEST_LIBRARIES gtest gtest_main)
        endif (GTEST_SRC_DIR AND GTEST_INCLUDE_DIRS) //one may be here
        endif (NOT GTEST_FOUND)
        
        Thanks
        
        Yu
        
        If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
        
        David Hansen - 2014-04-09
        
        Hi Yu,
        
        If you replace
        
        endif (NOT GTEST_FOUND)
        
        with
        
        endif (NOT GTEST_FOUND)
        set(GTEST_FOUND 0)
        
        this should disable all attempts to compile the tests.
        
        Best,
        
        David
        
        If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Michael Hansen - 2014-04-08

Hmmm, looks like gtPlus tries to compile some CUDA components.

Let me ask you, do you have MKL installed but not CUDA?

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Yu Cai - 2014-04-09
  
  Dear Dr Hansen
  
  I follow the steps for linux installation.
  
  Yes, I have the MKL installed. It has 30 days free use. I think mine is within 30 days.
  
  Thank for patience for help me on Gadgetron.
  
  Cheers
  
  Yu
  
  If you would like to use MKL (Intel Math Kernel Library), please download your installation file from Intel and do the installation. Here is what we did with MKL version 11.0.5.192:
  
  tar -xzvf l_mkl_11.0.5.192_intel64.tgz
  cd l_mkl_11.0.5.192_intel64/
  sudo ./install.sh
  
  Follow the instructions and add the following paths to your ~/.bashrc::
  
  export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/mkl/lib/intel64
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - Yu Cai - 2014-04-11
    
    Dear gadgetron expert
    
    With your help, finally make it compile it successfully. I will learn how to use it.
    
    Thanks
    
    Best
    
    Yu
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

Yu Cai - 2014-04-12

Dear Gadgetron experts

I compile it succseefully. I followed the examples of " hello word". However, when I run mriclient -d testdata.h5. It seems libiomp5.so file missed.

It shows the error

mriclient: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory

Thanks

Yu

If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
- Hui Xue - 2014-04-12
  
  Hi Yu,
  
  this .so file is a part of MKL, in the MKL_HOME\compiler\lib\intel64 folder. Do you add this folder into your path?
  
  regards
  
  Hui Xue
  
  Hui Xue
  Staff Scientist
  National Heart, Lung and Blood Institute
  National Institutes of Health
  10 Center Drive, Bethesda
  MD 20814
  
  Phone: +1 (301) 496-3052
  Cell: +1 (609) 712-3398
  Fax: +1 (301) 496-2389
  Email: hui.xue@nih.govhui.xue@nih.gov
  
  From: Yu Cai [caiyu27@users.sf.net]
  Sent: Saturday, April 12, 2014 4:00 PM
  To: [gadgetron:discussion]
  Subject: [gadgetron:discussion] question about installing GadgeTron on Windows 7 using VM player for Ubuntu
  
  Dear Gadgetron experts
  
  I compile it succseefully. I followed the examples of " hello word". However, when I run mriclient -d testdata.h5. It seems libiomp5.so file missed.
  
  It shows the error
  
  mriclient: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory
  
  Thanks
  
  Yu
  
  question about installing GadgeTron on Windows 7 using VM player for Ubuntu https://sourceforge.net/p/gadgetron/discussion/general/thread/bfc12c25/?limit=25#6846
  
  Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/gadgetron/discussion/general/
  
  To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
  
  If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
  - Yu Cai - 2014-04-12
    
    Dear Dr Xue
    
    Thank for help. In my version. It is located in directory /opt/intel/composer_xe_2013.5.192/compiler/lib/intel64/
    
    After I add this path, it works fine now.
    
    Best Regards
    
    Yu
    
    If you would like to refer to this comment somewhere else in this project, copy and paste the following link:

question about installing GadgeTron on Windows 7 using VM player for Ubuntu

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question about installing GadgeTron on Windows 7 using VM player for Ubuntu

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question about installing GadgeTron on Windows 7 using VM player for Ubuntu