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Sep 12, 2017  02:09 AM | Joses Ho
CCMAKE on Linux does not install all binaries
Hi,

I have followed the instructions that are floating in this forum (but curiously not in the docs):

tar -xvf CMTK-3.3.1-Source.tar
cd CMTK-3.3.1-Source
mkdir build
cd build
ccmake -C ../config/gcc-x86_64-sse.cmake ../

But the only executables that end up in build/bin are:

cmtk
cmtk_functions.sh
cmtk_locking_procmail.sh
cmtk_locking.sh
correct_dwi_distortion
correct_dwi_distortion_and_motion
correct_nex_motion
groupwise_reformat
iterative_shape_averaging
munger

Executables required for registration (eg registration, warp, affine) are not installed. 

What other steps do I need to take before I can successfully install all binaries?

Thanks,
Joses 

PS
in the config options I set as follows:

BASH_PATH /bin/bash
BUILD_APPS ON
BUILD_CONTRIB ON
BUILD_CONTRIB_MUNGER ON
BUILD_MANPAGES ON
BUILD_SHARED_LIBS ON
BUILD_TESTING ON
CMAKE_BACKWARDS_COMPATIBILITY 2.4
CMAKE_BUILD_TYPE CMAKE_CXX_FLAGS
CMAKE_INSTALL_PREFIX /usr/local
CMTK_BUILD_DCMTK ON
CMTK_BUILD_MXML ON
CMTK_BUILD_NRRD ON
CMTK_BUILD_SQLITE ON
CMTK_BUILD_ZLIB ON
CMTK_INSTALL_BIN_DIR bin
CMTK_INSTALL_DATA_DIR share/cmtk
CMTK_INSTALL_INCLUDE_DIR include/cmtk
CMTK_INSTALL_LIB_DIR lib/cmtk
CMTK_ROOT_PATH_SRI24 CMTK_ROOT_PATH_SRI24-NOTFOUND
CMTK_USE_BZIP2 ON
CMTK_USE_CUDA OFF
CMTK_USE_DCMTK ON
CMTK_USE_FFTW ON
CMTK_USE_LZMA ON
CMTK_USE_QT OFF
CMTK_USE_SMP ON
CMTK_USE_SQLITE ON
FFTWD_OMP_LIB FFTWD_OMP_LIB-NOTFOUND
FFTWD_THREADS_LIB /usr/lib64/libfftw3_threads.so
FFTWF_OMP_LIB FFTWF_OMP_LIB-NOTFOUND
FFTWF_THREADS_LIB /usr/lib64/libfftw3f_threads.so
FFTW_INCLUDE_PATH /usr/include
FIND_EXECUTABLE /bin/find
LIBINTL_LIBRARY LIBINTL_LIBRARY-NOTFOUND
NUMDIFF_USE_UNLOCKED_IO ON
Sep 12, 2017  06:09 AM | Greg Jefferis
CCMAKE on Linux does not install all binaries
The full set of executables can be found under lib/cmtk/bin iirc.

You can use the cmtk script to call them.

As for docs, I am seriously thinking about moving development to GitHub and at least having an up to date README there. Torsten?

Best,

Greg.



Sep 12, 2017  10:09 PM | Joses Ho
RE: CCMAKE on Linux does not install all bina
Hi Greg,

I do not find any folder lib/cmtk/bin, either inside the cmtk build folder or in local folders.

Calling the CMTK script produces the following:
./cmtk: line 47: ~/scratch/cmtk-build/bin/--help: No such file or directory

The only reason I am attempting a manual build from source is because the Fiji CMTK plugin does not install properly on Linux, which is a known problem in this forum. 

Moving the official development to Github would be a lot better; the NITRC website as a whole is slow, clunky, and difficult to work with.

Joses
Sep 13, 2017  03:09 PM | Greg Jefferis
RE: CCMAKE on Linux does not installall bina
Hi Joses,

Can you give some kind of output from the build process? Is there any error message?

You are right that the binaries should be found in the build/bin directory after the build. The lib/cmtk/bin directory is only when the built binaries are installed to their final location i.e. after doing

make install

If you want to experiment, try running ccmake without specifying the config e.g.

cd build
ccmake ..

and set the options and then run

make

Best,

Greg.

Sep 13, 2017  10:09 PM | Torsten Rohlfing - Google LLC
RE: CCMAKE on Linux does not install all bin
Hi Greg -

I do have to say, I passionately hate git, but if you see a benefit in moving to github, and you're willing to do the move, then I'd be fine with that.

:)