SIRF build fails - unable to disable synergistic code

[mastergari]

According to @KrisThielemans, setting DISABLE_Synergistic:BOOL=ON in <PATH TO>/builds/SIRF/build/CMakeCache.txt shouldn’t compile syn_utilities.cpp. However, calling make from SIRF/build/ returns:

/home/matthew/Programs/sirf/build/sources/SIRF/src/common/syn_utilities.cpp:32:10: fatal error: sirf/Gadgetron/gadgetron_data_containers.h: No such file or directory 
#include "sirf/Gadgetron/gadgetron_data_containers.h"

If I set DISABLE_Synergistic:BOOL=OFF, then make returns the same error as above. Also note that cmake returns:

-- One or more of the following components are missing: Registration, ISMRMRD and STIR (with ITK). Synergistic code will not be built.
-- Either Registration or ISMRMRD or STIR (with ITK) have not been built.

At first, it appears that I have successfully built Registration (NIFTYREG), ISMRMRD, and STIR (with ITK), and all packages show as Up-to-date when calling make install from <PATH TO>/builds/<PACKAGE>/build. However, when I try to enable the synergistic code, cmake returns -- ISMRMRD missing, and all of the ismrmrd programs in the INSTALL/bin directory return error while loading shared libraries: libismrmrd.so.1.7: cannot open shared object file: No such file or directory. I noticed that calling make install from ISMRMRD/build/ sets all runtime paths to "". I don't need ISMRMRD, but I cannot figure out how to properly build it in my attempt to bypass the synergistic code issue.

Any help is appreciated!

[mastergari]

I think part of my issue was that I had set DISABLE_GIT_CHECKOUT_Gadgetron:BOOL=OFF in build/CMakeCache.txt and DISABLE_Gadgetron:BOOL=ON in build/builds/SIRF/build/CMakeCache.txt. I was able to build SIRF to some extent after changing some of my cmake settings.

First, my ISMRMRD build failed with error message:

/usr/bin/ld: /home/matthew/Programs/sirf/build/INSTALL/lib/libhdf5.a(H5HFsection.c.o): relocation R_X86_64_PC32 against symbol 'H5E_HEAP_g' can not be used when making a shared object; recompile with -fPIC

so I recompiled HDF5 after adding -fPIC to CMAKE_C_FLAGS and CMAKE_CXX_FLAGS in builds/HDF5/build/CMakeCache.txt.

Next, the configure step for SIRF failed with error message (this appears to be a separate issue):

CMake Error at /home/matthew/Programs/sirf/build/INSTALL/share/cmake/hdf5/hdf5-config-version.cmake:18 (IF):
  if given arguments:
    "0" "EQUAL"
  Unknown arguments specified

so I commented out the IF ENDIF statements on line 18 in hdf5-config-version.cmake since there are missing arguments and a comment stating "not using this yet". Calling make or make SIRF from the build folder overwrites the cmake file, so I continued to the build/builds/SIRF/build folder.

While trying to build SIRF only, I received the error message:

/home/matthew/Programs/sirf/build/sources/SIRF/src/Registration/cReg/NiftiImageData3DDisplacement.cpp:33:10: fatal error: vtkSmartPointer.h: No such file or directory
 #include "vtkSmartPointer.h"

so I set DISABLE_VTK:BOOL=ON. Beyond this, I used to see the syn_utilities.cpp error mentioned in the first comment. However, adding -fPIC and DISABLE_Gadtron:BOOL=ON to their respective CMakeCache.txt files allowed me to complete the build, and all SIRF tests passed after installing the python dependencies in build/sources/SIRF/requirements.txt.