Installation issue on Linux Box/HPC cluster

[brangl]

Hi, I'm trying to install the CIP library and encountered the following errors. I've followed the github wiki and downloaded the develop branch. The problems are:

UPDATE: The first error only raises when I try to build on more than 2 cores (e.g. make -j 8 ). The second error persists.

1. It seems to be missing the itkMultiThreaderBase.h file:
   [ 53%] Linking CXX executable ../../bin/ConvertDicom
   In file included from /hdd_scratch3/br888855/ChestImagingPlatform/CommandLineTools/ExampleCLI/Testing/ExampleCLITest.cxx:1:0:
   /hdd_scratch3/br888855/ChestImagingPlatform/CommandLineTools/Testing/itkTestMain.h:41:10: fatal error: itkMultiThreaderBase.h: No such file or directory
   #include "itkMultiThreaderBase.h"
   ^~~~~~~~~~~~~~~~~~~~~~~~

2. It seems to be trying to use a C compiler to install C++ code:
   [ 54%] Built target ConvertDicom
   running build_ext
   skipping '/hdd_scratch3/br888855/ChestImagingPlatform/cip_python/utils/gco_python/gco_python.cpp' Cython extension (up-to-date)
   building 'pygco' extension
   /usr/bin/cc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/hdd_scratch3/br888855/ChestImagingPlatform/Utilities/GraphCutsOptimization -I/hdd_scratch3/br888855/ChestImagingPlatform-build/CIPPython-install/lib/python2.7/site-packages/numpy/core/include -I/hdd_scratch3/br888855/ChestImagingPlatform-build/CIPPython-install/include/python2.7 -c /hdd_scratch3/br888855/ChestImagingPlatform/cip_python/utils/gco_python/gco_python.cpp -o build/temp.linux-x86_64-2.7/hdd_scratch3/br888855/ChestImagingPlatform/cip_python/utils/gco_python/gco_python.o
   cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++ [enabled by default]
   In file included from /hdd_scratch3/br888855/ChestImagingPlatform-build/CIPPython-install/include/python2.7/Python.h:19:0,
   from /hdd_scratch3/br888855/ChestImagingPlatform/cip_python/utils/gco_python/gco_python.cpp:4:
   /usr/include/limits.h:124:26: error: no include path in which to search for limits.h

include_next <limits.h>

                      ^

In file included from /hdd_scratch3/br888855/ChestImagingPlatform/cip_python/utils/gco_python/gco_python.cpp:4:0:
/hdd_scratch3/br888855/ChestImagingPlatform-build/CIPPython-install/include/python2.7/Python.h:22:2: error: #error "Something's broken. UCHAR_MAX should be defined in limits.h."
#error "Something's broken. UCHAR_MAX should be defined in limits.h."
^
/hdd_scratch3/br888855/ChestImagingPlatform-build/CIPPython-install/include/python2.7/Python.h:26:2: error: #error "Python's source code assumes C's unsigned char is an 8-bit type."
#error "Python's source code assumes C's unsigned char is an 8-bit type."
^
In file included from /hdd_scratch3/br888855/ChestImagingPlatform-build/CIPPython-install/include/python2.7/Python.h:33:0,
from /hdd_scratch3/br888855/ChestImagingPlatform/cip_python/utils/gco_python/gco_python.cpp:4:
/usr/include/stdio.h:33:21: fatal error: stddef.h: No such file or directory

include <stddef.h>

                 ^

compilation terminated.
error: command '/usr/bin/cc' failed with exit status 1
make[5]: *** [cip_python/CMakeFiles/CIP_PYTHON] Error 1
make[4]: *** [cip_python/CMakeFiles/CIP_PYTHON.dir/all] Error 2

Any help greatly appreciated, thanks!

[rsanjoseestepar]

Hello,

Right now we are adapting the platform to use ITK version 5 and C++11, so some issues are expected, and the documentation is not yet updated.

On Cmake, be sure you have ITK_VERSION_MAYOR set to 5 and USE_BOOST set to OFF, and try to build again using 2 cores top.

If you still have problems, I recommend you to use the CIP docker (https://hub.docker.com/r/acilbwh/chestimagingplatform).

Hope this helps

[brangl]

Thanks - changing the ITK version to 5 and turning USE_BOOST to OFF again resulted in error 2. above. Using only 2 cores did not raise error 1.

I managed to use the docker version for the time being.