SIRF-SuperBuild build fails on Windows #197

evgueni-ovtchinnikov · 2019-01-24T12:49:21Z

SIRF-SuperBuild build fails on Windows with the error message from CMake:

8>  -- FFTW3 WINDOWS libraries: FFTW3F_LIBRARY-NOTFOUND
8>  CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
8>    Could NOT find FFTW3 (missing: FFTW3F_LIBRARY FFTW3_INCLUDE_DIR)
8>  Call Stack (most recent call first):
8>    C:/Program Files/CMake/share/cmake-3.12/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
8>    C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/lib/cmake/ISMRMRD/FindFFTW3.cmake:114 (find_package_handle_standard_args)
8>    src/xGadgetron/CMakeLists.txt:31 (find_package)

CMake GUI however displays both 'missing' items with correct values!

The text was updated successfully, but these errors were encountered:

rijobro · 2019-01-24T14:02:22Z

It looks like the error is coming from SIRF (thus xGadgetron), but I would have guessed that when you say you're looking at the CMake GUI, you're actually looking at the CMake of the superbuild. Is that correct?

If so, it sounds like FFTW3F_LIBRARY isn't being passed from the superbuild to SIRF. You could check this by looking at builds/SIRF/build/CMakeCache.txt and looking for FFTW3F_LIBRARY there.

rijobro · 2019-01-24T14:04:18Z

Here are the arguments in External_SIRF.cmake:

    CMAKE_ARGS
        -DCMAKE_PREFIX_PATH=${SUPERBUILD_INSTALL_DIR}
        -DCMAKE_LIBRARY_PATH=${SUPERBUILD_INSTALL_DIR}/lib
        -DCMAKE_INSTALL_PREFIX=${SIRF_Install_Dir}
        -DBOOST_INCLUDEDIR=${BOOST_ROOT}/include/
        -DBOOST_LIBRARYDIR=${BOOST_LIBRARY_DIR}
        -DBOOST_ROOT=${BOOST_ROOT}
        -DMatlab_ROOT_DIR=${Matlab_ROOT_DIR}
        -DMATLAB_ROOT=${Matlab_ROOT_DIR} # pass this for compatibility with old SIRF
        -DMATLAB_DEST_DIR=${MATLAB_DEST_DIR}
        -DSTIR_DIR=${STIR_DIR}
        -DHDF5_ROOT=${HDF5_ROOT}
        -DHDF5_INCLUDE_DIRS=${HDF5_INCLUDE_DIRS}
        -DISMRMRD_DIR=${ISMRMRD_DIR}
        -DSWIG_EXECUTABLE=${SWIG_EXECUTABLE}
        -DPYTHON_EXECUTABLE=${PYTHON_EXECUTABLE}
        -DPYTHON_INCLUDE_DIR=${PYTHON_INCLUDE_DIRS}
        -DPYTHON_LIBRARY=${PYTHON_LIBRARIES}
        -DPYTHON_DEST_DIR=${PYTHON_DEST_DIR}
        -DPYTHON_STRATEGY=${PYTHON_STRATEGY}
        -DNiftyReg_Binary_DIR=${NiftyReg_Binary_DIR}

It doesn't look like FFTW3F_LIBRARY is being passed, so maybe you just need to add it in.

evgueni-ovtchinnikov · 2019-01-24T15:20:54Z

Thanks, it worked!
I added to CMAKE_ARGS

		-DFFTW3_INCLUDE_DIR=${FFTW3_ROOT_DIR}
		-DFFTW3F_LIBRARY=${FFTW3F_LIBRARY}

where

  if (WIN32)
    set(FFTW3F_LIBRARY ${FFTW3_ROOT_DIR}/libfftw3f-3.lib)
  else()
    set(FFTW3F_LIBRARY ${FFTW3_ROOT_DIR}/libfftw3f.so)
  endif()

I hope this will not break anything - any comments anyone?

rijobro · 2019-01-24T15:30:16Z

I would have thought that you don't need to set any variables, since these would all be set in External_FFTW3.cmake.

When I'm debugging, I print all available CMake variables like this:

message(STATUS "print all variables...")
get_cmake_property(_variableNames VARIABLES)
list (SORT _variableNames)
foreach (_variableName ${_variableNames})
    message(STATUS "${_variableName}=${${_variableName}}")
endforeach()
message(FATAL_ERROR "all variables printed.")

If I were you, I would put this somewhere in your External_SIRF.cmake file, and check whether FFTW3F_LIBRARY is already correct (it would save you having to do an if/else).

evgueni-ovtchinnikov · 2019-01-24T15:48:16Z

will try later

now i have run into another problem when trying to SuperBuild with DEVEL_BUILD on:

8>  CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:2048 (message):
8>    Unable to find the requested Boost libraries.
8>
8>    Boost version: 1.65.1
8>
8>    Boost include path:
8>    C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/include/boost-1_65_1
8>
8>
8>    Could not find the following Boost libraries:
8>
8>            boost_system
8>            boost_filesystem
8>            boost_thread
8>            boost_date_time
8>            boost_chrono
8>
8>    Some (but not all) of the required Boost libraries were found.  You may
8>    need to install these additional Boost libraries.  Alternatively, set
8>    BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT
8>    to the location of Boost.
8>  Call Stack (most recent call first):
8>    src/xGadgetron/cGadgetron/CMakeLists.txt:18 (find_package)
8>
8>
8>  CMake Deprecation Warning at C:/Program Files/CMake/share/cmake-3.12/Modules/UseSWIG.cmake:492 (message):
8>    SWIG_ADD_MODULE is deprecated.  Use SWIG_ADD_LIBRARY instead.
8>  Call Stack (most recent call first):
8>    src/xGadgetron/pGadgetron/CMakeLists.txt:37 (SWIG_ADD_MODULE)
8>
8>
8>  CMake Error at C:/Program Files/CMake/share/cmake-3.12/Modules/FindBoost.cmake:2048 (message):
8>    Unable to find the requested Boost libraries.
8>
8>    Boost version: 1.65.1
8>
8>    Boost include path:
8>    C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/include/boost-1_65_1
8>
8>
8>    Could not find the following Boost libraries:
8>
8>            boost_system
8>            boost_thread
8>            boost_filesystem
8>
8>    Some (but not all) of the required Boost libraries were found.  You may
8>    need to install these additional Boost libraries.  Alternatively, set
8>    BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT
8>    to the location of Boost.
8>  Call Stack (most recent call first):
8>    src/xGadgetron/mGadgetron/CMakeLists.txt:21 (find_package)
8>
8>
8>  -- setup.py:pGadgetron<-sirf.Gadgetron
8>  -- setup.py:pSTIR<-sirf.STIR
8>  -- setup.py:pUtilities<-sirf.Utilities
8>  -- setup.py:pygadgetron<-sirf.pygadgetron
8>  -- setup.py:pystir<-sirf.pystir
8>  -- setup.py:pyiutilities<-sirf.pyiutilities
8>  -- setup.py:C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/python/setup.py
8>CUSTOMBUILD : CMake error : The following variables are used in this project, but they are set to NOTFOUND.
8>  -- Configuring incomplete, errors occurred!
8>  See also "C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/builds/SIRF/build/CMakeFiles/CMakeOutput.log".
8>  See also "C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/builds/SIRF/build/CMakeFiles/CMakeError.log".
8>  Please set them or make sure they are set and tested correctly in the CMake files:
8>  Boost_CHRONO_LIBRARY_DEBUG (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_CHRONO_LIBRARY_RELEASE (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_DATE_TIME_LIBRARY_DEBUG (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_DATE_TIME_LIBRARY_RELEASE (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_FILESYSTEM_LIBRARY_DEBUG (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_FILESYSTEM_LIBRARY_RELEASE (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_SYSTEM_LIBRARY_DEBUG (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_SYSTEM_LIBRARY_RELEASE (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_THREAD_LIBRARY_DEBUG (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>  Boost_THREAD_LIBRARY_RELEASE (ADVANCED)
8>      linked by target "cstir" in directory C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/sources/SIRF/src/xSTIR/cSTIR
8>
9>------ Skipped Build: Project: ALL_BUILD, Configuration: Release x64 ------
9>Project not selected to build for this solution configuration

BOOST_LIBRARYDIR was set as suggested (to Boost/bin.v2/libs)

rijobro · 2019-01-24T15:51:12Z

Not sure for Windows, but try setting BOOST_ROOT to C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/. If you can't seen an option for this in your CMake GUI, then try:

cmake . -DBOOST_ROOT=C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/

evgueni-ovtchinnikov · 2019-01-24T16:02:45Z

no, it does not help, same error message

rijobro · 2019-01-24T16:32:37Z

Well again, this looks like a SIRF error (not superbuild), so check the value of BOOST_ROOT in builds/SIRF/build/CMakeCache.txt.

KrisThielemans · 2019-01-24T23:05:56Z

I never succeeded to get CMake to correctly find a Boost version that we compile. It's a very complicated moving target with boost renaming libraries in the build schemes, and CMake trying to catch-up.

I very much recommend to install the Boost binaries, and set USE_SYSTEM_BOOST=ON.

KrisThielemans · 2019-01-25T00:08:16Z

Regarding the missing FFTW stuff, @evgueni-ovtchinnikov can you give more information on how you're running this? If USE_SYSTEM_FFTW3=ON, see #147.

Otherwise, I'm surprised as it searches for the library with find_library , see for example here. I thought this would go and search in our install directory., but I admit that I cannot see anything related to that in the find_library doc (but If it doesn't, how come USE_SYSTEM_FFTW3=OFF works apparently on the VM?)

KrisThielemans · 2019-01-25T00:10:06Z

See #7 for other remaining issues with the Windows build. Note however that I succesfully build on Windows 10 with CMake 3.13.2 with USE_SYSTEM_BOOST=ON and USE_SYSTEM_FFTW3=ON

evgueni-ovtchinnikov · 2019-01-31T14:40:45Z

same problem with boost on windows 7

all boost libraries are actually present in INSTALL/lib, but there are no respective dlls in INSTALL/bin, which is a likely reason for the error messages

moreover, there are no boost dlls in build/SIRF-SuperBuild at all

rijobro · 2019-01-31T15:06:30Z

Surely all the dlls belong in INSTALL/lib, and not in INSTALL/bin, so it's normal that there aren't any dlls in INSTALL/bin?

KrisThielemans · 2019-01-31T15:11:29Z

Please do not waste time trying to set USE_SYSTEM_BOOST=OFF on Windows. It's going to be a struggle. Instead, install the boost binaries, set the BOOST_ROOT environment (or CMake) variable.

evgueni-ovtchinnikov · 2019-02-01T10:57:33Z

no, it does not help, same error message

evgueni-ovtchinnikov · 2019-02-01T11:02:27Z

installed boost_1_65_1, boost is ok, back to fftw3 problem:

 -- FFTW3 WINDOWS libraries: FFTW3F_LIBRARY-NOTFOUND
10>  CMake Error at C:/Program Files/CMake/share/cmake-3.13/Modules/FindPackageHandleStandardArgs.cmake:137 (message):
10>    Could NOT find FFTW3 (missing: FFTW3F_LIBRARY FFTW3_INCLUDE_DIR)
10>  Call Stack (most recent call first):
10>    C:/Program Files/CMake/share/cmake-3.13/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE)
10>    C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/lib/cmake/ISMRMRD/FindFFTW3.cmake:114 (find_package_handle_standard_args)
10>    src/xGadgetron/CMakeLists.txt:36 (find_package)

cmake shows correct values for FFTW3F_LIBRARY and FFTW3_INCLUDE_DIR

KrisThielemans · 2019-02-01T15:33:23Z

This commit makes little sense to me, given the discussion in #147. Maybe I was incorrect there.

In any case,

if USE_SYSTEM_FFTW3=OFF, those variables aren't set.
it would need similar fixes for ISMRMRD and Gadgetron presumably.

Can we do this via a PR please?

rijobro · 2019-02-06T14:46:28Z

This re-closed itself automatically, not sure why.

casperdcl · 2019-02-06T15:22:13Z

because

75b7f6c Revert "added missing CMake FFTW variables to External_SIRF.cmake, fixes #197 (together with installing boost_1_65_1)"

includes the text

fixes #197

github being too clever...

rijobro · 2019-02-06T16:20:11Z

ah... Thanks!

evgueni-ovtchinnikov · 2019-02-08T16:59:43Z

my standalone SIRF has CMake option SIRF_INSTALL_DEPENDENCIES, which forces copying boost dlls to INSTALL/bin, whereas SIRF-SuperBuild does not have one, and Python and Matlab fail to load SIRF Gadgetron libraries

evgueni-ovtchinnikov · 2019-02-08T17:01:55Z

Matlab fails with the error message

    'There was an error loading the library "C:\Users\wps46139\Documents\GitHub\build\SIRF-SuperBuild\INSTALL\matlab\mgadgetron.mexw64"
     
     Missing symbol 'H5P_CLS_DATASET_CREATE_ID_g' in 'C:\Program Files\MATLAB\R2017a/bin/win64\hdf5.dll' required by 'C:\Users\wps46139\Documents\GitHub\build\SIRF-SuperBuild\INSTALL\bin\ismrmrd.dll->C:\Users\wps46139\Documents\GitHub\build\SIRF-SuperBuild\INSTALL\matlab\mgadgetron.mexw64'
     Missing symbol 'H5P_CLS_LINK_CREATE_ID_g' in 'C:\Program Files\MATLAB\R2017a/bin/win64\hdf5.dll' required by 'C:\Users\wps46139\Documents\GitHub\build\SIRF-SuperBuild\INSTALL\bin\ismrmrd.dll->C:\Users\wps46139\Documents\GitHub\build\SIRF-SuperBuild\INSTALL\matlab\mgadgetron.mexw64''

apparently there is a conflict between HDF5 libraries used by SuperBuild and matlab's ones

evgueni-ovtchinnikov · 2019-02-11T15:00:25Z

overwriting matlab hdf5 dlls (luckily, there are only two of them) does fix the problem, but it is hardly a solution many users would like :(

casperdcl · 2019-02-11T15:34:08Z

could prefix to matlab's path. Can also contact matlab to get them to update the dlls (I've done this before)

KrisThielemans · 2019-02-11T16:23:29Z

This is the same problem as what we're having with Boost https://github.com/CCPPETMR/SIRF/issues/240.

Like there, I think the best thing to do is to build SIRF with the same version as what is used by Matlab. That implies that we need to check what the HDF5 version is for different Matlab versions. Fun.

@evgueni-ovtchinnikov would you be able to send an email to Mathworks support requesting the relevant information (for both HDF5 and Boost). Best to explain them why. feel free to point them to this issue.

KrisThielemans · 2019-02-23T22:32:48Z

HDF5 info is in #208, Boost info is in #207

KrisThielemans · 2019-02-23T22:35:22Z

Proposed FFTW fix is in #204

KrisThielemans · 2020-12-21T15:39:52Z

I've tried this again with latest versions.

I had to update the HDF5 MD5SUM for some reason (will create a PR for this). When building HDF5, VS threw up a few dialog boxes with errors. These were presumably when CMake tests some functionality. Ignoring them, or Aborting them worked fine.
error in the unittests for JSON (fixed by upgrading Visual Studio and JSON library, PR set JSON to 3.9.1 and don't build tests by defaults #454 )
~~STIR getopt.c complained about non-existing strings.h~~ (Note: this disappeared after upgrading my VS 2019 to latest version)
some failures with ISMRMRD

I'll update this when I find more

KrisThielemans · 2020-12-21T16:32:46Z

Screenshot of error dialog when building HDF5. I'm guessing CMake really should execute this silently, but doesn't. (I have CMake 3.18.3)

This happens after

1>-- Checking for appropriate format for 64 bit long:

before every check like this

1>Width with l64 failed with result: 3
1>Width with l failed with result: 3
1>Width with L failed with result: 3
1>Width with q failed with result: 3

KrisThielemans · 2020-12-22T21:38:27Z

I get warnings when building STIR via the SIRF-SuperBuild:

Warning	C4530	C++ exception handler used, but unwind semantics are not enabled. Specify /EHsc [C:\Users\krisf\Documents\devel\buildVC\SIRF-SuperBuild\builds\STIR\build\src\spatial_transformation_buildblock\spatial_transformation_buildblock.vcxproj]

Clearly, /EHsc needs to be passed, but when I build STIR directly with CMake, I don't need to do anything. Why does this happen for the SuperBuild?

KrisThielemans · 2020-12-24T11:45:49Z

I get warnings when building STIR via the SIRF-SuperBuild:

Warning	C4530	C++ exception handler used, but unwind semantics are not enabled. Specify /EHsc [C:\Users\krisf\Documents\devel\buildVC\SIRF- SuperBuild\builds\STIR\build\src\spatial_transformation_buildblock\spatial_transformation_buildblock.vcxproj]

resolved this with 75281a5

KrisThielemans · 2020-12-24T11:46:34Z

I've resolved all the above problems now. SIRF builds without any problems with the SIRF-SuperBuild!

Sadly, all tests fail...

KrisThielemans · 2020-12-26T23:09:49Z

Tests failed due to path issues. I also needed SyneRBI/SIRF#840.

Setting the paths as in #460, all tests work!

C:\Users\krisf\Documents\devel\cmake\install\bin\ctest.exe -VVV -C RelWithDebInfo          Test project C:/Users/krisf/Documents/devel/buildVC/SIRF-SuperBuild/builds/SIRF/build
    Start 1: MR_TESTS_CPLUSPLUS
1/7 Test #1: MR_TESTS_CPLUSPLUS ...............   Passed    7.11 sec
    Start 2: MR_TESTS_MATLAB
2/7 Test #2: MR_TESTS_MATLAB ..................   Passed   27.02 sec
    Start 3: REG_TEST_CPLUSPLUS
3/7 Test #3: REG_TEST_CPLUSPLUS ...............   Passed   37.77 sec
    Start 4: REG_TEST_MATLAB
4/7 Test #4: REG_TEST_MATLAB ..................   Passed   25.18 sec
    Start 5: REG_TEST_MATLAB_SPM
5/7 Test #5: REG_TEST_MATLAB_SPM ..............   Passed   26.98 sec
    Start 6: PET_TESTS_CPLUSPLUS
6/7 Test #6: PET_TESTS_CPLUSPLUS ..............   Passed  156.87 sec
    Start 7: PET_TESTS_MATLAB
7/7 Test #7: PET_TESTS_MATLAB .................   Passed   15.91 sec

100% tests passed, 0 tests failed out of 7

You'll notice though that these were with MATLAB only as I currently don't have Python on my Windows laptop.

I'm 99% sure that I will have to disable MATLAB when building with Python and vice versa due to HDF5 version conflicts etc, but at least things are looking up!

KrisThielemans · 2020-12-28T17:21:20Z

I have now tested this with miniconda's Python 3.8. I've put in a small commits but it all works for me, although I do need .SyneRBI/SIRF#844 as well. Note that I did make a separate build for Python.

KrisThielemans · 2020-12-28T17:35:07Z

So, I believe i can close this now. There's 2 SIRF PRs pending, but as far as the SuperBuild goes, all is well.

Some info on my test environment (all very new):

Visual Studio 2019 version 16.8.3
CMake 3.19.2
MATLAB 2020b
Python 3.8 (via miniconda), and using https://github.com/SyneRBI/SIRF/wiki/SIRF-and-Python#using-anaconda (except that I didn't install h5py and libxml2. Note that h5py could potentially create conflicts with our own HDF5 build)
precompiled Boost 1.74.0
no FFT nor HDF5 libraries preinstalled

CMake Configuration:

STIR_TAG=release_4
SIRF_TAG=origin/master
BOOST_ROOT=c:\local\boost_1_74_0
either DISABLE_MATLAB or DISABLE_PYTHON=ON

run-time environment was as in #460

I built the RelWithDebInfo configuration. Debug worked for MATLAB, but wouldn't work for Python due to SyneRBI/SIRF#42

evgueni-ovtchinnikov closed this as completed in 5b8cb89 Feb 1, 2019

KrisThielemans reopened this Feb 1, 2019

rijobro closed this as completed in 75b7f6c Feb 6, 2019

rijobro reopened this Feb 6, 2019

KrisThielemans added this to the v2.1 milestone Feb 15, 2019

KrisThielemans mentioned this issue Feb 23, 2019

Need to use same HDF5 version as Matlab #208

Closed

KrisThielemans modified the milestones: v2.1, v2.2 Oct 6, 2019

KrisThielemans mentioned this issue Dec 21, 2020

Windows support #7

Closed

KrisThielemans mentioned this issue Dec 22, 2020

HDF5 1.8.12 configuration errors with Visual Studio #451

Closed

KrisThielemans mentioned this issue Dec 23, 2020

override CMAKE_CXX_FLAGS for Boost can cause problems #455

Open

KrisThielemans closed this as completed Dec 28, 2020

KrisThielemans mentioned this issue May 29, 2022

Windows: IMRMRD fails to link with self built Boost #720

Open

SIRF-SuperBuild build fails on Windows #197

SIRF-SuperBuild build fails on Windows #197

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