search

SyneRBI / SIRF-SuperBuild

SIRF CMake SuperBuild
http://www.ccpsynerbi.ac.uk
Apache License 2.0
15 stars 17 forks source link

Windows support #7

Closed KrisThielemans closed 3 years ago

KrisThielemans commented 7 years ago

At present, most configurations will fail for Windows. Probably our best strategy is to download precompiled packages and use those.

KrisThielemans commented 7 years ago

With CMake 3.9-rc4 I successfully built with pre-downloaded Boost, HDF5 and FFTW (as per the wiki) and at commit 0eabb888fd22412a1fc418063c08ed67c9adc463

(command lines were in Powershell)

cd C:\Users\krisf\Documents\devel\SIRF-SuperBuild-CMake3.9-64
~/Documents/devel\CMake-Build\INSTALL\bin/cmake  -DBOOST_ROOT=C:/Users/krisf/Documents/devel/boost_1_63_0   -DUSE_SYSTEM_Boost=On -DUSE_SYSTEM_HDF5=On -DCMAKE_GENERATOR_PLATFORM=x64   -DCMAKE_INSTALL_PREFIX=C:\Users\krisf\Documents\devel\SIRF-SuperBuild-CMake3.9-64/INSTALL -DUSE_SYSTEM_FFTW3=On -DFFTW3_ROOT_DIR=C:/Users/krisf/Documents/devel/fftw-3.3.5-dll64 C:/Users/krisf/Documents/devel/SIRF-SuperBuild
KrisThielemans commented 7 years ago

Some difficulties encountered with HDF5:

Summary:

KrisThielemans commented 7 years ago

Just checked that adding -DHDF5_USE_STATIC_LIBRARIES=1 still needs a change to FindHDF5 as the relevant lines there are only enabled on Unix. Fix is in https://gitlab.kitware.com/cmake/cmake/merge_requests/1023

So, sadly it seems that unless we can force CMake to find our Config-install of HDF5 (see https://gitlab.kitware.com/cmake/cmake/issues/17029), we can only build with an installed HDF5 in Program Files (at least until FindHDF5.cmake gets fixes)

KrisThielemans commented 6 years ago

Started testing with CMake 3.10.1 (which has the relevant fixes for FindHDF5.cmake).

Current problems:

  1. had to fix detection of x64
  2. CMAKE_INSTALL_PREFIX was not reset from the default (should normally have been set ok)
  3. USE_SYSTEM_HDF5 was not correctly honoured (When I ran CMake, it said it was using the system version, but Visual Studio went ahead and downloaded source and compiled anyway).
  4. ISMRMRD failed to link against own compiled HDF5 because that was compiled for 32-bit. message: 
    library machine type 'X86' conflicts with target machine type 'x64'
  5. When building in Debug-mode, Python link fails, see https://github.com/CCPPETMR/SIRF/issues/42

Items 2 and 3 might have been because I ran CMake a few times (with deleting the cache and without) before settling on USE_SYSTEM_HDF5=On. It's strange/undesirable though. Will need to check again later.

KrisThielemans commented 6 years ago

confirmed that when deleting the cache, configuring, and then clicking USE_SYSTEM_HDF5 does work as expected (also for CMAKE_INSTALL_PREFIX). Not sure how to reproduce the above problems 2 and 3 so I am going to ignore them...

KrisThielemans commented 6 years ago

CTest fails because config option isn't passed on:

ctest -VV -C Release
...
test 1
    Start 1: SIRF_TESTS

1: Test command: "C:\Program Files\CMake\bin\ctest.exe" "test"
...
1:     Start 1: PET_TEST1
1: Test not available without configuration.  (Missing "-C <config>"?)
1: 1/3 Test #1: PET_TEST1 ........................***Not Run   0.00 sec
...
Can we add this option on other systems?
KrisThielemans commented 6 years ago

Going to the relevant subdir, PET tests work after setting PYTHONPATH! In Powershell

cd SIRF-prefix\src\SIRF-build\src\xSTIR
Env:PYTHONPATH = "C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\python"
ctest -VV -C Release
...
100% tests passed, 0 tests failed out of 1

MR tests fail with error

1: Traceback (most recent call last):
1:   File "fully_sampled.py", line 22, in <module>
1:     from pGadgetron import *
1:   File "C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\python\pGadgetron.py", line 41, in
<module>
1:     import pygadgetron
1:   File "C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\python\pygadgetron.py", line 17, in
 <module>
1:     _pygadgetron = swig_import_helper()
1:   File "C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\python\pygadgetron.py", line 16, in
 swig_import_helper
1:     return importlib.import_module('_pygadgetron')
1:   File "C:\Users\krisf\Anaconda2\lib\importlib\__init__.py", line 37, in import_module
1:     __import__(name)
1: ImportError: DLL load failed: The specified module could not be found.

This means that a DLL isn't in the Path. Sadly, Windows doesn't say which one. Obvious candidate is the ISMRMRD DLL but the following didn't help

$env:Path += ";C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\bin"

@evgueni-ovtchinnikov , do you know how to set the PATH correctly?

KrisThielemans commented 6 years ago

Compilation problems should be fixed with #64.

Still need to fix above ctest and DLL problems, and also create .bat and .PS1 files with appropriate settings. @evgueni-ovtchinnikov and @paskino can you find the correct settings and then creating the configure file?

KrisThielemans commented 6 years ago

Currently tested with USE_SYSTEM_BOOST=ON only, but USE_SYSTEM_FFTW ON/OFF, USE_SYSTEM_HDF5 `ON/OFF'.

old version of HDF5 (1.8.15) with out-of-date conda gives

LINK : fatal error LNK1181: cannot open input file 'C:\aroot\stage\Library\lib\z.lib' [C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\ISMRMRD-prefix\src\ISMRMRD-build\ismrmrd.vcxproj]

This is resolved with a conda update hdf5.

KrisThielemans commented 6 years ago

Regarding ctest, need to call ctest in the SIRF-build with -C ${CMAKE_CFG_INTDIR} probably. However, this might then fail when using Makefiles as CMAKE_CFG_INTDIR might be set to . as opposed to empty (I checked that on the VM, both ctest -C and ctest -C . work fine though, so this should be safe). @rijobro, can you try this on Mac?

KrisThielemans commented 6 years ago

A few more fixes have been incorporated. All the ctest problems have now been fixed.

The above mentioned DLL problem was related to both FFTW and boost. dumpbin (part of the VS Toolkit) gave

 dumpbin /dependents _pygadgetron.pyd
    boost_filesystem-vc140-mt-1_63.dll
    boost_thread-vc140-mt-1_63.dll
    boost_system-vc140-mt-1_63.dll
    ismrmrd.dll
    libfftw3f-3.dll
    hdf5.dll
    ....

where I cut system libraries. Any DLLs in INSTALL/bin (such as ismrmd.dll) would be picked up if that's included in the PATH. I had to do the following (in Powershell):

 $Env:Path += ";C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\bin"
 $Env:Path += ";C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\FFTW"
 $Env:Path += ";c:/Users/krisf/Documents/devel/boost_1_63_0/lib64-msvc-14.0/"
 $Env:PYTHONPATH = "C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\python"
 $Env:MATLABPATH = "C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\matlab"

(The FFTW line would not be necessary when using a system-version presumably).

As an alternative, I guess we could copy the libraries in bin (ugly) or force static linking (probably best really).

Sadly, I still get a python crash when just loading an MR.AcquisitionData object (with filename). I guess a conflict between DLLs or something.

For MATLAB, I still have problems presumably also related to DLLs

>> [notfound, warnings] = loadlibrary('mgadgetron')
Error using loadlibrary
There was an error loading the library
"C:\Users\krisf\Documents\devel\build-VC\SIRF-SuperBuild-CMAKE3.10\INSTALL\matlab\mgadgetron.mexw64"
The specified procedure could not be found.

Caused by:
    Error using loaddefinedlibrary
    The specified procedure could not be found.
KrisThielemans commented 6 years ago
KrisThielemans commented 3 years ago

Closing this as very outdated. Updating #197 instead