Link with correct libraries #8

smistad · 2017-05-18T07:41:44Z

This will hopefully link the plugin with the external libraries on windows. FAST_LIBRARIES comes from FASTConfig.cmake and should contain FAST, zlib, OpenCL, ++

jonei · 2017-05-18T13:45:03Z

Now there are even more errors of the same type. FAST_LIBRARIES doesn't contain everything we need.
Hardcoding in "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v7.0/lib/x64/OpenCL.lib" in the same place, reduces the amount of errors to the same as before this change. Janne thought it might have something to do with how that string gets parsed, since it is in the FAST CMakeCache.txt file:
//Dependencies for the target
FAST_LIB_DEPENDS:STATIC=blablabla

jonei · 2017-05-19T08:27:53Z

Just a thought, can this have anything to do with OpenCL versions? Some of the symbols from the "unresolved external symbol" error messages i pasted i the previous pull request, seems to be used in the OpenCL 1.2 code, which we don't use to compile FAST. We use 1.1 I guess. Which versions of OpenCL and Cuda do you use? We are at Cuda 7.0.

jonei · 2017-05-24T10:37:46Z

${OPENCL_LIBRARIES} is still needed in the airways cmakelists
${FAST_LIBRARIES} is not needed
zlibstatic.lib: need to include this in a uniform way on all platforms

Need to handle std::string path; in Config.cpp in FAST. std::string is not working across dlls.

smistad · 2017-05-24T11:42:23Z

I'm working on the FAST part of it. Will let you know when I have figured it out

…airways filter

smistad · 2017-05-24T14:29:12Z

Ok. Please test the latest commit. I have only tested it on ubuntu. But I am able to build and link the FAST library on windows.

Note that FAST is now built as a shared library on windows (.dll).

jonei · 2017-05-24T16:01:55Z

So this broke the Mac build in 1000 pieces.
24-May-2017 16:59:30 [shell ###] std::atomic m_count;
FAST/Semaphore.hpp:187:10: error: no type named 'atomic' in namespace 'std'
build
Did you change any flags/settings or have you added new code using this C++11 construct? I think we have supported C++11 on Mac before, but I'm not sure.

Windows: Did manage to build everything manually and the airways dll loaded when I added FAST.dll to the path.

smistad · 2017-05-24T17:36:46Z

Fast and the airways plugin is built with c++ 11, and it is required. I haven't changed any of that. Will have to look into Mac another day.
Great. Does that mean the windows build is ok? Progress.

jonei · 2017-05-24T17:46:09Z

Yes, the windows build seems ok! But the automated tests doesn't run before all platforms are good.

jonei · 2017-05-25T11:30:06Z

Mac:
A.
In Cpp11.cmake, C++11 wasn't set for Mac. Don't know if this ever worked for OSX < 10.11 which I use. Please change
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang" OR CMAKE_COMPILER_IS_GNUCXX)
to
if (${CMAKE_CXX_COMPILER_ID} STREQUAL "AppleClang" OR CMAKE_COMPILER_IS_GNUCXX)

B.
In Utility.cpp, glFrustum is no longer found after you removed OpenGl, I suppose.
#include <OpenGL/gl.h> made it compile.

smistad · 2017-05-25T13:20:22Z

As of CMake 3.0.0 the CMAKE_<LANG>_COMPILER_ID value for Apple-provided Clang is now AppleClang. To test for both the Apple-provided Clang and the regular Clang use the following if condition:

if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
  # using regular Clang or AppleClang
endif()

https://stackoverflow.com/questions/10046114/in-cmake-how-can-i-test-if-the-compiler-is-clang

I have added this change and the GL include in Utility.cpp to FAST now.

jonei · 2017-05-25T16:04:51Z

Everything builds, but the VNNcl tests now seg faults on Linux (14.04). Any ideas?
If you build CustusX, you can try to run Catch from the build folder:
./Catch [unit][vnncl]

Typical output:

error:
SEGFAULT
(
1
)
[16:22:16.655][INFO] --- Initialize services for Catch...
[16:22:16.678][INFO] Installing all plugins...
[16:22:17.904][INFO] Starting plugin org.custusx.registration.gui
[16:22:17.908][INFO] Starting plugin org.custusx.filter.routetotarget
[16:22:17.911][INFO] Starting plugin org.custusx.registration.method.centerline
[16:22:17.913][INFO] Starting plugin org.custusx.acquisition
[16:22:17.915][INFO] Starting plugin org.custusx.help
[16:22:17.921][INFO] Starting plugin org.custusx.core.view
[16:22:18.063][INFO] Layout 0 changed to 3D ACS Connected
[16:22:18.064][INFO] Starting plugin org.custusx.core.state
[16:22:18.067][INFO] Found valid VLC application: /usr/bin/vlc
[16:22:18.068][INFO] Starting plugin org.custusx.registration.method.bronchoscopy
[16:22:18.071][INFO] Starting plugin org.custusx.registration
[16:22:18.072][INFO] Starting plugin org.custusx.core.tracking
[16:22:18.077][INFO] Starting plugin org.custusx.filter.airways
WARNING: NVIDIA platform was detected, disabling OpenGL interop
WARNING: Writing to directly to 3D textures/images is not supported on main device
[16:22:18.122][INFO] Starting plugin org.custusx.filter.accusurf
[16:22:18.125][INFO] Starting plugin org.custusx.core.video
[16:22:18.128][INFO] Starting plugin org.custusx.registration.method.manual
[16:22:18.131][INFO] Starting plugin org.custusx.calibration
[16:22:18.134][INFO] Starting plugin org.custusx.dicom
[16:22:18.137][INFO] Starting plugin org.custusx.filter.tubesegmentation
[16:22:18.141][INFO] Starting plugin org.custusx.training
[16:22:18.146][INFO] Starting plugin org.custusx.core.tracking.system.igstk
[16:22:18.150][INFO] Installing tracking system: org.custusx.core.tracking.system.igstk
[16:22:18.150][INFO] Starting plugin org.custusx.registration.method.commandline
[16:22:18.153][INFO] Starting plugin org.custusx.registration.method.plate
[16:22:18.159][INFO] Starting plugin org.custusx.core.openigtlink
[16:22:18.163][INFO] Installing tracking system: org.custusx.core.openigtlink
[16:22:18.163][INFO] Starting plugin org.custusx.registration.method.pointcloud
[16:22:18.169][INFO] Starting plugin org.custusx.usreconstruction
[16:22:18.173][INFO] Starting plugin org.custusx.registration.method.vessel
[16:22:18.178][INFO] Starting plugin org.custusx.core.patientmodel
[16:22:18.182][INFO] Starting plugin org.custusx.usreconstruction.vnncl
Found 1 OpenCL platforms.
1 platforms selected for inspection.
Platform 0: NVIDIA Corporation
Looking for GPU devices only.
1 devices found for this platform.
Inspecting device 0 with the name Quadro 4000
The device was accepted.
The platform NVIDIA CUDA was selected as the best platform.
A total of 1 devices were selected for the context from this platform:
Device 0: Quadro 4000
[16:22:18.228][INFO] Starting plugin org.custusx.filter.levelset
[16:22:18.232][INFO] Starting plugin org.custusx.usreconstruction.pnn
[16:22:18.236][INFO] Starting plugin org.custusx.registration.method.landmark
[16:22:18.239][DEBUG] --- End initialize services.
Found 1 OpenCL platforms.
1 platforms selected for inspection.
Platform 0: NVIDIA Corporation
Looking for GPU devices only.
1 devices found for this platform.
Inspecting device 0 with the name Quadro 4000
The device was accepted.
The platform NVIDIA CUDA was selected as the best platform.
A total of 1 devices were selected for the context from this platform:
Device 0: Quadro 4000
[16:22:18.285][INFO] Method: 3, radius: 10, planeMethod: 0, nClosePlanes: 8, nPlanes: 21, nStarts: 1
[16:22:18.285][INFO] Kernel path: /media/jenkins/bamboo/buildagent/xml-data/build-dir/CX-CO93-TPL/Installed/CustusX/config//shaders//kernels.cl
Created kernel with name voxel_methods
[16:22:18.291][INFO] Input dims: (21, 21, 21)
[16:22:18.291][INFO] Frames: 21, Blocks: 10, Frames per block: 2
[16:22:18.291][INFO] Allocating 1 big blocks outside of OpenCL
[16:22:18.291][INFO] Allocating 9 small blocks outside of OpenCL
[16:22:18.291][INFO] Allocating OpenCL input block buffers
[16:22:18.291][INFO] Allocating CL output buffer, size 9261
[16:22:18.291][INFO] Using 24276 of 2146631680 global memory
[16:22:18.291][INFO] Device has 49151 bytes of local

smistad · 2017-05-25T16:09:55Z

Is this on your machine? Maybe it is due to the upgrade from CUDA 7 to 8. Or it is due to the change we did in OpenCLUtilityLibrary

jonei · 2017-05-25T16:13:10Z

No, not mine. The Machine hasn't been touched as far as I know. Maybe OpenCLUtilityLibrary then.

jonei · 2017-05-26T12:44:49Z

I had to run all the software updates on the Linux machine and then it worked!
Merging this into the remove tsf/levelset branch and deleting the CX build folder made that branch green as well.

smistad · 2017-05-26T13:34:47Z

Great! I have done some improvements in the airways segmentation in FAST, and also added lung sac segmentation to the plugin. Will create a PR for it before the end of the day. Hopefully no build issues this time.

…ix/FX-31-inncorrect-zoom-after-running-rtt to develop * commit '94691f3875993f290e774f2dd235a14da810c2ac': FX-35: Updated function name. FX-15: We need to make sure that the slider changed signal is always triggered to set the camera correctly, in case the slider is already at the same position as the default.

Link with correct libraries

1266a8f

Updated FAST and OpenCLUtilityLibrary SHA's and some cmake stuff for …

973bb2b

…airways filter

jonei merged commit 8e0b83a into SINTEFMedtek:bugfix/FX-19-airwaysegmentation-algorithm-does-not May 24, 2017

blacksino mentioned this pull request Apr 12, 2019

segment fault/Ubuntu 16.04 #11

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Link with correct libraries #8

Link with correct libraries #8

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Link with correct libraries #8

Link with correct libraries #8

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