0003741: On MacOSX 10.6, link error when building with VTK6

ID	Project	Category	View Status	Date Submitted	Last Update

0003741	Slicer4	Core: Building (CMake, Superbuild)	public	2014-06-18 15:05	2017-06-10 08:51

Reporter	jcfr	Assigned To	jcfr
Priority	high	Severity	major	Reproducibility	have not tried
Status	closed	Resolution	fixed
Product Version
Target Version	Slicer 4.4.0	Fixed in Version	Slicer 4.4.0

Summary	0003741: On MacOSX 10.6, link error when building with VTK6
Description	Reported here some notes about the problem: //----------------------------- Dear CMake team, After transitioning Slicer to VTK6, on MacOSX I am facing a rather annoying issue. Until now I was ignoring the "duplicate dylib" warning since has explained in [1] it shouldn't prevent project from building successfully. But today .. I got the following error message: two level namespace mach-o files can link with at most 253 dylibs, this link would use 287 dylibs See [2] for full message. The link command (and modified for easier readability) confirms the duplicated libraries. See enclosed file [3] ... and looking at the list of CMake targets linked agsainst the problematic target .. I can also confirm that there are no duplicates. See enclosed file [4] The ideal solution would be to fix CMake issue #10179. Especially considering that such problem are becoming more and more relevant with project becoming more modular and their size increasing. In the short term, I was thinking about these options / dirty hacks: (1) create a wrapper script that would be invoked instead of the regular compiler. This script would remove the duplication starting with the end of the list. (2) is there anything that could be done to order the CMake targets to minimize the duplicated libraries ? (3) modify the ITK and VTK Slicer forks to combine library together ... Version of CMake: 2.8.10 OS: MacOSX 10.6 Thanks for your help and advices, Jc [1] http://public.kitware.com/Bug/view.php?id=10179#c19275 [2] http://slicer.cdash.org/viewBuildError.php?buildid=239124 [3] Slicer_r23343_macosx_modified_link_command_for_MRMLCLIPythonD.txt [4] Slicer_r23343_cmake_targets_for__MRMLCLIPythonD.txt //----------------------------- //----------------------------- Update: The issue does NOT occur on MacOSX 10.8 [1] using clang 4.1 [2] but it occurs on MacOSX 10.6 [3] using g++ 4.2.1 [4]. I will look into updating/install clang on MacOSX 10.6. [1] $ sw_vers ProductName: Mac OS X ProductVersion: 10.8.5 BuildVersion: 12F45 [2] $ c++ --version Apple clang version 4.1 (tags/Apple/clang-421.11.66) (based on LLVM 3.1svn) Target: x86_64-apple-darwin12.5.0 Thread model: posix [3] > sw_vers ProductName: Mac OS X ProductVersion: 10.6.8 BuildVersion: 10K549 [4] > c++ --version i686-apple-darwin10-g++-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) //----------------------------- //----------------------------- Update 0000002: On MacOSX 10.6 it seems that the version of g++ is compiled universal binary [1] and probably use the "nlist" structure that limit the the number of entries to 253. See [2]. Considering that the generated library are of type Mach-O 64-bit [3], that seems like a reasonable explanation Let's also note that hardware running the MacOSX 10.6 is a "Mac Pro (Mid 2010)" which has the 64-bit kernel enabled by default [4] ... I also tried to force it using systemsetup. See [5] To compare, I checked the type of executable on the MacOSX 10.8 and it return a single architecture. See [6] [1] > file /usr/bin/c++ /usr/bin/c++: Mach-O universal binary with 3 architectures /usr/bin/c++ (for architecture i386): Mach-O executable i386 /usr/bin/c++ (for architecture ppc7400): Mach-O executable ppc /usr/bin/c++ (for architecture x86_64): Mach-O 64-bit executable x86_64 [2] From https://developer.apple.com/library/mac/documentation/DeveloperTools/Conceptual/MachORuntime/Reference/reference.html#//apple_ref/doc/uid/20001298-BAJECHFH 8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------ If this file is a two-level namespace image (that is, if the MH_TWOLEVEL flag of the mach_header structure is set), the high 8 bits of n_desc specify the number of the library in which this undefined symbol is defined. Use the macro GET_LIBRARY_ORDINAL to obtain this value and the macro SET_LIBRARY_ORDINAL to set it. Zero specifies the current image. 1 through 253 specify the library number according to the order of LC_LOAD_DYLIB commands in the file. The value 254 is used for undefined symbols that are to be dynamically looked up (supported only in OS X v10.3 and later). For plug–ins that load symbols from the executable program they are linked against, 255 specifies the executable image. For flat namespace images, the high 8 bits must be 0. 8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------8<------ [3] > file VTKv6-build/lib/libvtkCommonCorePython27D-6.1.dylib VTKv6-build/lib/libvtkCommonCorePython27D-6.1.dylib: Mach-O 64-bit dynamically linked shared library x86_64 [4] http://support.apple.com/kb/HT3770 [5] http://support.apple.com/kb/HT3773 [6] $ file /usr/bin/c++ /usr/bin/c++: Mach-O 64-bit executable x86_64 //----------------------------- //----------------------------- Update 0000003: The nlist_64 structure [1] also specifies a small number (254) of library entries. See below. My first conclusion was incorrect and didn't really make sense. Instead, I think that newer version of the compiler (clang) are smarter about duplicated libraries and filter them out. 8<-----8<-----8<-----8<-----8<-----8<-----8<-----8<----- If this file is a two-level namespace image (that is, if the MH_TWOLEVEL flag of the mach_header structure is set), the high 8 bits of n_desc specify the number of the library in which this symbol is defined. Use the macro GET_LIBRARY_ORDINAL to obtain this value and the macro SET_LIBRARY_ORDINAL to set it. Zero specifies the current image. 1 through 254 specify the library number according to the order of LC_LOAD_DYLIB commands in the file. For plug–ins that load symbols from the executable program they are linked against, 255 specifies the executable image. For flat namespace images, the high 8 bits must be 0. 8<-----8<-----8<-----8<-----8<-----8<-----8<-----8<----- [1] https://developer.apple.com/library/mac/documentation/DeveloperTools/Conceptual/MachORuntime/Reference/reference.html#//apple_ref/doc/uid/20001298-CJBDFJFA //----------------------------- //----------------------------- Update 0000004: I installed llvm 3.1, upgraded to CMake 2.8.12. and started a build. See [1] Will keep you posted. Thanks Jc [1] http://slicer.cdash.org/index.php?project=Slicer4#Continuous //-----------------------------
Tags	No tags attached.

Import 2017-06-07 23:51:09: master 2ec6b84f 2014-06-18 19:03:39 jcfr Details Diff	COMP: On MacOSX, waiting issue 0003741 is solved uses VTK 5.10 As illustrated in the bug report [1], the maximum number of linked libraries is reached on MacOSX 10.6 (see below for an example of message) but there are no problem on MacOSX 10.8 (at least when targeting 10.9). // --------- ld: warning: duplicate dylib /path/to ... [...] ld: warning: duplicate dylib /path/to ... two level namespace mach-o files can link with at most 253 dylibs, this link would use 287 dylibs // --------- Waiting we come up with a solution or understand better the scope of the problem, this commit force the VTK version to 5.10. [1] http://na-mic.org/Mantis/view.php?id=3741 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23344 3bd1e089-480b-0410-8dfb-8563597acbee
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Import 2017-06-07 23:51:09: master 3619c674 2014-06-20 21:47:38 jcfr Details Diff	COMP: Specify minimum set of VTKv6 libraries. Fixes 0003741 The VTK utility: Utilities/Maintenance/WhatModulesVTK.py discovers which modules are used in a project. This patch modifies the Slicer CMakeLists.txt file to only load the vtk modules used by Slicer. This should reduce the number of libraries being linked. This commit also updates CTK project including a patch reducing the number of library associated with CTKImageProcessingITKCore library. // ---------------- $ git shortlog 48ef9aeb8..282abc7 --no-merges Jean-Christophe Fillion-Robin (1): CTKImageProcessingITKCore - With ITKv4, link only to the required libraries // ---------------- Co-authored-by: Jean-Christophe Fillion-Robin <jchris.fillionr@kitware.com> From: Bill Lorensen <bill.lorensen@gmail.com> git-svn-id: http://svn.slicer.org/Slicer4/trunk@23350 3bd1e089-480b-0410-8dfb-8563597acbee
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Import 2017-06-07 23:51:09: master dcf78181 2014-06-20 22:07:09 jcfr Details Diff	COMP: Re-enable VTKv6 on MacOSX. Since following commit r23350, issue 0003741 is resolved, this commit re-enables VTKv6 on MacOSX. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23352 3bd1e089-480b-0410-8dfb-8563597acbee
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Import 2017-06-07 23:51:09: master 211b7e68 2014-06-20 22:17:55 jcfr Details Diff	COMP: On MacOSX, waiting issue 0003741 is really solved uses VTK 5.10 It turns out that the test build I initiated managed to go way beyond the original stopping point [See r23344]. That said, there are still the same issue when building SubjectHierarchy, Annotations module ... This commits reverts back to VTK 5.10 for MacOSX. The solution gonna be to continue the work initiated in [1] and remove the top level call to "find_package()" and instead have every Slicer libraries/modules including his set of direct dependencies. [1] http://massmail.spl.harvard.edu/public-archives/slicer-devel/2014/015671.html git-svn-id: http://svn.slicer.org/Slicer4/trunk@23353 3bd1e089-480b-0410-8dfb-8563597acbee
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Import 2017-06-07 23:51:09: master f0f0df61 2014-07-03 21:34:23 jcfr Details Diff	COMP: Move most of find_package calls into each Slicer sub-project. To help address issue 0003741 [1], call to find_package associated to CTK, DCMTK, ITK and SlicerExecutionModel have been moved in every Slicer sub project, library or module expecting it. This allows to reduce both the number of include directories and the number of libraries passed to the compiler. Moving forward, every Slicer sub project, library or module will be responsible to call find_package (optionally specifying a list of components) and (if it applies) include the associated "use file". Note that call to find_package(VTK) is still done at the top-level, before moving the call to the expected sub-directories, the CTKConfig.cmake will have to be updated to call find_package(VTK) specifying the required components where it is needed. [1] http://na-mic.org/Mantis/view.php?id=3741 git-svn-id: http://svn.slicer.org/Slicer4/trunk@23413 3bd1e089-480b-0410-8dfb-8563597acbee
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Import 2017-06-07 23:51:09: master c1dd6356 2014-07-29 22:32:01 jcfr Details Diff	COMP: Specify list VTK_MAKE_INSTANTIATOR3 input as list of cxx files only. This commit fixes a build error introduced by kitware/VTK@5c3241b9d8 It ensures there are no duplicated entries in the instantiator files. The error (reported below) was first discovered when building Slicer on MacOSX 10.6 with the option VTK_ENABLE_KITS while working on issue 0003741. // ------------------------ $ make vtkSlicerTransformsModuleMRMLDisplayableManager/fast [ 59%] Building CXX object Modules/Loadable/Transforms/MRMLDM/CMakeFiles/vtkSlicerTransformsModuleMRMLDisplayableManager.dir/TransformsInstantiator.cxx.o /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx: In function 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()': /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:10: error: redefinition of 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()' /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:9: error: 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager2DNew()' previously defined here /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx: In function 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()': /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:12: error: redefinition of 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()' /path/to/Slicer-build/Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx:11: error: 'vtkObject* vtkInstantiatorvtkMRMLTransformsDisplayableManager3DNew()' previously defined here make[1]: * [Modules/Loadable/Transforms/MRMLDM/CMakeFiles/vtkSlicerTransformsModuleMRMLDisplayableManager.dir/TransformsInstantiator.cxx.o] Error 1 make: * [vtkSlicerTransformsModuleMRMLDisplayableManager/fast] Error 2 // ------------------------ The content of the associated instantiator file was: // --------------- $ cat Modules/Loadable/Transforms/MRMLDM/TransformsInstantiator.cxx [...] vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager2D) vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager2D) vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager3D) vtkInstantiatorNewMacro(vtkMRMLTransformsDisplayableManager3D) [...] // --------------- This commit avoid the duplicated entries in the instantiator file. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23508 3bd1e089-480b-0410-8dfb-8563597acbee
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Import 2017-06-07 23:51:09: master 6611ef5f 2014-07-29 23:00:19 jcfr Details Diff	COMP: Fix VTK6 link error on MacOSX 10.6. Fixes 0003741 To reduce the number of libraries passed to the linker, this commit build VTK6 with the VTK_ENABLE_KITS option enabled. If building on MacOSX 10.6 without CMake 3.0, it also updated the build system to output a fatal error message explaining that a more recent version of CMake is required. git-svn-id: http://svn.slicer.org/Slicer4/trunk@23509 3bd1e089-480b-0410-8dfb-8563597acbee
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Date Modified	Username	Field	Change
2014-06-18 15:05	jcfr	New Issue
2014-06-18 15:05	jcfr	Status	new => assigned
2014-06-18 15:05	jcfr	Assigned To	=> jcfr
2014-07-29 18:44	jcfr	Note Added: 0012290
2014-07-29 18:44	jcfr	Priority	normal => high
2014-07-29 18:44	jcfr	Severity	minor => major
2014-07-29 18:44	jcfr	Target Version	=> Slicer 4.4.0
2014-07-30 14:10	jcfr	Note Added: 0012299
2014-07-30 14:10	jcfr	Status	assigned => resolved
2014-07-30 14:10	jcfr	Fixed in Version	=> Slicer 4.4.0
2014-07-30 14:10	jcfr	Resolution	open => fixed
2014-08-29 07:48	jcfr	Status	resolved => closed
2014-08-29 07:49	jcfr	Relationship added	related to 0003809
2017-06-10 08:51	jcfr	Changeset attached	=> Slicer master 6611ef5f
2017-06-10 08:51	jcfr	Changeset attached	=> Slicer master c1dd6356
2017-06-10 08:51	jcfr	Changeset attached	=> Slicer master f0f0df61
2017-06-10 08:51	jcfr	Changeset attached	=> Slicer master 211b7e68
2017-06-10 08:51	jcfr	Changeset attached	=> Slicer master dcf78181
2017-06-10 08:51	jcfr	Changeset attached	=> Slicer master 3619c674
2017-06-10 08:51	jcfr	Changeset attached	=> Slicer master 2ec6b84f

jcfr 2014-07-29 18:44 administrator ~0012290	See r23508 - http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23508

jcfr 2014-07-30 14:10 administrator ~0012299	Fixed by the following revision: http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23520 http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23515 http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23514 http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23513 http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23512 http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23509 Note also that CMake 3.0.0 is required with the following patch: https://github.com/Kitware/CMake/commit/9f7e27fc3a2d2b1863147f235a2980de019ee7c9

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