Hi Dennis, with configuration I meant the CMAKE_BUILD_TYPE which on Linux is Debug by default. The bundle process parses every executable and library for their dependencies to pack everything together (and adjust the dependency paths) that's necessary to make the executables relocatable.
Best, Stefan From: Dennis, H. E. Cicada Brokaw [mailto:hbro...@iu.edu] Sent: Tuesday, October 15, 2019 10:39 PM To: Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de>; mitk-users@lists.sourceforge.net Subject: Re: Error during make install Hello Stefan, I appreciate your suggestion. I had built the DiffusionRelease configuration. The bundle process eventually completed after running for about one week. I have no idea what the bundle process does. I was simply wanting the executable binaries, and needed header files, and libraries to be placed in the correct installation location. I guess with make package, I could have taken the resulting tar ball and unarchived it in the installation location. Anyway, the installation seems to be working now, but no idea what it was doing with this bundle process or why it was taking so long. The destination location was on the same drive as the source (relative to the source directory, it was ../2018.04.2) And another strange thing about the installation, to me, is the placement of libraries in the bin directory. I don't understand why they are not put in the lib directory. Seems rather strange to me. Sincerely, Cicada Dennis ________________________________ From: Dinkelacker, Stefan <s.dinkelac...@dkfz-heidelberg.de<mailto:s.dinkelac...@dkfz-heidelberg.de>> Sent: Tuesday, October 8, 2019 4:01 AM To: Dennis, H. E. Cicada Brokaw; mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Subject: [External] RE: Error during make install This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external sources. Hi Dennis, I recommend to create a relocatable package/tarball with "make package" instead of using "make install". Also make sure to build in Release configuration as we do not support installing of debug builds in general. Regarding the loooong bundle process it is supposed to take only a few minutes indeed. It's just a wild guess but it might be related to network drive access in your specific configuration? Best, Stefan From: Dennis, H. E. Cicada Brokaw [mailto:hbro...@iu.edu] Sent: Wednesday, October 2, 2019 5:25 PM To: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Subject: Re: [mitk-users] Error during make install I found that I was able to avoid the below error by adding the installation directories to: PATH LD_LIBRARY_PATH CPATH When I did the change, it is possible all I needed to change was LD_LIBRARY_PATH, or PATH, but when I made the change, I changed all of them. Now the program runs for a very, very, very long time. I do not understand what it is doing or why. All I want to do is install the binaries, libraries, headers, and resources into the install location. I was using the command "make install" Is there some other command that means what I am wanting to do? Why is it taking days to do what should be simple copy operations? It is spending hours and hours and days on the following (preparing a bundle)?: globbed plugins: /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_FastSymmetricForcesDemons_MultiRes_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_LevelSetMotion_MultiRes_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_affine_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_rigid_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_translation_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_Rigid_ICP_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_Rigid_closedform_points_default.so Using MITK version of BundleUtilities.cmake Using MITK version of GetPrerequisites.cmake MITK fixup_bundle fixup_bundle app='/N/soft/rhel7/mitk/2018.04.2/bin/MitkTractDensity' libs='/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_FastSymmetricForcesDemons_MultiRes_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_LevelSetMotion_MultiRes_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_affine_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_rigid_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_translation_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_Rigid_ICP_default.so;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_Rigid_closedform_points_default.so' dirs='/N/soft/rhel7/mitk/MITK-2018.04.2_build/MITK-build/bin;/N/soft/rhel7/mitk/MITK-2018.04.2_build/MITK-build/bin/plugins;/N/soft/rhel7/mitk/MITK-2018.04.2_build/MITK-build/lib;/N/soft/rhel7/mitk/MITK-2018.04.2_build/MITK-build/lib/plugins;/N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/bin/.;/N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/lib/.;/N/soft/rhel7/qt/5.12.2/5.12.2/gcc_64/lib/.;/N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/lib/vigra/lib;/N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/src/MatchPoint-build/lib;/N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/src/CTK-build/CMakeExternals/Install/bin;/N/soft/rhel7/mitk/MITK-2018.04.2_venv/bin/.;/N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/src/CTK-build/CTK-build/bin/.;/N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/src/CTK-build/qRestAPI-build/.;/gpfs/hps/soft/rhel7/mitk/2018.04.2/bin' ignoreItems='' fixup_bundle: preparing... ________________________________ From: Dennis, H. E. Cicada Brokaw <hbro...@iu.edu<mailto:hbro...@iu.edu>> Sent: Wednesday, September 25, 2019 3:24 PM To: mitk-users@lists.sourceforge.net<mailto:mitk-users@lists.sourceforge.net> Subject: [mitk-users] Error during make install I am building the 2018.04.2 release from source (I am doing this for an HPC cluster that is running RHEL7 as its OS, and we do not install software on all of the nodes, but rather in a centrally available mounted directory system-so we cannot install in the default locations). I was able to run make and eventually succeeded in getting it to complete without an error. When I configured I set the install directory, so when I do make install, make does install to that directory. But during the make install I am running into the following error: ... Analyzed prerequisites of /N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/lib/./../lib/../lib/libgdcmexpat.so.2.0 Analyzed prerequisites of /N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/lib/./../lib/../lib/libgdcmzlib.so.2.6 Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_FastSymmetricForcesDemons_MultiRes_default.so Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_LevelSetMotion_MultiRes_default.so Analyzed prerequisites of /N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/lib/./libMAPAlgorithmsITK-0.13.so.0.13 Analyzed prerequisites of /N/soft/rhel7/mitk/MITK-2018.04.2_build/ep/lib/./../lib/libMAPUtilities-0.13.so.0.13 Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_affine_default.so Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_rigid_default.so Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_MultiModal_translation_default.so Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_Rigid_ICP_default.so Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_Rigid_closedform_points_default.so -- warning: cannot resolve item 'libofstd.so.13' possible problems: need more directories? need to use InstallRequiredSystemLibraries? run in install tree instead of build tree? -- warning: gp_resolved_file_type non-absolute file 'libofstd.so.13' returning type 'other' -- possibly incorrect -- warning: cannot resolve item 'libofstd.so.13' possible problems: need more directories? need to use InstallRequiredSystemLibraries? run in install tree instead of build tree? Analyzed prerequisites of /N/soft/rhel7/mitk/2018.04.2/bin/ofstd_tests -- warning: cannot resolve item 'libofstd.so.13' possible problems: need more directories? need to use InstallRequiredSystemLibraries? run in install tree instead of build tree? CMake Error at /N/soft/rhel7/mitk/MITK-2018.04.2/CMake/BundleUtilities.cmake:441 (file): file READ_ELF given FILE "libofstd.so.13" that does not exist. Call Stack (most recent call first): /N/soft/rhel7/mitk/MITK-2018.04.2/CMake/BundleUtilities.cmake:497 (get_item_rpaths) /N/soft/rhel7/mitk/MITK-2018.04.2/CMake/BundleUtilities.cmake:634 (set_bundle_key_values) /N/soft/rhel7/mitk/MITK-2018.04.2/CMake/BundleUtilities.cmake:912 (get_bundle_keys) MITK-build/Modules/DiffusionImaging/FiberTracking/cmdapps/Fiberfox/cmake_install.cmake:195 (fixup_bundle) MITK-build/Modules/DiffusionImaging/FiberTracking/cmake_install.cmake:42 (include) MITK-build/Modules/DiffusionImaging/cmake_install.cmake:43 (include) MITK-build/cmake_install.cmake:157 (include) cmake_install.cmake:93 (include) make: *** [install] Error 1 The library about which the complaint is made is there: $ ls -la ./ep/src/DCMTK-build/lib/libofstd.so* lrwxrwxrwx 1 hbrokaw hpc 14 Sep 19 16:24 ./ep/src/DCMTK-build/lib/libofstd.so -> libofstd.so.13 -rwxr-xr-x 2 hbrokaw hpc 323192 Sep 19 16:24 ./ep/src/DCMTK-build/lib/libofstd.so.13 -rwxr-xr-x 2 hbrokaw hpc 323192 Sep 19 16:24 ./ep/src/DCMTK-build/lib/libofstd.so.3.6.3 and $ ls -la ../2018.04.2/lib64/libofstd* lrwxrwxrwx 1 hbrokaw hpc 14 Sep 19 21:53 ../2018.04.2/lib64/libofstd.so -> libofstd.so.13 -rwxr-xr-x 2 hbrokaw hpc 323192 Sep 19 16:24 ../2018.04.2/lib64/libofstd.so.13 -rwxr-xr-x 2 hbrokaw hpc 323192 Sep 19 16:24 ../2018.04.2/lib64/libofstd.so.3.6.3 Originally, the libofstd.so.13 files were soft links to libofstd.so.3.6.3 in the same directory. I tried changing it to a hard link to see if that would change the error, but the error is the same. I would also note that there is a suprising amount of time taken (hours of time) after the following line is printed: Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_FastSymmetricForcesDemons_MultiRes_default.so before the next line is printed: Analyzed prerequisites of /gpfs/hps/soft/rhel7/mitk/2018.04.2/bin/mdra-0-13_MITK_LevelSetMotion_MultiRes_default.so Any assistance would be appreciated. I am used to "make install" simply copying lots of files to the destination location (in this case the destination is ../2018.04.2 - the absolute path is: /gpfs/hps/soft/rhel7/mitk/2018.04.2) This "make install" seems to be doing some sort of testing and I believe it has not finished copying all of the files that need to be in the installation directory before it is having this error. Sincerely, Cicada Dennis
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