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>
Sent: Wednesday, September 25, 2019 3:24 PM
To: 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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