[SyneRBI/SIRF-SuperBuild] curl linking problem for ISMRMD with system HDF5 on Ubuntu 22.04 (Issue #935)
Cate-Gascoigne
When choosing USE_SYSTEM_HDF5=ON, CMake finds the Ubuntu hdf5 libraries. However, we get the following error
cd /home/cate/devel/build/builds/ISMRMRD/build/utilities && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ismrmrd_generate_cartesian_shepp_logan.dir/link.txt --verbose=ON
/usr/bin/c++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -Wall -std=c++11 -Werror -O3 -DNDEBUG -rdynamic CMakeFiles/ismrmrd_generate_cartesian_shepp_logan.dir/generate_cartesian_shepp_logan.cpp.o CMakeFiles/ismrmrd_generate_cartesian_shepp_logan.dir/ismrmrd_phantom.cpp.o -o ismrmrd_generate_cartesian_shepp_logan -Wl,-rpath,/home/cate/devel/build/builds/ISMRMRD/build:/home/cate/anaconda3/lib:/usr/lib/x86_64-linux-gnu/hdf5/serial: ../libismrmrd.so.1.13.7 /home/cate/anaconda3/lib/libboost_program_options.so.1.82.0 -lfftw3 -lfftw3f /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /usr/lib/x86_64-linux-gnu/libpugixml.so.1.12
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_global_init@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_perform@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_slist_free_all@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_setopt@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_init@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_slist_append@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_cleanup@CURL_OPENSSL_4'
/usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_global_cleanup@CURL_OPENSSL_4'
collect2: error: ld returned 1 exit status
@KrisThielemans thinks this is because APT installs HDF5 with its hdf5-config.cmake, and CMake does not know it needs to link with curl.
Adding -lcurl to the above line resolves this, but this is not really a SIRF or even ISMRMRD problem.
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Edoardo Pasca
Discussion with @KrisThielemans
Possible solutions:
- we ask ubuntu to package the
hdf5-config.cmake - we ask CMake to attempt to test for the
curllinking - we take libhdf5 from conda
- we default build HDF5
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Kris Thielemans
@paskino I tried this on the 3.6.0 VM and there it works. I found this is because on that system h5cc is installed, and CMake's FindHDF5.cmake uses it to find compilation and linking problems. So, I think the easiest solution is to install h5cc and h5c++.
On debian/ubuntu, this can be done with
sudo apt install hd5-helpers
which we do for our VM/docker
https://github.com/SyneRBI/SIRF-SuperBuild/blob/5f1a7f498bf6f41551c19eb53798b5d33af43eec/docker/build_system-ubuntu.sh#L56-L59
Could you confirm that on the system where you had problems, h5cc was not installed, and that it gets fixed if you do? If so, I suggested we add a some lines to https://github.com/SyneRBI/SIRF-SuperBuild?tab=readme-ov-file#faqs, pointing to here, and close this issue.
PS: We do recommend already to our users to use that install script, https://github.com/SyneRBI/SIRF/wiki/SIRF-SuperBuild-Ubuntu#1-install-dependencies-via-apt
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Kris Thielemans
I've created https://gitlab.kitware.com/cmake/cmake/-/issues/26654, but don't really expect a fix in CMake.
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Kris Thielemans
Decision is to set the
USE_SYSTEM_HDF5=OFFas default behaviour
we already do https://github.com/SyneRBI/SIRF-SuperBuild/blob/5f1a7f498bf6f41551c19eb53798b5d33af43eec/SuperBuild.cmake#L189
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Edoardo Pasca
I tested the docker build on master:
docker build . --build-arg NUM_PARALLEL_BUILDS=1 --build-arg RUN_CTEST=0 --target=build --no-cache
hdf5-helpers seems installed however the build fails with the default USE_SYSTEM_HDF5=ON
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Kris Thielemans
Does it fail with the above error? is h5cc on the image? What's the CMake log for ISMRMD? Ideally you add -DHDF5_FIND_DEBUG=ON.
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Edoardo Pasca
That's what CMake finds. I think the problem is that HDF5 is installed both by conda and on ubuntu system if BUILD_CIL=ON (via the dependency on h5py). CMake does not manage to separate the 2.
CMake SuperBuild log
HDF5_C_COMPILER_EXECUTABLE /opt/conda/bin/h5cc
HDF5_C_INCLUDE_DIR /usr/include/hdf5/serial
HDF5_DIFF_EXECUTABLE /opt/conda/bin/h5diff
HDF5_DIR HDF5_DIR-NOTFOUND
HDF5_IS_PARALLEL OFF
HDF5_SOURCE_DIR /opt/SIRF-SuperBuild/sources/HDF5
HDF5_TAG hdf5-1_10_1
HDF5_URL https://github.com/HDFGroup/hdf5/
HDF5_hdf5_LIBRARY_DEBUG HDF5_hdf5_LIBRARY_DEBUG-NOTFOUND
HDF5_hdf5_LIBRARY_RELEASE /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
CMake ISMRMRD log
HDF5_C_COMPILER_EXECUTABLE /opt/conda/bin/h5cc
HDF5_C_INCLUDE_DIR /usr/include/hdf5/serial
HDF5_C_LIBRARIES /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
HDF5_DIFF_EXECUTABLE /opt/conda/bin/h5diff
HDF5_DIR HDF5_DIR-NOTFOUND
HDF5_FIND_DEBUG ON
HDF5_INCLUDE_DIRS /usr/include/hdf5/serial
HDF5_IS_PARALLEL OFF
HDF5_LIBRARIES /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
HDF5_hdf5_LIBRARY_DEBUG HDF5_hdf5_LIBRARY_DEBUG-NOTFOUND
HDF5_hdf5_LIBRARY_RELEASE /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
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Edoardo Pasca
I tried not to install the hdf5 packages below
https://github.com/SyneRBI/SIRF-SuperBuild/blob/5f1a7f498bf6f41551c19eb53798b5d33af43eec/docker/build_gadgetron-ubuntu.sh#L8-L13
However libarmadillo-dev depends on a whole lot of hdf5 libraries and ancillary hdf5 packages.
I suggest to move the installation of h5py for CIL after the build stage.
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Kris Thielemans
I did a test on my local machine with a new conda env with only h5py (conda create -n test h5py) and the following CMakeLists.txt:
cmake_minimum_required(VERSION 3.14.0)
PROJECT(TESTHDF5)
find_package(HDF5 COMPONENTS C)
Running with cmake -S . -B build/ -DHDF5_FIND_DEBUG=ON, I get
HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
-- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
<snip>
Root cause therefore: h5py depends on hdf5, which installs all include files and libraries as well as h5cc. However, trying to use h5cc leads to
h5cc cmake_hdf5_test.c
/home/sirfuser/mambaforge/envs/test/bin/h5cc: 1: eval: x86_64-conda-linux-gnu-cc: not found
Indeed, https://github.com/SyneRBI/SIRF/wiki/Building-SIRF-and-CIL-with-conda says to add cxx-compiler. Adding that to my conda env means that CMake finds the conda version of hdf5 and all is well.
Summary: when using conda, install both h5py and cxx-compiler.
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Kris Thielemans
I suggest to move the installation of
h5pyfor CIL after the build stage
While this might build, I think it's a failing strategy unfortunately. Reason: we build with system hdf5, and then install conda hdf5, so any python program will use the conda hdf5 shared library at run-time, while ISMRMRD, STIR and possibly ITK assume it will be the system hdf5. In my experience, this can easily lead to segfaults. (libgcc shared libraries are backwards compatible somehow, hdf5 shared libraries are not).
The only case where this might be safe is if we are NOT using the conda env where CIL is installed. I have no idea if this is the case, but it seems unlikely.
I see 3 solutions:
- remove h5py requirement from CIL (why does it need it anyway?), even if only for our own builds. However, this is probably not a good strategy, as people might install h5py anyway (maybe sirf-exercises do already)
- forget about most apt packages and use conda packages instead (see the wiki page, but it will need work for gadgetron).
- continue mixing apt and conda, and pray that hdf5 (or other libraries) don't trip us up.
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Edoardo Pasca
On the VM we use the system python, while on docker we install conda or better conda is installed by the base image to run jupyter.
I agree that it is dangerous, but I thought that once built the libraries would find the linked libraries. I must be wrong.
Several CIL requirements are needed for reading scanner data such as h5py and dxchange. We can debate whether this is a requirement or just a piece of software that makes the functionality more complete. For us here the important bits of CIL are in the optimisation framework which doesn't really depend on those packages.
However, this docker image is the base of the joined courses that we've been running, therefore we've kept the full list of dependencies.
If I remember correctly Gadgetron used to be tested only on Ubuntu, relying on dependencies available on apt.
It may not be a bad idea to use conda packages all the way through. Gadgetron has a list in their meta.yaml which can be used.
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Edoardo Pasca
paskino left a comment (SyneRBI/SIRF-SuperBuild#935)The HDF5 version on Ubuntu 22.04 is 1.10.7. The versions available on conda-forge do not have that!
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Edoardo Pasca
paskino left a comment (SyneRBI/SIRF-SuperBuild#935)Looking deeper in the issue, our base image quay.io/jupyter/scipy-notebook:ubuntu-22.04 does already contain both h5py and hdf5
# Name Version Build Channel
hdf5 1.14.3 nompi_hdf9ad27_105 conda-forge
h5py 3.11.0 nompi_py311h439e445_102 conda-forge
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Casper da Costa-Luis
Closed #935 as completed via #946.
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