[SyneRBI/SIRF-SuperBuild] docker: pin Ubuntu 22.04 (PR #946)
Casper da Costa-Luis
- fixes #945
You can view, comment on, or merge this pull request online at:
https://github.com/SyneRBI/SIRF-SuperBuild/pull/946
Commit Summary
- 87bd329 docker: pin Ubuntu 22.04
File Changes
(1 file)
- M Dockerfile (2)
Patch Links:
- https://github.com/SyneRBI/SIRF-SuperBuild/pull/946.patch
- https://github.com/SyneRBI/SIRF-SuperBuild/pull/946.diff
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- fffb950 debug revert
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 64b2194 debug revert
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 0abf592 debug revert
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Casper da Costa-Luis
@casperdcl pushed 2 commits.
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)similar libcurl linker error:
#26 47.21 : && /usr/lib/ccache/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -Wall -std=c++11 -Werror -O3 -DNDEBUG -rdynamic utilities/CMakeFiles/ismrmrd_test_xml.dir/ismrmrd_test_xml.cpp.o -o utilities/ismrmrd_test_xml -Wl,-rpath,/opt/SIRF-SuperBuild/builds/ISMRMRD/build:/usr/lib/x86_64-linux-gnu/hdf5/serial:/opt/conda/lib: libismrmrd.so.1.13.7 /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /opt/conda/lib/libpugixml.so.1.15 && :
#26 47.21 /usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_global_init@CURL_OPENSSL_4'
#26 47.21 /usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_perform@CURL_OPENSSL_4'
#26 47.21 /usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_slist_free_all@CURL_OPENSSL_4'
#26 47.21 /usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_setopt@CURL_OPENSSL_4'
#26 47.21 /usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_init@CURL_OPENSSL_4'
#26 47.21 /usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_slist_append@CURL_OPENSSL_4'
#26 47.21 /usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_easy_cleanup@CURL_OPENSSL_4'
#26 47.21 /usr/bin/ld: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so: undefined reference to `curl_global_cleanup@CURL_OPENSSL_4'
#26 47.21 collect2: error: ld returned 1 exit status
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)I wonder if fixing #934 might be easier...
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)#937 was along the way to do that (despite the title). However, it's obviously strange that our GHA work ok now, but docker doesn't, so probably some missing package somewhere.
The above linking error is caused by the system HDF5 not coming with hdf5-config.cmake. So CMake tries to get the information from h5cc. If that fails, it goes and finds some libraries, but has no clue what to link with, so really it should have given up already, but it valiantly forges ahead.
We normally really on the 2nd step, but we see
https://github.com/SyneRBI/SIRF-SuperBuild/actions/runs/14171846317/job/39697234560#step:9:8335
#26 2.089 -- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
#26 2.101 -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so (found suitable version "1.10.7", minimum required is "1.8")
#26 2.101 -- USING the system HDF5, found HDF5_INCLUDE_DIRS=/usr/include/hdf5/serial, HDF5_C_LIBRARY_hdf5=,HDF5_LIBRARIES=/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
Sadly, CMake doesn't tell us why the HDF5 C compiler wrapper failed. It's stored in a log file though (can't remember which one). Maybe you could check if h5cc is really installed, although it should be
https://github.com/SyneRBI/SIRF-SuperBuild/blob/b56b85bb4066fa6cffa854bbb0bcd5ed7804159d/docker/build_system-ubuntu.sh#L56-L59
Try and put
h5cc -showconfig h5c++ -showconfig
before calling CMake. You can just as well stop the actual build for now while debugging.
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)looks like 'tis using conda
0.385 SUMMARY OF THE HDF5 CONFIGURATION
0.385 =================================
0.385
0.385 General Information:
0.385 -------------------
0.385 HDF5 Version: 1.14.3
0.385 Configured on: Wed Jan 22 03:13:54 UTC 2025
0.385 Configured by: conda@6f7718f776d2
0.385 Host system: x86_64-conda-linux-gnu
0.385 Uname information: Linux 6f7718f776d2 6.5.0-1025-azure #26~22.04.1-Ubuntu SMP Thu Jul 11 22:33:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
0.385 Byte sex: little-endian
0.385 Installation point: /opt/conda
0.385
0.385 Compiling Options:
0.385 ------------------
0.385 Build Mode: production
0.385 Debugging Symbols: no
0.385 Asserts: no
0.385 Profiling: no
0.385 Optimization Level: high
0.385
0.385 Linking Options:
0.385 ----------------
0.385 Libraries: shared
0.385 Statically Linked Executables:
0.385 LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib
0.385 H5_LDFLAGS:
0.385 AM_LDFLAGS: -L/opt/conda/lib -L/opt/conda/lib
0.385 Extra libraries: -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm
0.385 Archiver: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-ar
0.385 AR_FLAGS: cr
0.385 Ranlib: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-ranlib
0.385
0.385 Languages:
0.385 ----------
0.385 C: yes
0.385 C Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-cc
0.385 CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include
0.385 H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API -I/home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/work/src/H5FDsubfiling
0.385 AM_CPPFLAGS: -I/opt/conda/include -I/opt/conda/include
0.385 C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/work=/usr/local/src/conda/hdf5-1.14.3 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix
0.385 H5 C Flags: -std=c99 -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wshadow -Wundef -Wwrite-strings -pedantic -Wno-c++-compat -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wc11-c2x-compat -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -s -Wbad-function-cast -Wcast-align -Wformat -Wimplicit-function-declaration -Wint-to-pointer-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-but-set-variable -Wunused-variable -Wunused-function -Wunused-parameter -Wincompatible-pointer-types -Wint-conversion -Wshadow -Wrestrict -Wcast-function-type -Wmaybe-uninitialized -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wstrict-overflow=2 -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
0.385 AM C Flags:
0.385 Shared C Library: yes
0.385 Static C Library: no
0.385
0.385
0.385 Fortran: yes
0.385 Fortran Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-gfortran
0.385 Fortran Flags:
0.385 H5 Fortran Flags: -std=f2008 -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Winteger-division -Wfrontend-loop-interchange -fdiagnostics-urls=never -fno-diagnostics-color -s -Wno-unused-dummy-argument -Wno-array-temporaries -O3
0.385 AM Fortran Flags:
0.385 Shared Fortran Library: yes
0.385 Static Fortran Library: no
0.385 Module Directory: ${includedir}
0.385
0.385 C++: yes
0.385 C++ Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-c++
0.385 C++ Flags: -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/work=/usr/local/src/conda/hdf5-1.14.3 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix
0.385 H5 C++ Flags: -std=c++11 -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wno-deprecated-copy -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -s -Wcast-align -Wmissing-declarations -Wpacked -Wredundant-decls -Wswitch -Wunused-but-set-variable -Wunused-function -Wunused-variable -Wunused-parameter -Wshadow -O3
0.385 AM C++ Flags:
0.385 Shared C++ Library: yes
0.385 Static C++ Library: no
0.385
0.385 Java: no
0.385
0.385
0.385 Features:
0.385 ---------
0.385 Parallel HDF5: no
0.385 Parallel Filtered Dataset Writes: no
0.385 Large Parallel I/O: no
0.385 High-level library: yes
0.385 Dimension scales w/ new references: no
0.385 Build HDF5 Tests: yes
0.385 Build HDF5 Tools: yes
0.385 Build GIF Tools: yes
0.385 Threadsafety: yes
0.385 Default API mapping: v114
0.385 With deprecated public symbols: yes
0.385 I/O filters (external): deflate(zlib),szip(encoder)
0.385 Map (H5M) API: no
0.385 Direct VFD: yes
0.385 Mirror VFD: no
0.385 Subfiling VFD: no
0.385 (Read-Only) S3 VFD: yes
0.385 (Read-Only) HDFS VFD: no
0.385 Packages w/ extra debug output: none
0.385 API tracing: no
0.385 Using memory checker: yes
0.385 Function stack tracing: no
0.385 Use file locking: best-effort
0.385 Strict file format checks: no
0.385 Optimization instrumentation: no
0.389 SUMMARY OF THE HDF5 CONFIGURATION
0.389 =================================
0.389
0.389 General Information:
0.389 -------------------
0.389 HDF5 Version: 1.14.3
0.389 Configured on: Wed Jan 22 03:13:54 UTC 2025
0.389 Configured by: conda@6f7718f776d2
0.389 Host system: x86_64-conda-linux-gnu
0.389 Uname information: Linux 6f7718f776d2 6.5.0-1025-azure #26~22.04.1-Ubuntu SMP Thu Jul 11 22:33:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
0.389 Byte sex: little-endian
0.389 Installation point: /opt/conda
0.389
0.389 Compiling Options:
0.389 ------------------
0.389 Build Mode: production
0.389 Debugging Symbols: no
0.389 Asserts: no
0.389 Profiling: no
0.389 Optimization Level: high
0.389
0.389 Linking Options:
0.389 ----------------
0.389 Libraries: shared
0.389 Statically Linked Executables:
0.389 LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/opt/conda/lib -Wl,-rpath-link,/opt/conda/lib -L/opt/conda/lib
0.389 H5_LDFLAGS:
0.389 AM_LDFLAGS: -L/opt/conda/lib -L/opt/conda/lib
0.389 Extra libraries: -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm
0.389 Archiver: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-ar
0.389 AR_FLAGS: cr
0.389 Ranlib: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-ranlib
0.389
0.389 Languages:
0.389 ----------
0.389 C: yes
0.389 C Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-cc
0.389 CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /opt/conda/include
0.389 H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API -I/home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/work/src/H5FDsubfiling
0.389 AM_CPPFLAGS: -I/opt/conda/include -I/opt/conda/include
0.389 C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/work=/usr/local/src/conda/hdf5-1.14.3 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix
0.389 H5 C Flags: -std=c99 -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wshadow -Wundef -Wwrite-strings -pedantic -Wno-c++-compat -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wc11-c2x-compat -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -s -Wbad-function-cast -Wcast-align -Wformat -Wimplicit-function-declaration -Wint-to-pointer-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-but-set-variable -Wunused-variable -Wunused-function -Wunused-parameter -Wincompatible-pointer-types -Wint-conversion -Wshadow -Wrestrict -Wcast-function-type -Wmaybe-uninitialized -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wno-jump-misses-init -Wstrict-overflow=2 -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -O3
0.389 AM C Flags:
0.389 Shared C Library: yes
0.389 Static C Library: no
0.389
0.389
0.389 Fortran: yes
0.389 Fortran Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-gfortran
0.389 Fortran Flags:
0.389 H5 Fortran Flags: -std=f2008 -Waliasing -Wall -Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow -pedantic -Wintrinsics-std -Wimplicit-procedure -Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all -Wno-c-binding-type -Winteger-division -Wfrontend-loop-interchange -fdiagnostics-urls=never -fno-diagnostics-color -s -Wno-unused-dummy-argument -Wno-array-temporaries -O3
0.389 AM Fortran Flags:
0.389 Shared Fortran Library: yes
0.389 Static Fortran Library: no
0.389 Module Directory: ${includedir}
0.389
0.389 C++: yes
0.389 C++ Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/_build_env/bin/x86_64-conda-linux-gnu-c++
0.389 C++ Flags: -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /opt/conda/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/hdf5_1737515482579/work=/usr/local/src/conda/hdf5-1.14.3 -fdebug-prefix-map=/opt/conda=/usr/local/src/conda-prefix
0.389 H5 C++ Flags: -std=c++11 -Wall -Wcast-qual -Wconversion -Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wnon-virtual-dtor -Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef -Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile -Wno-deprecated-copy -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -s -Wcast-align -Wmissing-declarations -Wpacked -Wredundant-decls -Wswitch -Wunused-but-set-variable -Wunused-function -Wunused-variable -Wunused-parameter -Wshadow -O3
0.389 AM C++ Flags:
0.389 Shared C++ Library: yes
0.389 Static C++ Library: no
0.389
0.389 Java: no
0.389
0.389
0.389 Features:
0.389 ---------
0.389 Parallel HDF5: no
0.389 Parallel Filtered Dataset Writes: no
0.389 Large Parallel I/O: no
0.389 High-level library: yes
0.389 Dimension scales w/ new references: no
0.389 Build HDF5 Tests: yes
0.389 Build HDF5 Tools: yes
0.389 Build GIF Tools: yes
0.389 Threadsafety: yes
0.389 Default API mapping: v114
0.389 With deprecated public symbols: yes
0.389 I/O filters (external): deflate(zlib),szip(encoder)
0.389 Map (H5M) API: no
0.389 Direct VFD: yes
0.389 Mirror VFD: no
0.389 Subfiling VFD: no
0.389 (Read-Only) S3 VFD: yes
0.389 (Read-Only) HDFS VFD: no
0.389 Packages w/ extra debug output: none
0.389 API tracing: no
0.389 Using memory checker: yes
0.389 Function stack tracing: no
0.389 Use file locking: best-effort
0.389 Strict file format checks: no
0.389 Optimization instrumentation: no
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)(I didn't know we could use html summary/details on GitHub. nice!)
It looks like h5cc is installed from conda hdf5, which is probably installed via h5py. However, somewhat crazily, the h5cc actually cannot compile anything, as it depends on c-compiler which we don't have currently. (IMHO, conda -hdf5 should therefore NOT include h5cc...). More info is in #935.
As I argued in #935: installing h5py means we now have 2 HDF5 versions installed (system and conda). I suppose we didn't have this before on docker, because we didn't install relevant CIL dependencies (or only installed it after building, although that's still dangerous, as anything in python would have a run-time of the conda-forge hdf5, while we would have compiled with system hdf5, which is a lot older, and I'm not so sure how good that'd work).
I guess I'd try the following:
- add
cxx-compilerandc-compilerto our .yml file, or have a "build .yml") - make sure that conda installs all of that before any cmake
- update hash for STIR in version_config.cmake to 4f73a6cf9b9ba78c4b0e259c3fd4d890b592077d (as we need UCL/STIR#1580)
- activate env and run CMake (it should pick up conda-forge's c,c++ compilers and h5cc)
Our wiki page says however we might have a problem with CCPi-Regularisation-Toolkit, but I cannot remember what that was. Maybe @paskino knows.
If that doesn't work, we'll have to finish #937 or port bits from it (That PR got confused by trying Ubuntu 24.04, recent Gadgetron and all that, but I think we should avoid that for now).
sigh
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)Tried adding the c{,xx}-compiler & bumping STIR, and now the error is:
CMake Error at /usr/local/share/cmake-3.29/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find Boost (missing: system) (found suitable version "1.74.0",
minimum required is "1.71.0")
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)that's weird, as boost system is installed (and is found in the action log). can you push or send log?
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- 1054166 fix conda hdf5
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)sure; #946/runs/14196702767/job/39773433531
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)I couldn't find the doc for this, but apparently, gcc 13.3 is too recent for boost 1.74.0. Solution: add boost to requirements.yml. And off we are on the slippery slope...
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@KrisThielemans pushed 1 commit.
- 4350226 add boost to requirements.yml
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)fails on (unrelated)
#15 14.15 + mamba list python
#15 14.15 + grep '^python '
#15 14.15 + tr -s ' '
#15 14.15 + cut -d ' ' -f 1,2
I have no idea why this happens (and have seen it before)
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- f60491d add boost to requirements.yml
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)You reverted the submodule. I just force-pushed to remove the change.
You probably need to:
git fetch git reset --hard origin/docker-bump git submodule update
btw current error is now fftw3 related:
FFTW3 UNIX libraries: FFTW3_LIBRARY-NOTFOUND CMake Error at /usr/local/share/cmake-3.29/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find FFTW3 (missing: FFTW3_LIBRARY) Call Stack (most recent call first): /usr/local/share/cmake-3.29/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE) CMake/FindFFTW3.cmake:114 (find_package_handle_standard_args) SuperBuild/External_FFTW3.cmake:96 (find_package) CMake/ExternalProjectDependency.cmake:593 (include) SuperBuild/External_ISMRMRD.cmake:31 (ExternalProject_Include_Dependencies) CMake/ExternalProjectDependency.cmake:593 (include) SuperBuild/External_SIRF.cmake:42 (ExternalProject_Include_Dependencies) CMake/ExternalProjectDependency.cmake:593 (include) CMake/ExternalProjectDependency.cmake:639 (ExternalProject_Include_Dependencies) SuperBuild.cmake:325 (ExternalProject_Include_Dependencies) CMakeLists.txt:42 (include)
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Oops, sorry.
I haven't checked why this is the case, but the easiest will be to add fftw as well. Of course, we'll soon end up where @paskino was...
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)Adding fftw/fftw-static to conda (and even adding -DFFTW3_ROOT_DIR=${CONDA_DIR}) makes no difference to the error...
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- b0f51b5 pin conda cxx-compiler to 1.5.2
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Adding
fftw/fftw-statictoconda(and even adding-DFFTW3_ROOT_DIR=${CONDA_DIR}) makes no difference to the error...
This makes very little sense to me, but I'm now trying to force conda to use g++-11 (otherwise we'll have Gadgetron failures anyway)
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Pinning the C++ compiler apparently still needs boost package (i.e. it isn't happ with the apt one), and presumably all the others as well. Also, for whatever reason this gives us hdf4.
By the way, I see
#17 1.398 Warning: 'conda-forge' already in 'channels' list, moving to the top
#17 1.452 warning libmamba 'repo.anaconda.com', a commercial channel hosted by Anaconda.com, is used.
#17 1.452
#17 1.452 warning libmamba Please make sure you understand Anaconda Terms of Services.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Pinning the C++ compiler apparently still needs boost package (i.e. it isn't happy with the apt one), and presumably all the others as well.
I tried this in the VM. The APT libraries are in /usr/lib/x86_64-linux-gnu/. When using the system (i.e. APT) g++, CMake find the libraries there. When using the conda g++, CMake doesn't look there at all (it does look in /usr/lib). Presumably this is for a good reason...
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)So, we seem to be stuck here. if we need 'h5py` for CIL (@paskino @gfardell, please confirm), I see 2 options:
- go conda all the way (as started in #937), but pinning cxx-compiler
- stick to APT for now, remove
h5pyfromrequirements.ymland try pip (trying to math hdf5 version to the apt one)
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Casper da Costa-Luis
@casperdcl pushed 5 commits.
- 37ce0bc minor linting
- afa218c conda fftw3
- bd23056 WIP: drop cil deps
- 2057cc8 pip install cil
- a903cc4 conda CIL dependencies & pip CIL by default
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@casperdcl pushed 11 commits.
- 1244da0 docker: pin Ubuntu 22.04
- eedd2d4 debug revert
- 2c7cce8 bump docker-stacks
- 37790f2 fix conda hdf5
- c95576d add boost to requirements.yml
- 7b37a05 pin conda cxx-compiler to 1.5.2
- fce1fcb minor linting
- 0889931 conda fftw3
- 7ae9e15 WIP: drop cil deps
- 5279c34 pip install cil
- 47e6315 conda CIL dependencies & pip CIL by default
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Casper da Costa-Luis
@casperdcl pushed 2 commits.
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)I've brute-forced fixes for
- the HDF5/cURL liker error on
External_ISMRMRD.cmake - the compiler standard version on
External_siemens_to_ismrmrd.cmake
There's now just this error:
ProjDataGEHDF5.cxx:(.text+0x847): undefined reference to stir::GE::RDF_HDF5::GEHDF5Wrapper::read_sinogram(stir::Array<3, unsigned char>&, std::array<unsigned long, 3ul> const&, std::array<unsigned long, 3ul> const&)
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)I'm not sure. It's vaguely similar to UCL/STIR#1202. Could try to use a newer version of STIR. Possibly it's a STIR bug, although I have no clue why it would come up now.
However, if you have to patch ISMRMRD to link with HDF5, you'll have patch STIR and SIRF as well.
As discussed at length in #935: there's 2 versions of HDF5 libraries here: conda and apt. ISMRMRD [https://github.com/SyneRBI/SIRF-SuperBuild/actions/runs/15468133565/job/43545150850?pr=946#step:9:7945](got built with the APT version) as did STIR. However, CMake isn't happy with h5cc (I can't remember why), and therefore doesn't know linking options for hdf5, hence the linking error.
(As stated in #935 as well: as the APT and conda HDF5 versions are so wildly different, I'd imagine this will cause run-time conflicts when running from conda's python (but maybe not).)
I'm not sure how to get out of this swamp TBH. In #937, we started on using conda for nearly everything on docker, but that also got complicated (one reason being that the VM and GHA don't). Sigh.
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Casper da Costa-Luis
casperdcl left a comment (SyneRBI/SIRF-SuperBuild#946)Could try to use a newer version of STIR
I tried using DEVEL_BUILD i.e. STIR master, which still fails.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)sorry, I only now see that this linking error is when building SIRF. STIR itself installed fine. It seems to be STIR's "circular library dependency problem", which seems only mentioned in one of our oldest issues UCL/STIR#6.
But I have no clue why this appears here, and not in other SIRF builds (SIRF Actions are fine).
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)(As stated in #935 as well: as the APT and conda HDF5 versions are so wildly different, I'd imagine this will cause run-time conflicts when running from conda's python (but maybe not).)
also for curl now
Cannot generate a safe runtime search path for target ismrmrd because files
in some directories may conflict with libraries in implicit directories:
runtime library [libcurl.so.4] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
/opt/conda/lib
and in other places libunwind.so.8, liblapacke.so.3, libopenblas.so.0, libgomp.so.1.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)As I now spotted that we have still have conda h5py, can we just try to make sure that isn't installed (or force remove it before building), which will make the curl linking problem disappear, not sure about the STIR linking problem though.
If that seems to work, it might be safest to build our own HDF5 as well as install libhdf5 with conda, with matched versions, but we need to get through the build errors first.
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KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)regarding
There's now just this error:
ProjDataGEHDF5.cxx:(.text+0x847): undefined reference to stir::GE::RDF_HDF5::GEHDF5Wrapper::read_sinogram(stir::Array<3, unsigned char>&, std::array<unsigned long, 3ul> const&, std::array<unsigned long, 3ul> const&)
presumably from UCL/STIR:src/buildblock/ProjDataGEHDF5.cxx:82
To diagnose if this is a STIR recursive library problem, let's try the following.
- execute the original line separately to see if we have the same error
- then execute the modified line by adding
libIO.aone more time, see below
cd /opt/SIRF-SuperBuild/builds/SIRF/build
/usr/lib/ccache/g++ -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -O3 -DNDEBUG /opt/SIRF-SuperBuild/INSTALL/lib/objects-Release/stir_registries/buildblock/buildblock_registries.cxx.o /opt/SIRF-SuperBuild/INSTALL/lib/objects-Release/stir_registries/data_buildblock/data_buildblock_registries.cxx.o /opt/SIRF-SuperBuild/INSTALL/lib/objects-Release/stir_registries/IO/IO_registries.cxx.o /opt/SIRF-SuperBuild/INSTALL/lib/objects-Release/stir_registries/recon_buildblock/recon_buildblock_registries.cxx.o /opt/SIRF-SuperBuild/INSTALL/lib/objects-Release/stir_registries/Shape_buildblock/Shape_buildblock_registries.cxx.o /opt/SIRF-SuperBuild/INSTALL/lib/objects-Release/stir_registries/modelling_buildblock/modelling_registries.cxx.o /opt/SIRF-SuperBuild/INSTALL/lib/objects-Release/stir_registries/spatial_transformation_buildblock/spatial_transformation_registries.cxx.o /opt/SIRF-SuperBuild/INSTALL/lib/objects-Release/stir_registries/scatter_buildblock/scatter_registries.cxx.o src/Registration/cReg/CMakeFiles/sirf_flip_or_mirror_image.dir/sirf_flip_or_mirror_image.cpp.o -o src/Registration/cReg/sirf_flip_or_mirror_image -Wl,-rpath,/opt/SIRF-SuperBuild/INSTALL/lib:/opt/conda/lib:/usr/lib/x86_64-linux-gnu/hdf5/serial: src/Registration/cReg/libReg.a src/common/libcsirf.a src/Synergistic/cSyn/libcsyn.a src/xGadgetron/cGadgetron/libcgadgetron.a src/xSTIR/cSTIR/libcstir.a src/Registration/cReg/libReg.a src/common/libcsirf.a src/Synergistic/cSyn/libcsyn.a src/xGadgetron/cGadgetron/libcgadgetron.a src/xSTIR/cSTIR/libcstir.a src/Registration/NiftyMoMo/libNiftyMoMo.a /opt/SIRF-SuperBuild/INSTALL/lib/libreg_nifti.a /opt/SIRF-SuperBuild/INSTALL/lib/libz.a /opt/SIRF-SuperBuild/INSTALL/lib/libreg_png.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_ReadWriteImage.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_maths.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_tools.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_globalTrans.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_localTrans.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_measure.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_resampling.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_blockMatching.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_femTrans.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_aladin.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_f3d.a /opt/SIRF-SuperBuild/INSTALL/lib/libreg_nifti.a /opt/SIRF-SuperBuild/INSTALL/lib/libz.a /opt/SIRF-SuperBuild/INSTALL/lib/libreg_png.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_ReadWriteImage.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_maths.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_tools.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_globalTrans.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_localTrans.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_measure.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_resampling.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_blockMatching.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_femTrans.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_aladin.a /opt/SIRF-SuperBuild/INSTALL/lib/lib_reg_f3d.a /opt/SIRF-SuperBuild/INSTALL/lib/libgadgetron_toolbox_cpunfft.so.4.5.0 /opt/SIRF-SuperBuild/INSTALL/lib/libgadgetron_toolbox_cpufft.so.4.5.0 /opt/SIRF-SuperBuild/INSTALL/lib/libgadgetron_toolbox_cpucore_math.so.4.5.0 -llapacke /usr/lib/x86_64-linux-gnu/liblapacke.so /usr/lib/x86_64-linux-gnu/libopenblas.so /usr/lib/x86_64-linux-gnu/libfftw3.so /usr/lib/x86_64-linux-gnu/libfftw3f.so /opt/SIRF-SuperBuild/INSTALL/lib/libgadgetron_toolbox_hostutils.so.4.5.0 /opt/SIRF-SuperBuild/INSTALL/lib/libgadgetron_core.so.4.5.0 /opt/SIRF-SuperBuild/INSTALL/lib/libgadgetron_toolbox_cpucore.so.4.5.0 /opt/SIRF-SuperBuild/INSTALL/lib/libismrmrd.so.1.13.7 /opt/conda/lib/libpugixml.so.1.15 /usr/lib/x86_64-linux-gnu/libcurl.so /opt/SIRF-SuperBuild/INSTALL/lib/libgadgetron_toolbox_log.so.4.5.0 src/iUtilities/libiutilities.a /usr/lib/x86_64-linux-gnu/libboost_system.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_filesystem.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_thread.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_atomic.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_date_time.so.1.74.0 /usr/lib/x86_64-linux-gnu/libboost_chrono.so.1.74.0 /opt/SIRF-SuperBuild/INSTALL/lib/libanalytic_FBP3DRP.a /opt/SIRF-SuperBuild/INSTALL/lib/libanalytic_FBP2D.a /opt/SIRF-SuperBuild/INSTALL/lib/libanalytic_SRT2D.a /opt/SIRF-SuperBuild/INSTALL/lib/libanalytic_SRT2DSPECT.a /opt/SIRF-SuperBuild/INSTALL/lib/libiterative_OSMAPOSL.a /opt/SIRF-SuperBuild/INSTALL/lib/libiterative_KOSMAPOSL.a /opt/SIRF-SuperBuild/INSTALL/lib/libiterative_OSSPS.a /opt/SIRF-SuperBuild/INSTALL/lib/libscatter_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/librecon_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/libparallelproj_c.so.1.9.0 /opt/SIRF-SuperBuild/INSTALL/lib/libdisplay.a /opt/SIRF-SuperBuild/INSTALL/lib/libspatial_transformation_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/libShape_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/libIO.a /opt/SIRF-SuperBuild/INSTALL/lib/libmodelling_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/libIO.a /opt/SIRF-SuperBuild/INSTALL/lib/libmodelling_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/liblistmode_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/libdata_buildblock.a \
/opt/SIRF-SuperBuild/INSTALL/lib/libIO.a \
/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so /opt/SIRF-SuperBuild/INSTALL/lib/libITKLabelMap-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKMathematicalMorphology-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKFastMarching-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKImageFeature-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKSmoothing-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKOptimizers-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKPolynomials-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKBiasCorrection-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKColormap-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKConvolution-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKStatistics-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkNetlibSlatec-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKSpatialObjects-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKPath-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKFFT-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKDenoising-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKDiffusionTensorImage-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOJPEG2000-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkopenjpeg-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKQuadEdgeMeshFiltering-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKTestKernel-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOBMP-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOGDCM-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkgdcmMSFF-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkgdcmDICT-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkgdcmIOD-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkgdcmDSED-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkgdcmCommon-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOGIPL-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOJPEG-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOMeshBYU-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOMeshFreeSurfer-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOMeshGifti-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKgiftiio-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKEXPAT-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOMeshOBJ-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOMeshOFF-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOMeshVTK-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOMeshBase-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKQuadEdgeMesh-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKMesh-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOMeta-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKMetaIO-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIONIFTI-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKTransform-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKniftiio-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKznz-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIONRRD-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKNrrdIO-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOPNG-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkpng-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOTIFF-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitktiff-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkzlib-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkjpeg-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOVTK-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKIOImageBase-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKCommon-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkdouble-conversion-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitksys-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libITKVNLInstantiation-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkvnl_algo-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkvnl-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkv3p_netlib-5.2.so.1 /opt/SIRF-SuperBuild/INSTALL/lib/libitkvcl-5.2.so.1 -lm -lm -ldl /opt/SIRF-SuperBuild/INSTALL/lib/libnumerics_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/libeval_buildblock.a /opt/SIRF-SuperBuild/INSTALL/lib/libbuildblock.a /usr/lib/gcc/x86_64-linux-gnu/11/libgomp.so /usr/lib/x86_64-linux-gnu/libpthread.a -Wl,-rpath-link,/opt/SIRF-SuperBuild/INSTALL/libIf this is a STIR bug, then we can set -DSTIR_DISABLE_HDF5=ON when building the docker image for now.
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Edoardo Pasca
@paskino pushed 1 commit.
- cefd9c9 update python and CIL version, update base nvidia docker image for build to CUDA 11.8
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Casper da Costa-Luis
@casperdcl pushed 14 commits.
- 261c356 bump docker-stacks, pin Ubuntu 22.04
- 3cd015b fix conda hdf5
- 2d5b532 add boost to requirements.yml
- d8a4914 pin conda cxx-compiler to 1.5.2
- 258e8f9 minor linting
- b27ddf1 conda fftw3
- 1e188a1 HDF5 link CURL
- d99f901 fix siemens_to_ismrmrd build
- 9f580e3 docker: update python & cuda versions
- 339ce52 cil: numpy<2
- 951f6b4 pip install cil
- 6a22b35 update docs
- fabe799 TODO: REVERT: DEBUGGING
- f7e1b70 fix parallelproj openmp linking
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Casper da Costa-Luis
Casper da Costa-Luis
@casperdcl pushed 14 commits.
- b26e6ac bump docker-stacks, pin Ubuntu 22.04
- e6b452c fix conda hdf5
- d206a7e add boost to requirements.yml
- 1af30be pin conda cxx-compiler to 1.5.2
- 962a578 minor linting
- 30cf858 conda fftw3
- c6053f0 HDF5 link CURL
- bea7b2f fix siemens_to_ismrmrd build
- ab9043e docker: update python & cuda versions
- 1fdc502 cil: numpy<2
- 08deca6 pip install cil
- a0a2911 TODO: REVERT: DEBUGGING
- b6921c2 fix parallelproj openmp linking
- 0e6846c fix CIL maybe
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Casper da Costa-Luis
@casperdcl pushed 10 commits.
- 41dd61a fix conda hdf5
- dfae1ca add boost to requirements.yml
- 837e655 pin conda cxx-compiler to 1.5.2
- 573b133 conda fftw3
- 05ef210 HDF5 link CURL
- 6068d5c fix siemens_to_ismrmrd build
- 894ef8b cil: numpy>=2
- e82668c pip install cil
- 1f13bb1 TODO: REVERT: DEBUGGING
- f1aa187 fix parallelproj openmp linking
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Casper da Costa-Luis
@casperdcl pushed 4 commits.
- 622808f cil: numpy>=2
- 19b7a07 pip install cil
- fc9d190 TODO: REVERT: DEBUGGING
- 03c1dd5 fix parallelproj openmp linking
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Casper da Costa-Luis
@casperdcl pushed 12 commits.
- 5d60b2a fix conda hdf5
- 8cd0c52 add boost to requirements.yml
- ef284e0 pin conda cxx-compiler to 1.5.2
- 7f7edc6 conda fftw3
- b2236d7 HDF5 link CURL
- be90d9a fix siemens_to_ismrmrd build
- 4d62b2b cil: numpy>=2
- 1c12aef pip install cil
- 213efde TODO: REVERT: DEBUGGING
- 4b78e7d fix parallelproj openmp linking
- 26c5954 drop astra GPU
- 52a3bfc self-hosted conda channel for speed & reliability
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Casper da Costa-Luis
@casperdcl pushed 3 commits.
- a312248 drop astra GPU
- 3e3d972 self-hosted conda channel for speed & reliability
- 41aef66 DEBUG:NOWARN
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- f703523 wip
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Casper da Costa-Luis
@casperdcl pushed 4 commits.
- 666f50c revert boost to 1.85
- 5d84184 stir lib hell
- c2bf90e partial reverts
- 4a4fb31 STIR_DISABLE_HDF5 work-around
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Casper da Costa-Luis
@casperdcl pushed 2 commits.
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Kris Thielemans
@KrisThielemans requested changes on this pull request.
some tiny comments. Should we merge this asap?
don't forget to re-instate c-cpp.yml
> @@ -11,7 +11,7 @@ Options: $(sed -rn 's/^\s*(\w)\) .*;; # (.*)$/ -\1: \2/p' "$0") Docker Compose Options: Forwarded to 'docker compose build/run', e.g.: - $0 -b -- --build-arg BUILD_CIL=ON --build-arg EXTRA_BUILD_FLAGS="-DCIL_TAG=origin/master" + $0 -b -- --build-arg USE_ITK=OFF --build-arg EXTRA_BUILD_FLAGS="-DCIL_TAG=origin/master"
setting ITK=OFF will break lots of exercises, so would have to re-enable this before merging. However, I see that ITK is being used anyway, so not sure what this is supposed to do.
> @@ -158,14 +150,6 @@ set(DEFAULT_SPM_TAG r7771) set(DEFAULT_JSON_URL https://github.com/nlohmann/json) set(DEFAULT_JSON_TAG v3.11.3) -# CCPi CIL -# minimum supported version of CIL supported is > 22.1.0 or from commit a6062410028c9872c5b355be40b96ed1497fed2a
Even if we don't build CIL, we should have some control somewhere on installed CIL version via pip. Where is this configured?
In CMakeLists.txt:
> @@ -23,13 +23,14 @@ if (WIN32) cmake_minimum_required( VERSION 3.20.0 FATAL_ERROR) else() cmake_minimum_required( VERSION 3.16.2 FATAL_ERROR) + add_compile_options(-w)
will have to be removed, or at least checked on compiler version
In Dockerfile:
> @@ -90,6 +92,7 @@ RUN BUILD_FLAGS="-G Ninja\
-DGadgetron_USE_CUDA=${Gadgetron_USE_CUDA}\
-DBUILD_CIL=${BUILD_CIL}" \
EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS}" \
+ FFTW3_ROOT_DIR="${CONDA_DIR}" \
but you set USE_SYSTEM_FFTW3 off. Are we installing in CONDA_DIR?
In patches/ismrmrd-1.37.7.patch:
> @@ -0,0 +1,19 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 26eb693..3f8dbc3 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -230,7 +230,13 @@ set_target_properties(ismrmrd
+ PROPERTIES
+ EXPORT_NAME ISMRMRD)
+
+-target_link_libraries(ismrmrd ${ISMRMRD_TARGET_LINK_LIBS})
++find_package(CURL REQUIRED)
ah well...
> @@ -31,9 +31,9 @@ else() # ISMRMRD needs more recent 1.68.0 so let's just say 1.71.0 as well set(Boost_REQUIRED_VERSION 1.71.0) endif() -set(Boost_VERSION 1.88.0) -set(Boost_URL http://downloads.sourceforge.net/project/boost/boost/${Boost_VERSION}/boost_1_88_0.zip) -set(Boost_MD5 2f3b4bc30f3b2cb33a4b51af02831013) +set(Boost_VERSION 1.85.0)
add a comment on why this version
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Casper da Costa-Luis
@casperdcl pushed 16 commits.
- c26b512 fix conda hdf5: use cxx-compiler, boost, fftw3
- bfc30dc HDF5 link CURL
- e3134d7 fix siemens_to_ismrmrd build
- 15cd2d0 cil: numpy>=2
- 07baab0 pip install cil
- 03f2805 fix parallelproj openmp linking
- 54adf2c drop astra GPU
- 48a4660 self-hosted conda channel for speed & reliability
- c3057d9 Build boost & fftw3
- 05fe02b revert boost to 1.85
- 24b7f27 bump STIR
- 54a9a33 minor fixes
- 6a1449c fix missing packages
- 30390a0 TODO: REVERT: DEBUG: NOWARN
- 9908ede TODO: REVERT: DEBUGGING
- 3dff418 TODO: REVERT: skip tests for now
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Casper da Costa-Luis
@casperdcl commented on this pull request.
In Dockerfile:
> -ARG USE_SYSTEM_Boost="ON" -ARG USE_SYSTEM_FFTW3="ON" +ARG USE_SYSTEM_Boost="OFF" +ARG USE_SYSTEM_FFTW3="OFF"
might revert this
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Casper da Costa-Luis
> ARG USE_SYSTEM_Armadillo="ON" -ARG USE_SYSTEM_Boost="ON" -ARG USE_SYSTEM_FFTW3="ON" +ARG USE_SYSTEM_Boost="OFF" +ARG USE_SYSTEM_FFTW3="OFF"
might revert this?
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Kris Thielemans
@KrisThielemans commented on this pull request.
In Dockerfile:
> ARG USE_SYSTEM_Armadillo="ON" -ARG USE_SYSTEM_Boost="ON" -ARG USE_SYSTEM_FFTW3="ON" +ARG USE_SYSTEM_Boost="OFF" +ARG USE_SYSTEM_FFTW3="OFF"
If you can, would be good
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Casper da Costa-Luis
@casperdcl pushed 9 commits.
- 8ec6a23 build boost, use system fftw3
- 03ff039 revert boost to 1.85
- bdbd7bf bump STIR
- ff44800 minor CIL & Exercises fixes
- 088babc fix missing packages
- 3da30ed TODO: REVERT: DEBUG: NOWARN
- f3fbea3 TODO: REVERT: DEBUGGING
- 0e25976 TODO: REVERT: skip tests for now
- e9e5d50 docker: STIR_DISABLE_HDF5=ON
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Kris Thielemans
@KrisThielemans commented on this pull request.
> @@ -139,7 +140,7 @@ set(DEFAULT_parallelproj_TAG v1.10.2) ## STIR set(STIR_REQUIRED_VERSION "6.3.0") set(DEFAULT_STIR_URL https://github.com/UCL/STIR) -set(DEFAULT_STIR_TAG rel_6.3.0) +set(DEFAULT_STIR_TAG "0e667f713967f45f76cbb906805e3058e9e09f20") # 2024-11-12⬇️ Suggested change
-set(DEFAULT_STIR_TAG "0e667f713967f45f76cbb906805e3058e9e09f20") # 2024-11-12 +set(DEFAULT_STIR_TAG "ec3a5670f9b63cb10f4bebce6edf22d6f028a6fb") # 2024-11-28
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- 8a62b7b use STIR of 28Nove2025
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Kris Thielemans
@KrisThielemans commented on this pull request.
In .github/workflows/docker.yml:
> @@ -88,7 +88,7 @@ jobs:
name: build
run: |
# rebuild sirf image
- ./docker/compose.sh -bR${{ matrix.type == 'gpu' && 'g' || 'c' }} -- --build-arg BUILD_CIL=ON
+ ./docker/compose.sh -bR${{ matrix.type == 'gpu' && 'g' || 'c' }} -- --build-arg STIR_DISABLE_HDF5=ON
⬇️ Suggested change
- ./docker/compose.sh -bR${{ matrix.type == 'gpu' && 'g' || 'c' }} -- --build-arg STIR_DISABLE_HDF5=ON
+ ./docker/compose.sh -bR${{ matrix.type == 'gpu' && 'g' || 'c' }} -- --build-arg BUILD_CIL=ON
In .github/workflows/docker.yml:
> @@ -172,7 +172,7 @@ jobs:
name: build
run: |
# rebuild sirf image
- ./docker/compose.sh -dbR${{ matrix.type == 'gpu' && 'g' || 'c' }}
+ ./docker/compose.sh -dbR${{ matrix.type == 'gpu' && 'g' || 'c' }} -- --build-arg STIR_DISABLE_HDF5=ON
⬇️ Suggested change
- ./docker/compose.sh -dbR${{ matrix.type == 'gpu' && 'g' || 'c' }} -- --build-arg STIR_DISABLE_HDF5=ON
+ ./docker/compose.sh -dbR${{ matrix.type == 'gpu' && 'g' || 'c' }}
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- 47fd955 atte,pt to re-enable STIR HDF5
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Still failing to link HDF5.
I see https://github.com/SyneRBI/SIRF-SuperBuild/actions/runs/19774393591/job/56664507472#step:9:27016
- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
that's weird though, as we have hdf5-helpers, see here
@casperdcl can you get access to the https://cmake.org/cmake/help/latest/manual/cmake-configure-log.7.html on your docker build?
TBH, I can't see anything immediatelly wrong with what CMake then found, but as I'm desperate...
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)ok. I think I've found it.
For whatever reason, h5cc doesn't work in the docker image (and there's no hdf5-config). That means CMake has to make guesses. In particular, H5_BUILT_AS_DYNAMIC_LIB is probably not set, as HDF5_DEFINITIONS is listed as empty. As we're using the .so, we are missing the definition H5CPP_DLL, that is used for pretty much all HDF5 C++ classes, e.g. here and required to make the definitions visible.
So, work-around: define H5_BUILT_AS_DYNAMIC_LIB somehow everywhere. Better solution: figure out why h5cc doesn't work.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Comment on h5cc not working is at #946 (comment) and refers to #935 (comment). Those say however that this is because there's a h5cc from conda (with system gcc), which I'm not sure is currently the case.
If the cmake configure log is too hard, the following should tell us
cat <<EOF > cmake_hdf5_test.cpp
#include <H5Cpp.h>
int main() { return 0; }
EOF
h5c++ cmake_hdf5_test.cpp
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Obviously, the fact that h5cc doesn't work also explains why we need the curl work-around. I forgot...
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)So, we have https://github.com/SyneRBI/SIRF-SuperBuild/blob/47fd955c42f9c247825eb33d1e3a61dbefb01815/docker/requirements.yml#L39
This installs h5cc and h5c++ but they don't work, as we don't install cxx-compiler.
Obviously, we've gone round this loop about 50 times by now.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)I've fine-tuned the conda installation and put it all in a script. This works on the tomography server. See the wiki page.
The message for this PR is: using cxx-compiler=1.5.2 (i.e. g++ 11) and -DGadgetron_TAG=avoid_test_compilation_error -DGadgetron_URL=https://github.com/SyneRBI/gadgetron.git -DISMRMRD_TAG=v1.14.3 does the trick.
As we're using conda for various installs including h5py already for the docker image, there seems little point in not going further. In fact, it feels safer, as we'll always use the same HDF5 version. We could therefore do this all this, and probably skip running build_system-ubuntu.sh and build_gadgetron-ubuntu.sh.
If this is a step too far, I suggest we just install cxx-compiler=1.5.2 and update version_config.cmake. It should pick up the conda hdf5 then anyway.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Note that this doesn't need STIR master. 6.3.0 is fine
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)I believe there's a bug in FindHDF5, which should have set H5_BUILT_AS_DYNAMIC_LIB https://gitlab.kitware.com/cmake/cmake/-/issues/27431
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- baa0644 CMake USE_SYSTEM_HDF5 shared library work-around
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Kris Thielemans
@KrisThielemans commented on this pull request.
In SuperBuild/External_ISMRMRD.cmake:
> @@ -58,10 +58,18 @@ if(NOT ( DEFINED "USE_SYSTEM_${externalProjName}" AND "${USE_SYSTEM_${externalPr
endif()
endif ()
+ if (${${proj}_TAG} STREQUAL "v1.13.7")
we'll have to check for Linux , as this will likely break windows or even MacOS builds
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Kris Thielemans
@KrisThielemans pushed 1 commit.
- c08a5f3 CMake USE_SYSTEM_HDF5 shared library work-around
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)HDF5_definitions is set, but not sure if it's used. In any case, still failing, but I can't see why as
[output clipped, log limit 2MiB reached]
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- e0ac229 docker: STIR_DISABLE_HDF5=ON
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Casper da Costa-Luis
@casperdcl commented on this pull request.
> @@ -139,7 +140,7 @@ set(DEFAULT_parallelproj_TAG v1.10.2) ## STIR set(STIR_REQUIRED_VERSION "6.3.0") set(DEFAULT_STIR_URL https://github.com/UCL/STIR) -set(DEFAULT_STIR_TAG rel_6.3.0) +set(DEFAULT_STIR_TAG "0e667f713967f45f76cbb906805e3058e9e09f20") # 2024-11-12⬇️ Suggested change
-set(DEFAULT_STIR_TAG "0e667f713967f45f76cbb906805e3058e9e09f20") # 2024-11-12 +set(DEFAULT_STIR_TAG rel_6.3.0)
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Casper da Costa-Luis
@casperdcl pushed 13 commits.
- 40eee6f fix conda hdf5: use cxx-compiler, boost, fftw3
- d35e3d8 HDF5 link CURL
- 5cb9f71 fix siemens_to_ismrmrd build
- fbd2d3a cil: numpy>=2
- 90fa00b pip install cil
- 772a5e2 fix parallelproj openmp linking
- 01972f9 drop astra GPU
- 123c2e3 self-hosted conda channel for speed & reliability
- a0e77a6 build boost, use system fftw3
- 40d2cc3 revert boost to 1.85
- b45d766 minor CIL & Exercises fixes
- 15f5c7e fix missing packages
- 72f0244 docker: STIR_DISABLE_HDF5=ON
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- b33b196 unify CIL tests
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Casper da Costa-Luis
@casperdcl pushed 2 commits.
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Casper da Costa-Luis
@casperdcl pushed 14 commits.
- 1dd8866 HDF5 link CURL
- 8a10f4e fix siemens_to_ismrmrd build
- 18084ab cil: numpy>=2
- 42d4472 pip install cil
- 6055df8 fix parallelproj openmp linking
- 68b2b92 drop astra GPU
- c276adb self-hosted conda channel for speed & reliability
- 8850620 build boost, use system fftw3
- 31598a9 revert boost to 1.85
- 1125702 minor CIL & Exercises fixes
- 717d6c2 fix missing packages
- c887e98 docker: STIR_DISABLE_HDF5=ON
- 3f862c1 unify CIL tests
- df59c4c separate build & test
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Casper da Costa-Luis
@casperdcl pushed 1 commit.
- a5eb327 separate build & test
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Casper da Costa-Luis
Merged #946 into master.
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Kris Thielemans
KrisThielemans left a comment (SyneRBI/SIRF-SuperBuild#946)Great! Thanks a lot
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