Your message dated Thu, 29 Sep 2022 11:53:06 +0000 with message-id <e1ods6e-00evgx...@fasolo.debian.org> and subject line Bug#995224: fixed in relion 3.1.3-2 has caused the Debian Bug report #995224, regarding relion-cuda: FTBFS with cub 1.14 to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 995224: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=995224 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: relion-cuda Version: 3.1.0-2 Severity: serious Tags: ftbfs sid bookworm Justification: fails to build from source Hi, relion-cuda FTBFS with cub 1.14 which was just uploaded to unstable: make[4]: Entering directory '/build/relion-cuda-3.1.0/build' [ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o cd /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -E make_directory /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/. cd /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D build_configuration:STRING=Release -D generated_file:STRING=/build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o -D generated_cubin_file:STRING=/build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o.cubin.txt -P /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.Release.cmake -- Removing /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o /usr/bin/cmake -E rm -f /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o -- Generating dependency file: /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.NVCC-depend /usr/bin/nvcc -M -D__CUDACC__ /build/relion-cuda-3.1.0/src/acc/cuda/cuda_projector_plan.cu -o /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o.NVCC-depend -ccbin /usr/bin/cc -m64 -DINSTALL_LIBRARY_DIR=/usr/lib/ -DSOURCE_DIR=/build/relion-cuda-3.1.0/src/ -DACC_CUDA=2 -DACC_CPU=1 -DCUDA -DALLOW_CTF_IN_SGD -DHAVE_SINCOS -DHAVE_TIFF -Xcompiler ,\"-g\",\"-O2\",\"-ffile-prefix-map=/build/relion-cuda-3.1.0=.\",\"-fstack-protector-strong\",\"-Wformat\",\"-Werror=format-security\",\"-O3\",\"-DNDEBUG\" -arch=sm_35 -D__INTEL_COMPILER --default-stream per-thread --disable-warnings -DNVCC -I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/relion-cuda-3.1.0 -I/usr/lib/fltk -I/usr/include/x86_64-linux-gnu nvcc warning : The 'compute_35', 'compute_37', 'compute_50', 'sm_35', 'sm_37' and 'sm_50' architectures are deprecated, and may be removed in a future release (Use -Wno-deprecated-gpu-targets to suppress warning). In file included from /usr/include/thrust/system/cuda/config.h:33, from /usr/include/thrust/system/cuda/detail/execution_policy.h:35, from /usr/include/thrust/iterator/detail/device_system_tag.h:23, from /usr/include/thrust/iterator/detail/iterator_facade_category.h:22, from /usr/include/thrust/iterator/iterator_facade.h:37, from /build/relion-cuda-3.1.0/src/acc/cuda/cub/device/../iterator/arg_index_input_iterator.cuh:48, from /build/relion-cuda-3.1.0/src/acc/cuda/cub/device/device_reduce.cuh:41, from /build/relion-cuda-3.1.0/src/acc/cuda/cuda_utils_cub.cuh:16, from /build/relion-cuda-3.1.0/src/acc/cuda/cuda_projector_plan.cu:10: /usr/include/cub/util_namespace.cuh:46:2: error: #error CUB requires a definition of CUB_NS_QUALIFIER when CUB_NS_PREFIX/POSTFIX are defined. 46 | #error CUB requires a definition of CUB_NS_QUALIFIER when CUB_NS_PREFIX/POSTFIX are defined. | ^~~~~ CMake Error at relion_gpu_util_generated_cuda_projector_plan.cu.o.Release.cmake:220 (message): Error generating /build/relion-cuda-3.1.0/build/src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o make[4]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/build.make:1439: src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o] Error 1 make[4]: Leaving directory '/build/relion-cuda-3.1.0/build' This seems to be the Breaking Change described in https://github.com/NVIDIA/cub/releases/tag/1.14.0: #350: When the CUB_NS_[PRE|POST]FIX macros are set, CUB_NS_QUALIFIER must also be defined to the fully qualified CUB namespace (e.g. #define CUB_NS_QUALIFIER ::foo::cub). Note that this is handled automatically when using the new [THRUST_]CUB_WRAPPED_NAMESPACE mechanism. Andreas
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--- Begin Message ---Source: relion Source-Version: 3.1.3-2 Done: Andreas Beckmann <a...@debian.org> We believe that the bug you reported is fixed in the latest version of relion, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 995...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Beckmann <a...@debian.org> (supplier of updated relion package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 29 Sep 2022 13:27:08 +0200 Source: relion Architecture: source Version: 3.1.3-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Beckmann <a...@debian.org> Closes: 995224 Changes: relion (3.1.3-2) unstable; urgency=medium . [ Andreas Beckmann ] * Team upload. * Cherry-pick upstream fixes related to cub. (Closes: #995224) * Simplify debian/rules. * Fix missing hardening flags. * Build for Architecture: any. * Standards-Version: 4.6.1. * Fix some typos found by Lintian. . [ Andreas Tille ] * Enable uscan to create a sensible download name Checksums-Sha1: f546c8e49de452859968b9e4bf6b904d22f7f348 2136 relion_3.1.3-2.dsc 1584abd61543e983d61f29da10fb70d8a1e451e8 11148 relion_3.1.3-2.debian.tar.xz e509d4fa01034893e2311748ebb65a3a0d7d57ba 10279 relion_3.1.3-2_source.buildinfo Checksums-Sha256: c5519e6ea35040cb8e82478991993a405a30940ee349f983ec3bd842962768e9 2136 relion_3.1.3-2.dsc 8d71c4e8f13a42caa2a067cf681a1648b90f02882dd32c11d551c5f30fd567d8 11148 relion_3.1.3-2.debian.tar.xz 1821cd29fbf0ded1886745df06926735304fe4dd92d92bbc4a1751c84dfbfe89 10279 relion_3.1.3-2_source.buildinfo Files: b69285d1394bc2c419fa6baa2c7517d7 2136 science optional relion_3.1.3-2.dsc d04ab7f6bf49905529c227c525473bcd 11148 science optional relion_3.1.3-2.debian.tar.xz 11b9a17e76a486c897bc592ca7907ecb 10279 science optional relion_3.1.3-2_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJEBAEBCAAuFiEE6/MKMKjZxjvaRMaUX7M/k1np7QgFAmM1gZQQHGFuYmVAZGVi aWFuLm9yZwAKCRBfsz+TWentCL6mD/4kiMFN1FrxsvYIdg1/Q//diHtJ5MWg5g+v riMSsE4UVR/pjVTTML57GagnLV1Ojyp+8sWHs4zYgnWVDHWrQIlAKyUX8kbzjeT4 /g0HNLgrwAdVfpr+x520PG25sYz6M8KIsbvcTPujxDsLw9gjNLcusk3VDKfArY1H 7IJJgJn8t1T8fq9rEwud08RjEYMJLxa8U9uThBz8/zvvl14pH/bPPeng8X5NUKE9 RiRKO2FLKBZq1QW9aHEJmSmRkuEjEV2ijrqE0fPjQ8M2MmPnZCHvnxNsQSauQOo9 PzbjUdcPTrx4FDWVeuFHyAK79c8lzNqfwViNHngt44lKfWBVr+LipyXJJXtdChJV sZoKo1lpISppPLPQP4XZYQiAGU7GkixAeO5Qkohb7X8y3no0V3GVhakSxUeTPWem liyrXclAmxtxiKYCGcV0Ov1JLuOLLnq/E2pwzE8+ushYp1RUbOWQ2sZIQ4zhtkDA bCybEPsUKVFBzJ7WCQyy55jy9///hRLX/O6UbOMvcGFTfr5WA19Z/hIFGAlz1Ro7 g5zLRSURtcp8rgjkSJ2lT8j1O1esHsljslL7ypn++NeAJHMQ6D8aFFTLiYQ2sPzK hedMwNepBYUFkoqRMRv/w6Fs4d/8rWz1Hoq2TJEGnCW9x0RroYktl3grcOg/4djg H+N8il7hVA== =3PJ5 -----END PGP SIGNATURE-----
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