Your message dated Thu, 29 Sep 2022 15:09:04 +0000 with message-id <[email protected]> and subject line Bug#995224: fixed in relion-cuda 3.1.3-1 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 [email protected] immediately.) -- 995224: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=995224 Debian Bug Tracking System Contact [email protected] 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-cuda Source-Version: 3.1.3-1 Done: Andreas Beckmann <[email protected]> We believe that the bug you reported is fixed in the latest version of relion-cuda, 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 [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Beckmann <[email protected]> (supplier of updated relion-cuda 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 [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 29 Sep 2022 14:56:00 +0200 Source: relion-cuda Binary: relion-cuda relion-cuda-dbgsym relion-gui-cuda relion-gui-cuda-dbgsym Architecture: source amd64 Version: 3.1.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Beckmann <[email protected]> Description: relion-cuda - parallel toolkit for 3D reconstructions in cryo-electron microsco relion-gui-cuda - toolkit for 3D reconstructions in cryo-electron microscopy (gui a Closes: 995224 Changes: relion-cuda (3.1.3-1) unstable; urgency=medium . * Team upload. * New upstream version. * Build using cuda-gcc. . 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 . relion (3.1.3-1) unstable; urgency=medium . * Fix watchfile to detect new versions on github * New upstream version * Standards-Version: 4.6.0 (routine-update) * Update renamed lintian tag names in lintian overrides. * Mark autopkgtest superficial . relion (3.1.0-4) unstable; urgency=medium . * Drop useless get-orig-source target (routine-update) * Remove trailing whitespace in debian/changelog (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Trim trailing whitespace. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Build-Depends: fluid Checksums-Sha1: 7b3728ef9960bf4cb89e351b1da7464cadcc49d7 2197 relion-cuda_3.1.3-1.dsc c6ca397db6c711f87305bd803f672345f7487bae 2345487 relion-cuda_3.1.3.orig.tar.gz 1299d7eafefba5149b8c8f01581787b428ef9f84 12128 relion-cuda_3.1.3-1.debian.tar.xz 2c530b9101cb47f764e25bc00a1ecc40ffe3f96e 727155464 relion-cuda-dbgsym_3.1.3-1_amd64.deb be99a4f5e8e05a3f09696f83f557a97242537138 13568 relion-cuda_3.1.3-1_amd64.buildinfo 9b49d34887741c8f50e87b2af642e9e8778462a6 80185276 relion-cuda_3.1.3-1_amd64.deb 4144e8cbc52d1045c24833ef96b81eddca65a41e 52254104 relion-gui-cuda-dbgsym_3.1.3-1_amd64.deb 2c6e420dae61100cd7f3e78b7f1172f5eb43170f 5778664 relion-gui-cuda_3.1.3-1_amd64.deb Checksums-Sha256: 623ec7a43d938cc0f511a296b66f03d30b708ce28d79fcb5b7d2687f85d1aaaf 2197 relion-cuda_3.1.3-1.dsc f10934058e0670807b7004899d7b5103c21ad77841219352c66a33f98586d42e 2345487 relion-cuda_3.1.3.orig.tar.gz 0bac55b40f202b25042f005235765c9992ac53a7a10582a6147cf7067f9c9dbf 12128 relion-cuda_3.1.3-1.debian.tar.xz b0523534621ff1ce928fd03f6ed725c0d98e8e2b83bcf0df1d728f2240506dc1 727155464 relion-cuda-dbgsym_3.1.3-1_amd64.deb 3319bfc24ec27340095f960e46b45e2c7a2af309e15575c8ccfa216aa84eefd6 13568 relion-cuda_3.1.3-1_amd64.buildinfo 0366d392096925c5aff14ef65818537cf3b9f6df84129c854043b1f47decab72 80185276 relion-cuda_3.1.3-1_amd64.deb 776b25888df088738d4402218b2234e0ac053fe7e51d4c9120b472048bc23d43 52254104 relion-gui-cuda-dbgsym_3.1.3-1_amd64.deb a4d809d5c5b185810e871a94ab7feb218d61bce3b93ef1d947b9f08f5daf8765 5778664 relion-gui-cuda_3.1.3-1_amd64.deb Files: 5cf6ebf4eddd0feffc0e1cf0ab700e57 2197 contrib/science optional relion-cuda_3.1.3-1.dsc 5ddaf9afe51d743c5f58f625d9fd1cb7 2345487 contrib/science optional relion-cuda_3.1.3.orig.tar.gz 66f2f466d18b1162b5872bf7460be574 12128 contrib/science optional relion-cuda_3.1.3-1.debian.tar.xz 4cf20e508ab1b54f0a7c93451b332ef6 727155464 contrib/debug optional relion-cuda-dbgsym_3.1.3-1_amd64.deb 4059baeeb7b9b01cb7677cc1ccabf2a6 13568 contrib/science optional relion-cuda_3.1.3-1_amd64.buildinfo e21bb713f0e181645f1553f9f498bbe7 80185276 contrib/science optional relion-cuda_3.1.3-1_amd64.deb 454b3b386ca58e344d5d03e8842dc9d1 52254104 contrib/debug optional relion-gui-cuda-dbgsym_3.1.3-1_amd64.deb 103d46c3bba9edadd7f844530e91dff1 5778664 contrib/science optional relion-gui-cuda_3.1.3-1_amd64.deb -----BEGIN PGP SIGNATURE----- iQJEBAEBCAAuFiEE6/MKMKjZxjvaRMaUX7M/k1np7QgFAmM1oc8QHGFuYmVAZGVi aWFuLm9yZwAKCRBfsz+TWentCEjSD/4oUNbWlnbitOg/r5M+WIJV64j1f/VA6UiJ zU9nCkVe9rK4A9K6zUCbO79Wq4IlCc3G/f4ePBsJ/IP1lzGZbfAevRVDpEQOPgC5 ApN7FpULswBxHnWppANePiL5N2lYzsrcmd5LZhks02U9iyvCSlbSV3SDsMP5rHFM w1Z/SO30TM9ovitdrpgOP3fa6GSJvT0HaGF5sIG8wCmyDW6pLRO5Op9XlFfzbnr9 XlOxPNsXvktuRTy+lmZY1x4Kj6oRxwpX2xmIKQLssSR9cQ5Qrs1kcDhGIwLEt+HI ysZoY7uPsbXb/+5b3wMWo8lQtb8c+SEwR/TYjeREQYbKc3wnU2jEXlbFCl/x+14y BudCg4kPEFZ9mtwe+CyLHQtf61JfAM6nKz/Rtv6e7QxUKI931Oqrpfsj4JESxWRI Luj+EhAGOGEDbAT28LT593F5p7/5Dc1qfa0iD4qDTOgRBMCXMEBmG/Jk6tnJjFw/ BmsJpgX2wMNpXIYehdZWStOcmNjT/nOKiDMRwXo+yQOQfEZpHF7bC5bbsMoQxD67 QC1dMixL7xXbeGeVO7xeRtcm96O8+IL0jXhKrsYHLQ3RM0yHMCv3mDPXZmnDUcpm fPXIaiRFo+AFEjTXA4STMkaCRIi1vpE0ALWK1pRUN6xgByPI6v4tegd12AFnvp+G stNSP4rYLA== =i3ZB -----END PGP SIGNATURE-----
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