Your message dated Thu, 29 Sep 2022 15:09:04 +0000
with message-id <e1odv9s-00flxb...@fasolo.debian.org>
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 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
--- End Message ---
--- Begin Message ---
Source: relion-cuda
Source-Version: 3.1.3-1
Done: Andreas Beckmann <a...@debian.org>
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 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-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 ftpmas...@ftp-master.debian.org)
-----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
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Beckmann <a...@debian.org>
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
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