Opened 2 years ago
Last modified 4 weeks ago
#31088 new defect
GH Actions: WSL workflow fails with failed syscalls
Reported by: | mkoeppe | Owned by: | |
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Priority: | critical | Milestone: | sage-9.9 |
Component: | porting | Keywords: | |
Cc: | gh-tobiasdiez | Merged in: | |
Authors: | Reviewers: | ||
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | Stopgaps: |
Description (last modified by )
Also reported in https://groups.google.com/g/sage-devel/c/jE6qf0MqriQ/m/cdsEC8SkAgAJ
To fix this, we should probably follow the guidance added in #32714, putting as much of the build in the Linux filesystem.
Change History (17)
comment:1 Changed 2 years ago by
comment:3 Changed 2 years ago by
Thanks for letting us know, and thanks for all your work in the past months.
comment:4 Changed 22 months ago by
Milestone: | sage-9.3 → sage-9.4 |
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comment:5 Changed 19 months ago by
Milestone: | sage-9.4 → sage-9.5 |
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comment:6 Changed 16 months ago by
It now fails during the installation of flint
Attempting to download package flint-2.7.1.tar.gz from mirrors Downloading the Sage mirror list Searching fastest mirror 295ms: http://ftp.leg.uct.ac.za/pub/packages/sage/ 578ms: http://ftp.ntua.gr/pub/sagemath/ 180ms: http://ftp.rediris.es/mirror/sagemath/ 200ms: http://ftp.riken.jp/sagemath/ 327ms: http://ftp.sun.ac.za/ftp/pub/mirrors/www.sagemath.org/ 420ms: http://ftp.yz.yamagata-u.ac.jp/pub/math/sage/ 376ms: http://linorg.usp.br/sage/ 479ms: http://mirror.aarnet.edu.au/pub/sage/ 942ms: http://mirror.ufs.ac.za/sagemath/ 346ms: http://mirror.yandex.ru/mirrors/sage.math.washington.edu/ 80ms: http://mirrors.mit.edu/sage/ 395ms: http://mirrors.tuna.tsinghua.edu.cn/sagemath/ 621ms: http://mirrors.ustc.edu.cn/sagemath/ 26ms: http://mirrors.xmission.com/sage/ 697ms: http://sage.mirror.garr.it/mirrors/sage/ 784ms: http://sagemath.c3sl.ufpr.br/ 600ms: http://sagemath.mirror.ac.za/ 589ms: http://www-ftp.lip6.fr/pub/math/sagemath/ 430ms: http://www.mirrorservice.org/sites/www.sagemath.org/ 357ms: https://mirror-hk.koddos.net/sagemath/ 124ms: https://mirror.csclub.uwaterloo.ca/sage/ 491ms: https://mirror.dogado.de/sage/ WARNING [mirror_list|_rank_mirrors:136]: [Errno 111] Connection refused: https://mirror.koddos.net/sagemath/ 227ms: https://mirror.lyrahosting.com/sagemath/ 797ms: https://mirror.marwan.ma/sage/ 51ms: https://mirror.rcg.sfu.ca/mirror/sage/ WARNING [mirror_list|_rank_mirrors:136]: [Errno 111] Connection refused: https://mirrors.nju.edu.cn/sagemath/ 641ms: https://mirrors.up.pt/pub/sage/ Fastest mirror: http://mirrors.xmission.com/sage/ http://mirrors.xmission.com/sage/spkg/upstream/flint/flint-2.7.1.tar.gz [......................................................................] flint-2.7.1 ==================================================== Setting up build directory for flint-2.7.1 Finished extraction No patch files found in ../patches **************************************************** Host system: Linux fv-az159-516 4.4.0-17763-Microsoft #2183-Microsoft Sat Sep 11 15:52:00 PST 2021 x86_64 x86_64 x86_64 GNU/Linux **************************************************** C compiler: gcc C compiler version: Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Ubuntu 9.3.0-17ubuntu1~20.04' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-HskZEa/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu Thread model: posix gcc version 9.3.0 (Ubuntu 9.3.0-17ubuntu1~20.04) **************************************************** Package 'flint' is currently not installed No legacy uninstaller found for 'flint'; nothing to do Configuring FLINT. Configuring...x86_64-Linux Testing __builtin_popcountl...yes Testing native popcount...yes Testing __thread...yes Testing fenv...yes Testing cpu_set_t...yes FLINT was successfully configured. Building flint-2.7.1 make AT= QUIET_CC= QUIET_CXX= QUIET_AR= sed "s/ /,/g;s/.*/&,/g" qadic/CPimport.txt > build/CPimport.h if [ "1" -eq "1" ]; then \ make shared; \ fi gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c printf.c -o build/printf.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c fprintf.c -o build/fprintf.lo; In file included from /usr/include/stdio.h:39, from fprintf.c:13: /usr/include/x86_64-linux-gnu/bits/types/__fpos_t.h:5:10: fatal error: /mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include/bits/types/__mbstate_t.h: Invalid argument 5 | #include <bits/types/__mbstate_t.h> | ^~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. make[7]: *** [Makefile:265: build/fprintf.lo] Error 1 gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c sprintf.c -o build/sprintf.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c scanf.c -o build/scanf.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c fscanf.c -o build/fscanf.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c sscanf.c -o build/sscanf.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c clz_tab.c -o build/clz_tab.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c memory_manager.c -o build/memory_manager.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c version.c -o build/version.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c profiler.c -o build/profiler.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c thread_support.c -o build/thread_support.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c exception.c -o build/exception.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c hashmap.c -o build/hashmap.lo; gcc -fPIC -O2 -g -march=native -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1/src/build -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -I/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/include -c inlines.c -o build/inlines.lo; mkdir -p build/interfaces make[7]: Target 'shared' not remade because of errors. make[6]: *** [Makefile:176: library] Error 2 make[6]: Target 'all' not remade because of errors. make[5]: *** [Makefile:103: verbose] Error 2 ******************************************************************************** Error building flint-2.7.1 ******************************************************************************** real 0m4.011s user 0m1.594s sys 0m2.219s ************************************************************************ Error installing package flint-2.7.1 ************************************************************************ Please email sage-devel (http://groups.google.com/group/sage-devel) explaining the problem and including the log files /mnt/d/a/sage/sage/logs/pkgs/flint-2.7.1.log and /mnt/d/a/sage/sage/config.log Describe your computer, operating system, etc. If you want to try to fix the problem yourself, *don't* just cd to /mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1 and type 'make' or whatever is appropriate. Instead, the following commands setup all environment variables correctly and load a subshell for you to debug the error: (cd '/mnt/d/a/sage/sage/.tox/local-sudo-ubuntu-standard/local/var/tmp/sage/build/flint-2.7.1' && '/mnt/d/a/sage/sage/sage' --buildsh) When you are done debugging, you can type "exit" to leave the subshell. ************************************************************************
Seems to be a version mismatch between flint and bits. I cannot reproduce it locally.
comment:7 Changed 16 months ago by
Looks to me like a failed system call when accessing this header file. Is this appearing in more than one run?
comment:8 Changed 16 months ago by
Yes, flint fails since 9.4.beta6 see https://github.com/sagemath/sage/actions/workflows/ci-wsl.yml
comment:10 Changed 16 months ago by
WSL 1 is the only supported version (WSL 2 would require a self-hosted runner).
comment:11 Changed 13 months ago by
Description: | modified (diff) |
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Summary: | GH Actions: WSL workflow: No space left on device → GH Actions: WSL workflow fails with failed syscalls |
comment:13 Changed 12 months ago by
Description: | modified (diff) |
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comment:14 Changed 12 months ago by
Priority: | major → critical |
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This ticket needs some care so that we can update our instructions for WSL to something that actually works.
comment:15 Changed 9 months ago by
Milestone: | sage-9.6 → sage-9.7 |
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comment:16 Changed 5 months ago by
Milestone: | sage-9.7 → sage-9.8 |
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comment:17 Changed 4 weeks ago by
Milestone: | sage-9.8 → sage-9.9 |
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Tobias, when you have a chance, could you try to fix up the WSL workflow please? It's been failing consistently for months now