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Installation issue: clingo won't build on rhel8 #24450
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bootstrapAnything that has to do with Spack building its own dependencies.Anything that has to do with Spack building its own dependencies.build-error
Description
Trying to use clingo on rhel8 with gcc 8.3 installed through the system package provider.
Steps to reproduce the issue
$ spack find -b
==> Showing internal bootstrap store at "/home/s3j/.spack/bootstrap/store"
==> 15 installed packages
-- linux-rhel8-x86_64 / [email protected] -------------------------------
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
$ spack solve zlib
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/libiconv-1.16-eovfptqgoevl6gbuiiyhftvw37refjqt
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/libsigsegv-2.13-qrt5iqfwmvyau3qd7kriuejxi6nu4p5p
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/berkeley-db-18.1.40-hehtgcsh3q7zgedcegu7hmi2567rgszs
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/pkgconf-1.7.4-nueqgwm4c7it36pvhxs4x4lgcrda56tf
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/zlib-1.2.11-xqjeqtupcfqqqlaw5ehjlfjjly7zoe3b
[+] /projects/spack/opt/spack/gcc-8.3.1/python/nebkli6 (external python-3.8-3h77chnfvzfaatvkl4g6pkhqkt56ghtq)
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/re2c-1.2.1-43fryz3s27sm7qifg6hog7ozl3dvcnt4
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/diffutils-3.7-plskmdavt46a43qpdrddkmnbs7ubjvtt
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/m4-1.4.19-huzbxrt35xu5fr663j6edplbiwdxbyar
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/ncurses-6.2-tpaqywgi3r7p5f63emxcmpb4ysecgr3g
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/readline-8.1-d7jrl65krlltqovoywp7slaxuvwu3cse
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/gdbm-1.19-jwxbrshhi5xffsub35vbjmwxzg5he4vu
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/perl-5.34.0-dt5v7fy5smkbprv6alljhjdqgmbfi3cy
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/bison-3.7.6-xgsrixaol5mfixde6qfmo4lemjvgu3zj
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/openssl-1.1.1k-hey4lyw73kzqdjtpyt5uotiz7rxvziel
[+] /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/cmake-3.20.3-cdl7x2lzwjysfhrhz23abh6pk5g4z5wq
==> Installing clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g
==> No binary for clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g found: installing from source
==> Using cached archive: /projects/spack/var/spack/cache/_source-cache/git//potassco/clingo.git/2a025667090d71b2c9dce60fe924feb6bde8f667.tar.gz
==> Warning: Fetching from mirror without a checksum!
This package is normally checked out from a version control system, but it has been archived on a spack mirror. This means we cannot know a checksum for the tarball in advance. Be sure that your connection to this mirror is secure!
==> Already patched clingo-bootstrap
==> clingo-bootstrap: Executing phase: 'cmake'
==> Error: ProcessError: Command exited with status 1:
'cmake' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:STRING=/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g' '-DCMAKE_BUILD_TYPE:STRING=Release' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF' '-DCMAKE_INSTALL_RPATH:STRING=/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/lib;/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/lib64;/projects/spack/opt/spack/gcc-8.3.1/python/nebkli6/lib' '-DCMAKE_PREFIX_PATH:STRING=/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/bison-3.7.6-xgsrixaol5mfixde6qfmo4lemjvgu3zj;/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/cmake-3.20.3-cdl7x2lzwjysfhrhz23abh6pk5g4z5wq;/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/re2c-1.2.1-43fryz3s27sm7qifg6hog7ozl3dvcnt4;/projects/spack/opt/spack/gcc-8.3.1/python/nebkli6' '-DCLINGO_REQUIRE_PYTHON=ON' '-DCLINGO_BUILD_WITH_PYTHON=ON' '-DPYCLINGO_USER_INSTALL=OFF' '-DPYCLINGO_USE_INSTALL_PREFIX=ON' '-DCLINGO_BUILD_WITH_LUA=OFF' '-DCLINGO_BUILD_PY_SHARED:STRING=OFF' '-DPython_EXECUTABLE:STRING=/projects/spack/opt/spack/gcc-8.3.1/python/nebkli6/bin/python3.8' '-DPython_INCLUDE_DIR:STRING=/projects/spack/opt/spack/gcc-8.3.1/python/nebkli6/include/python3.8' '-DCLINGO_BUILD_APPS:STRING=OFF' '/tmp/s3j/spack-stage/spack-stage-clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/spack-src'
4 errors found in build log:
3 ==> [2021-06-21-12:48:38.693436] 'cmake' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:STRING=/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-
8.3.1/clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g' '-DCMAKE_BUILD_TYPE:STRING=Release' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-D
CMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=OFF' '-DCMAKE_INSTALL_RPATH:STRING=/home/s3j/.spack/bootstrap/store/linux-rh
el8-x86_64/gcc-8.3.1/clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/lib;/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/clingo-
bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/lib64;/projects/spack/opt/spack/gcc-8.3.1/python/nebkli6/lib' '-DCMAKE_PREFIX_PATH:STRING=/home/s3j/.
spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/bison-3.7.6-xgsrixaol5mfixde6qfmo4lemjvgu3zj;/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gc
c-8.3.1/cmake-3.20.3-cdl7x2lzwjysfhrhz23abh6pk5g4z5wq;/home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/re2c-1.2.1-43fryz3s27sm7qifg6hog7o
zl3dvcnt4;/projects/spack/opt/spack/gcc-8.3.1/python/nebkli6' '-DCLINGO_REQUIRE_PYTHON=ON' '-DCLINGO_BUILD_WITH_PYTHON=ON' '-DPYCLINGO_USER_INSTALL=OF
F' '-DPYCLINGO_USE_INSTALL_PREFIX=ON' '-DCLINGO_BUILD_WITH_LUA=OFF' '-DCLINGO_BUILD_PY_SHARED:STRING=OFF' '-DPython_EXECUTABLE:STRING=/projects/spack/
opt/spack/gcc-8.3.1/python/nebkli6/bin/python3.8' '-DPython_INCLUDE_DIR:STRING=/projects/spack/opt/spack/gcc-8.3.1/python/nebkli6/include/python3.8' '
-DCLINGO_BUILD_APPS:STRING=OFF' '/tmp/s3j/spack-stage/spack-stage-clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/spack-src'
4 -- The CXX compiler identification is GNU 8.3.1
5 -- Detecting CXX compiler ABI info
6 -- Detecting CXX compiler ABI info - failed
7 -- Check for working CXX compiler: /projects/spack/lib/spack/env/gcc/g++
8 -- Check for working CXX compiler: /projects/spack/lib/spack/env/gcc/g++ - broken
>> 9 CMake Error at /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/cmake-3.20.3-cdl7x2lzwjysfhrhz23abh6pk5g4z5wq/share/cmake-3.20/Modules/CM
akeTestCXXCompiler.cmake:59 (message):
10 The C++ compiler
11
12 "/projects/spack/lib/spack/env/gcc/g++"
13
14 is not able to compile a simple test program.
15
...
21 gmake[1]: Entering directory '/tmp/s3j/spack-stage/spack-stage-clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/spack-build-e7xfph2/CMakeFi
les/CMakeTmp'
22 Building CXX object CMakeFiles/cmTC_096bc.dir/testCXXCompiler.cxx.o
23 /projects/spack/lib/spack/env/gcc/g++ -static-libstdc++ -static-libgcc -Wl,--exclude-libs,ALL -o CMakeFiles/cmTC_096bc.dir/testCXXCompiler.cxx.
o -c /tmp/s3j/spack-stage/spack-stage-clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/spack-build-e7xfph2/CMakeFiles/CMakeTmp/testCXXCompiler.
cxx
24 Linking CXX executable cmTC_096bc
25 /home/s3j/.spack/bootstrap/store/linux-rhel8-x86_64/gcc-8.3.1/cmake-3.20.3-cdl7x2lzwjysfhrhz23abh6pk5g4z5wq/bin/cmake -E cmake_link_script CMakeFi
les/cmTC_096bc.dir/link.txt --verbose=1
26 /projects/spack/lib/spack/env/gcc/g++ -static-libstdc++ -static-libgcc -Wl,--exclude-libs,ALL -static-libstdc++ -static-libgcc -Wl,--exclude-libs
,ALL -rdynamic CMakeFiles/cmTC_096bc.dir/testCXXCompiler.cxx.o -o cmTC_096bc
>> 27 /usr/bin/ld: cannot find -lstdc++
>> 28 collect2: error: ld returned 1 exit status
>> 29 gmake[1]: *** [CMakeFiles/cmTC_096bc.dir/build.make:99: cmTC_096bc] Error 1
30 gmake[1]: Leaving directory '/tmp/s3j/spack-stage/spack-stage-clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/spack-build-e7xfph2/CMakeFil
es/CMakeTmp'
31 gmake: *** [Makefile:127: cmTC_096bc/fast] Error 2
32
33
34
35
See build log for details:
/tmp/s3j/spack-stage/spack-stage-clingo-bootstrap-spack-e7xfph2po6helmzwem56dkslzlxgzb2g/spack-build-out.txtInformation on your system
- Spack: 0.16.2-3213-7b6ca59038
- Python: 3.8.5
- Platform: linux-rhel8-haswell
- Concretizer: clingo
Additional information
I tried the solution from #22720 , but found the same error as in #24417
$ spack find -b
==> Showing internal bootstrap store at "/home/s3j/.spack/bootstrap/store"
==> 15 installed packages
-- linux-rhel8-x86_64 / [email protected] -------------------------------
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
$ spack -d solve zlib
==> [2021-06-21-12:55:42.947580] Imported solve from built-in commands
==> [2021-06-21-12:55:42.948825] Imported solve from built-in commands
==> [2021-06-21-12:55:42.952282] Reading config file /projects/spack/etc/spack/defaults/config.yaml
==> [2021-06-21-12:55:42.979847] Reading config file /projects/spack/etc/spack/config.yaml
==> [2021-06-21-12:55:42.983750] DATABASE LOCK TIMEOUT: 3s
==> [2021-06-21-12:55:42.983836] PACKAGE LOCK TIMEOUT: No timeout
==> [2021-06-21-12:55:42.984407] DATABASE LOCK TIMEOUT: 3s
==> [2021-06-21-12:55:42.984488] PACKAGE LOCK TIMEOUT: No timeout
==> [2021-06-21-12:55:42.984602] [BOOTSTRAP CONFIG SCOPE] name=_builtin
==> [2021-06-21-12:55:42.985087] [BOOTSTRAP CONFIG SCOPE] name=defaults, path=/projects/spack/etc/spack/defaults
==> [2021-06-21-12:55:42.985167] [BOOTSTRAP CONFIG SCOPE] name=defaults/linux, path=/projects/spack/etc/spack/defaults/linux
==> [2021-06-21-12:55:42.985245] [BOOTSTRAP CONFIG SCOPE] name=system, path=/etc/spack
==> [2021-06-21-12:55:42.985307] [BOOTSTRAP CONFIG SCOPE] name=system/linux, path=/etc/spack/linux
==> [2021-06-21-12:55:42.985376] [BOOTSTRAP CONFIG SCOPE] name=site, path=/projects/spack/etc/spack
==> [2021-06-21-12:55:42.985434] [BOOTSTRAP CONFIG SCOPE] name=site/linux, path=/projects/spack/etc/spack/linux
==> [2021-06-21-12:55:42.985501] [BOOTSTRAP CONFIG SCOPE] name=user, path=/home/s3j/.spack
==> [2021-06-21-12:55:42.985559] [BOOTSTRAP CONFIG SCOPE] name=user/linux, path=/home/s3j/.spack/linux
==> [2021-06-21-12:55:42.990699] [BOOTSTRAP ROOT SPEC] clingo: clingo-bootstrap@spack+python %gcc target=x86_64
==> [2021-06-21-12:55:42.990788] [BOOTSTRAP MODULE clingo] Try importing from Python
==> [2021-06-21-12:55:42.991149] [BOOTSTRAP MODULE clingo] Try installed specs with query 'clingo-bootstrap@spack+python %gcc target=x86_64 ^[email protected] '
==> [2021-06-21-12:55:43.067358] Imported buildcache from built-in commands
==> [2021-06-21-12:55:43.072523] Imported buildcache from built-in commands
==> [2021-06-21-12:55:43.081336] [BOOTSTRAP MODULE clingo] Try installing 'clingo-bootstrap@spack%gcc+python arch=linux-None-x86_64 ^[email protected]' from binary cache
==> [2021-06-21-12:57:02.819228] FileNotFoundError: [Errno 2] No such file or directory: '/home/s3j/.spack/bootstrap/store/linux-rhel5-x86_64/gcc-9.3.0/clingo-bootstrap-spack-kt74l7kjzrlp3cgtj2576o33mhsrgyrw'
==> [2021-06-21-12:57:02.824619] Error: 'overrides-1'
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bootstrapAnything that has to do with Spack building its own dependencies.Anything that has to do with Spack building its own dependencies.build-error