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Installation issue: clingo won't build on rhel8 #24450

@sethrj

Description

@sethrj

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.txt

Information on your system

  • Spack: 0.16.2-3213-7b6ca59038
  • Python: 3.8.5
  • Platform: linux-rhel8-haswell
  • Concretizer: clingo

Additional information

@alalazo

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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