spack install failed with bootstrapping
卫焕
首次使用spack时报错，
[tools_adm@computing-host-001 ~]$ spack install python
==> Bootstrapping clingo from pre-built binaries
==> Bootstrapping clingo from sources
==> Error: cannot bootstrap the "clingo" Python module from spec "clingo-bootstrap@spack+python %gcc target=x86_64" due to the following failures:
'spack-install' raised ConflictsInSpecError: Conflicts in concretized spec "clingo-bootstrap@spack%gcc@4.8.5~docs~ipo+python~static_libstdcpp build_type=Release arch=linux-centos7-x86_64/6hb2rkn"
List of matching conflicts for spec:
clingo-bootstrap@spack%gcc@4.8.5~docs~ipo+python~static_libstdcpp build_type=Release arch=linux-centos7-x86_64
^bison@3.8.2%gcc@4.8.5 arch=linux-centos7-x86_64
^diffutils@3.8%gcc@4.8.5 arch=linux-centos7-x86_64
^libiconv@1.16%gcc@4.8.5 libs=shared,static arch=linux-centos7-x86_64
^m4@1.4.19%gcc@4.8.5+sigsegv patches=9dc5fbd0d5cb1037ab1e6d0ecc74a30df218d0a94bdd5a02759a97f62daca573,bfdffa7c2eb01021d5849b36972c069693654ad826c1a20b53534009a4ec7a89 arch=linux-centos7-x86_64
^libsigsegv@2.13%gcc@4.8.5 arch=linux-centos7-x86_64
^perl@5.34.0%gcc@4.8.5+cpanm+shared+threads arch=linux-centos7-x86_64
^berkeley-db@18.1.40%gcc@4.8.5+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-centos7-x86_64
^bzip2@1.0.8%gcc@4.8.5~debug~pic+shared arch=linux-centos7-x86_64
^gdbm@1.19%gcc@4.8.5 arch=linux-centos7-x86_64
^readline@8.1%gcc@4.8.5 arch=linux-centos7-x86_64
^ncurses@6.2%gcc@4.8.5~symlinks+termlib abi=none arch=linux-centos7-x86_64
^pkgconf@1.8.0%gcc@4.8.5 arch=linux-centos7-x86_64
^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64
^cmake@3.21.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-centos7-x86_64
^openssl@1.1.1l%gcc@4.8.5~docs certs=system arch=linux-centos7-x86_64
^python@3.6%gcc@4.8.5+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib arch=linux-centos7-x86_64
^re2c@2.2%gcc@4.8.5 arch=linux-centos7-x86_64
1. "%gcc@:5" conflicts with "clingo-bootstrap" [C++14 support is required to bootstrap clingo]
Please run `spack -d spec zlib` for more verbose error messages
[tools_adm@computing-host-001 ~]$ spack install python
==> Bootstrapping clingo from pre-built binaries
==> Bootstrapping clingo from sources
==> Error: cannot bootstrap the "clingo" Python module from spec "clingo-bootstrap@spack+python %gcc target=x86_64" due to the following failures:
'spack-install' raised ConflictsInSpecError: Conflicts in concretized spec "clingo-bootstrap@spack%gcc@4.8.5~docs~ipo+python~static_libstdcpp build_type=Release arch=linux-centos7-x86_64/6hb2rkn"
List of matching conflicts for spec:
clingo-bootstrap@spack%gcc@4.8.5~docs~ipo+python~static_libstdcpp build_type=Release arch=linux-centos7-x86_64
^bison@3.8.2%gcc@4.8.5 arch=linux-centos7-x86_64
^diffutils@3.8%gcc@4.8.5 arch=linux-centos7-x86_64
^libiconv@1.16%gcc@4.8.5 libs=shared,static arch=linux-centos7-x86_64
^m4@1.4.19%gcc@4.8.5+sigsegv patches=9dc5fbd0d5cb1037ab1e6d0ecc74a30df218d0a94bdd5a02759a97f62daca573,bfdffa7c2eb01021d5849b36972c069693654ad826c1a20b53534009a4ec7a89 arch=linux-centos7-x86_64
^libsigsegv@2.13%gcc@4.8.5 arch=linux-centos7-x86_64
^perl@5.34.0%gcc@4.8.5+cpanm+shared+threads arch=linux-centos7-x86_64
^berkeley-db@18.1.40%gcc@4.8.5+cxx~docs+stl patches=b231fcc4d5cff05e5c3a4814f6a5af0e9a966428dc2176540d2c05aff41de522 arch=linux-centos7-x86_64
^bzip2@1.0.8%gcc@4.8.5~debug~pic+shared arch=linux-centos7-x86_64
^gdbm@1.19%gcc@4.8.5 arch=linux-centos7-x86_64
^readline@8.1%gcc@4.8.5 arch=linux-centos7-x86_64
^ncurses@6.2%gcc@4.8.5~symlinks+termlib abi=none arch=linux-centos7-x86_64
^pkgconf@1.8.0%gcc@4.8.5 arch=linux-centos7-x86_64
^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64
^cmake@3.21.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs~qt build_type=Release arch=linux-centos7-x86_64
^openssl@1.1.1l%gcc@4.8.5~docs certs=system arch=linux-centos7-x86_64
^python@3.6%gcc@4.8.5+bz2+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix~tkinter~ucs4+uuid+zlib arch=linux-centos7-x86_64
^re2c@2.2%gcc@4.8.5 arch=linux-centos7-x86_64
1. "%gcc@:5" conflicts with "clingo-bootstrap" [C++14 support is required to bootstrap clingo]
Please run `spack -d spec zlib` for more verbose error messages
根据报错提示，需要一个支持C++14的编译器，我安装了一个新版的gcc/11.2.0，并将其bin目录加到了PATH变量，
According to the error message, we need a compiler which support C++14. I installed gcc/11.2.0 and set it's bin directory to PATH environment variable.
[tools_adm@computing-host-001 ~]$ setenv PATH /tools/oss/gcc/11.2.0/bin:$PATH
[tools_adm@computing-host-001 ~]$ spack -d spec zlib %gcc@11.2.0
==> [2022-05-24-10:03:13.206293] Imported spec from built-in commands
==> [2022-05-24-10:03:13.211112] Imported spec from built-in commands
Input spec
--------------------------------
zlib%gcc@11.2.0
Concretized
--------------------------------
==> [2022-05-24-10:03:13.222579] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/config.yaml
==> [2022-05-24-10:03:13.298617] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/bootstrap.yaml
==> [2022-05-24-10:03:13.333346] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/config.yaml
==> [2022-05-24-10:03:13.387447] DATABASE LOCK TIMEOUT: 3s
==> [2022-05-24-10:03:13.387643] PACKAGE LOCK TIMEOUT: No timeout
==> [2022-05-24-10:03:13.388771] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/bootstrap.yaml
==> [2022-05-24-10:03:13.412265] DATABASE LOCK TIMEOUT: 3s
==> [2022-05-24-10:03:13.412528] PACKAGE LOCK TIMEOUT: No timeout
==> [2022-05-24-10:03:13.412772] [BOOTSTRAP CONFIG SCOPE] name=_builtin
==> [2022-05-24-10:03:13.413841] [BOOTSTRAP CONFIG SCOPE] name=defaults, path=/tools/oss/spack-0.17.2/etc/spack/defaults
==> [2022-05-24-10:03:13.413961] [BOOTSTRAP CONFIG SCOPE] name=defaults/linux, path=/tools/oss/spack-0.17.2/etc/spack/defaults/linux
==> [2022-05-24-10:03:13.414080] [BOOTSTRAP CONFIG SCOPE] name=bootstrap, path=/home/tools_adm/.spack/bootstrap/config
==> [2022-05-24-10:03:13.414180] [BOOTSTRAP CONFIG SCOPE] name=bootstrap/linux, path=/home/tools_adm/.spack/bootstrap/config/linux
==> [2022-05-24-10:03:13.416454] Reading config file /home/tools_adm/.spack/bootstrap/config/linux/compilers.yaml
==> [2022-05-24-10:03:13.504704] [BOOTSTRAP ROOT SPEC] clingo-bootstrap@spack+python %gcc target=x86_64
==> [2022-05-24-10:03:13.504904] [BOOTSTRAP MODULE clingo] Try importing from Python
==> [2022-05-24-10:03:13.505664] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/bootstrap.yaml
==> [2022-05-24-10:03:13.533487] Bootstrapping clingo from pre-built binaries
==> [2022-05-24-10:03:13.539614] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/config.yaml
==> [2022-05-24-10:03:13.602270] DATABASE LOCK TIMEOUT: 3s
==> [2022-05-24-10:03:13.602520] PACKAGE LOCK TIMEOUT: No timeout
==> [2022-05-24-10:03:13.656899] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/mirrors.yaml
==> [2022-05-24-10:03:14.404023] Cached index for https://mirror.spack.io/bootstrap/github-actions/v0.1 already up to date
==> [2022-05-24-10:03:14.477810] Imported buildcache from built-in commands
==> [2022-05-24-10:03:14.502955] Imported buildcache from built-in commands
==> [2022-05-24-10:05:40.274042] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/config.yaml
==> [2022-05-24-10:05:40.351266] Reading config file /home/tools_adm/.spack/bootstrap/config/linux/config.yaml
==> [2022-05-24-10:05:40.627291] [BOOTSTRAP MODULE clingo] The installed spec "clingo-bootstrap@spack+python %gcc target=x86_64 ^python@3.6 /vcipwnf57slgoo7busvvkzjkk7vydeb5" provides the "clingo" Python module
==> [2022-05-24-10:05:40.691909] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/repos.yaml
==> [2022-05-24-10:05:40.876049] Reading config file /home/tools_adm/.spack/linux/compilers.yaml
==> [2022-05-24-10:05:40.914061] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/config.yaml
==> [2022-05-24-10:05:40.969529] Reading config file /tools/oss/spack-0.17.2/etc/spack/defaults/packages.yaml
==> [2022-05-24-10:05:41.244816] build(zlib)
zlib@1.2.11%gcc@11.2.0+optimize+pic+shared arch=linux-centos7-sandybridge
问题解决。
Done.
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