Error: The "config" section of the configuration needs to be written to disk, but is currently using a deprecated format. Please update it using:

[abhisheks1460]

While installing any package i m receiving this error ,I m suing spack version 0.17.1.

===========================================================

#spack install aoflagger ==> Warning: config:terminal_title has been replaced by install_status and is ignored ==> Error: The "config" section of the configuration needs to be written to disk, but is currently using a deprecated format. Please update it using:

spack config [--scope=<scope>] update config

Note that previous versions of Spack will not be able to use the updated configuration.

==========================================================================

   #spack -d install aoflagger

==> [2024-04-29-19:50:14.468797] Reading config from file /home/apps/spack/etc/spack/defaults/config.yaml ==> [2024-04-29-19:50:14.527210] Imported install from built-in commands ==> [2024-04-29-19:50:14.529002] Imported install from built-in commands ==> [2024-04-29-19:50:14.529951] Reading config from file /home/apps/spack/etc/spack/defaults/concretizer.yaml ==> [2024-04-29-19:50:14.544507] Reading config from file /home/apps/spack/etc/spack/defaults/repos.yaml ==> [2024-04-29-19:50:14.910647] Reading config from file /home/apps/spack/etc/spack/defaults/packages.yaml ==> [2024-04-29-19:50:14.959354] Reading config from file /home/apps/spack/etc/spack/compilers.yaml ==> [2024-04-29-19:50:15.081911] '/usr/bin/gcc' '-v' '/tmp/spack-implicit-link-infot1frek1s/main.c' '-o' '/tmp/spack-implicit-link-infot1frek1s/output' ==> [2024-04-29-19:50:15.171557] '/opt/ohpc/pub/compiler/gcc/8.3.0/bin/gcc' '-v' '/tmp/spack-implicit-link-infohq8396fg/main.c' '-o' '/tmp/spack-implicit-link-infohq8396fg/output' ==> [2024-04-29-19:50:15.282409] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-12.1.0/gcc-12.2.0-5episdn64ynux75ivyfkodajcog7gaxb/bin/gcc' '-v' '/tmp/spack-implicit-link-info3h0wa5y0/main.c' '-o' '/tmp/spack-implicit-link-info3h0wa5y0/output' ==> [2024-04-29-19:50:15.413727] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-12.1.0/gcc-13.1.0-pq36qqwphwaii23k3capyyajavo2w2td/bin/gcc' '-v' '/tmp/spack-implicit-link-infog0kbkiys/main.c' '-o' '/tmp/spack-implicit-link-infog0kbkiys/output' ==> [2024-04-29-19:50:15.549506] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-12.2.0/nvhpc-22.7-qthdnnsghzce7imwkw74ogv6yuqegxh6/Linux_x86_64/22.7/compilers/bin/nvc' '-v' '/tmp/spack-implicit-link-infozkd0z658/main.c' '-o' '/tmp/spack-implicit-link-infozkd0z658/output' ==> [2024-04-29-19:50:15.798894] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-11.2.0/gcc-11.3.0-ctdmhs3sgm2ppuxyyf5vkemmkhh7fyj5/bin/gcc' '-v' '/tmp/spack-implicit-link-infov767494e/main.c' '-o' '/tmp/spack-implicit-link-infov767494e/output' ==> [2024-04-29-19:50:15.952202] '/home/apps/spack/opt/spack/linux-centos7-skylake_avx512/gcc-8.3.0/intel-oneapi-compilers-2021.4.0-6646aaqgo7fktbu3bqqghjcmruodstdc/compiler/2021.4.0/linux/bin/intel64/icc' '-v' '/tmp/spack-implicit-link-infou4cuprs0/main.c' '-o' '/tmp/spack-implicit-link-infou4cuprs0/output' ==> [2024-04-29-19:50:16.132784] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-11.2.0/intel-oneapi-compilers-2022.0.1-ksraq7ruceaa3h4wpxe5q34s6o25kl6m/compiler/2022.0.1/linux/bin/intel64/icc' '-v' '/tmp/spack-implicit-link-infoyj8stmc1/main.c' '-o' '/tmp/spack-implicit-link-infoyj8stmc1/output' ==> [2024-04-29-19:50:16.346983] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-11.2.0/intel-oneapi-compilers-2022.0.1-ksraq7ruceaa3h4wpxe5q34s6o25kl6m/compiler/2022.0.1/linux/bin/icx' '-v' '/tmp/spack-implicit-link-info1nav6ptq/main.c' '-o' '/tmp/spack-implicit-link-info1nav6ptq/output' ==> [2024-04-29-19:50:16.532826] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-11.3.0/gcc-12.1.0-6ii3twpqhl3quisppdm2fl46fy2kh7dn/bin/gcc' '-v' '/tmp/spack-implicit-link-infoenr7lcgl/main.c' '-o' '/tmp/spack-implicit-link-infoenr7lcgl/output' ==> [2024-04-29-19:50:16.670591] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-12.1.0/intel-oneapi-compilers-2022.1.0-stuxtrpa3qzgxaf7xdmyjgrrzqd6jyy5/compiler/2022.1.0/linux/bin/intel64/icc' '-v' '/tmp/spack-implicit-link-infoq9cz102r/main.c' '-o' '/tmp/spack-implicit-link-infoq9cz102r/output' ==> [2024-04-29-19:50:16.881922] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-12.1.0/intel-oneapi-compilers-2022.1.0-stuxtrpa3qzgxaf7xdmyjgrrzqd6jyy5/compiler/2022.1.0/linux/bin/icx' '-v' '/tmp/spack-implicit-link-infoi1nttfh_/main.c' '-o' '/tmp/spack-implicit-link-infoi1nttfh_/output' ==> [2024-04-29-19:50:17.097961] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-12.1.0/intel-oneapi-compilers-2023.0.0-rbsfm5ke3oyu2wwz3sazavywg2xn2we5/compiler/2023.0.0/linux/bin/intel64/icc' '-v' '/tmp/spack-implicit-link-infodh4zxoba/main.c' '-o' '/tmp/spack-implicit-link-infodh4zxoba/output' ==> [2024-04-29-19:50:17.330328] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-12.1.0/intel-oneapi-compilers-2023.0.0-rbsfm5ke3oyu2wwz3sazavywg2xn2we5/compiler/2023.0.0/linux/bin/icx' '-v' '/tmp/spack-implicit-link-info86magks5/main.c' '-o' '/tmp/spack-implicit-link-info86magks5/output' ==> [2024-04-29-19:50:17.557036] '/home/apps/spack/opt/spack/linux-centos7-cascadelake/gcc-13.1.0/nvhpc-23.7-snu63rlj6laeai5qyp436vlr6estme5i/Linux_x86_64/23.7/compilers/bin/nvc' '-v' '/tmp/spack-implicit-link-infopg5b8hau/main.c' '-o' '/tmp/spack-implicit-link-infopg5b8hau/output' ==> [2024-04-29-19:50:17.808153] DATABASE LOCK TIMEOUT: 60s ==> [2024-04-29-19:50:17.808483] PACKAGE LOCK TIMEOUT: No timeout ==> [2024-04-29-19:50:20.320362] Reading config from file /home/apps/spack/etc/spack/defaults/mirrors.yaml ==> [2024-04-29-19:50:20.330523] Reading config from file /home/apps/spack/etc/spack/defaults/bootstrap.yaml ==> [2024-04-29-19:50:20.342392] Reading config from file /home/apps/spack/etc/spack/defaults/repos.yaml ==> [2024-04-29-19:50:20.347229] [BOOTSTRAP CONFIG SCOPE] name=_builtin ==> [2024-04-29-19:50:20.347708] Reading config from file /home/apps/spack/etc/spack/defaults/bootstrap.yaml ==> [2024-04-29-19:50:20.357165] [BOOTSTRAP CONFIG SCOPE] name=defaults, path=/home/apps/spack/etc/spack/defaults ==> [2024-04-29-19:50:20.357212] [BOOTSTRAP CONFIG SCOPE] name=defaults/linux, path=/home/apps/spack/etc/spack/defaults/linux ==> [2024-04-29-19:50:20.357247] [BOOTSTRAP CONFIG SCOPE] name=bootstrap, path=/root/.spack/bootstrap/config ==> [2024-04-29-19:50:20.357271] [BOOTSTRAP CONFIG SCOPE] name=bootstrap/linux, path=/root/.spack/bootstrap/config/linux ==> [2024-04-29-19:50:20.358470] Reading config from file /home/apps/spack/etc/spack/defaults/config.yaml ==> [2024-04-29-19:50:20.387547] Reading config from file /root/.spack/bootstrap/config/linux/config.yaml ==> [2024-04-29-19:50:20.421226] Warning: config:terminal_title has been replaced by install_status and is ignored ==> [2024-04-29-19:50:20.423065] DATABASE LOCK TIMEOUT: 3s ==> [2024-04-29-19:50:20.423231] PACKAGE LOCK TIMEOUT: No timeout ==> [2024-04-29-19:50:20.423931] Reading config from file /home/apps/spack/etc/spack/defaults/packages.yaml ==> [2024-04-29-19:50:20.520733] Reading config from file /root/.spack/bootstrap/config/packages.yaml ==> [2024-04-29-19:50:20.530168] Reading config from file /root/.spack/bootstrap/config/linux/compilers.yaml ==> [2024-04-29-19:50:20.559649] Reading config from file /home/apps/spack/etc/spack/defaults/config.yaml Traceback (most recent call last): File "/home/apps/spack/bin/spack", line 52, in sys.exit(main()) File "/home/apps/spack/lib/spack/spack_installable/main.py", line 42, in main sys.exit(spack.main.main(argv)) File "/home/apps/spack/lib/spack/spack/main.py", line 1068, in main return _main(argv) File "/home/apps/spack/lib/spack/spack/main.py", line 1021, in _main return finish_parse_and_run(parser, cmd_name, args, env_format_error) File "/home/apps/spack/lib/spack/spack/main.py", line 1051, in finish_parse_and_run return _invoke_command(command, parser, args, unknown) File "/home/apps/spack/lib/spack/spack/main.py", line 648, in _invoke_command return_val = command(parser, args) File "/home/apps/spack/lib/spack/spack/cmd/install.py", line 354, in install install_without_active_env(args, install_kwargs, reporter_factory) File "/home/apps/spack/lib/spack/spack/cmd/install.py", line 466, in install_without_active_env concrete_specs = concrete_specs_from_cli(args, install_kwargs) + concrete_specs_from_file(args) File "/home/apps/spack/lib/spack/spack/cmd/install.py", line 434, in concrete_specs_from_cli args.spec, concretize=True, tests=install_kwargs["tests"] File "/home/apps/spack/lib/spack/spack/cmd/init.py", line 177, in parse_specs spec.concretize(tests=tests) File "/home/apps/spack/lib/spack/spack/spec.py", line 2988, in concretize self._new_concretize(tests) File "/home/apps/spack/lib/spack/spack/spec.py", line 2961, in _new_concretize result = solver.solve([self], tests=tests, allow_deprecated=allow_deprecated) File "/home/apps/spack/lib/spack/spack/solver/asp.py", line 3645, in solve setup, specs, reuse=reusable_specs, output=output, allow_deprecated=allow_deprecated File "/home/apps/spack/lib/spack/spack/solver/asp.py", line 806, in solve self.control = control or default_clingo_control() File "/home/apps/spack/lib/spack/spack/solver/asp.py", line 92, in default_clingo_control control = clingo().Control() File "/home/apps/spack/lib/spack/spack/solver/core.py", line 132, in clingo clingo_mod = _bootstrap_clingo() File "/home/apps/spack/lib/spack/spack/solver/core.py", line 197, in _bootstrap_clingo with spack.bootstrap.ensure_bootstrap_configuration(): File "/usr/lib64/python3.6/contextlib.py", line 81, in enter return next(self.gen) File "/home/apps/spack/lib/spack/spack/bootstrap/config.py", line 105, in ensure_bootstrap_configuration with _ensure_bootstrap_configuration(): File "/usr/lib64/python3.6/contextlib.py", line 81, in enter return next(self.gen) File "/home/apps/spack/lib/spack/spack/bootstrap/config.py", line 172, in _ensure_bootstrap_configuration spack.config.set("config", user_configuration["config"]) File "/home/apps/spack/lib/spack/spack/config.py", line 966, in set return CONFIG.set(path, value, scope) File "/home/apps/spack/lib/spack/spack/config.py", line 395, in _method return method(self, *args, **kwargs) File "/home/apps/spack/lib/spack/spack/config.py", line 665, in set self.update_config(path, value, scope=scope) File "/home/apps/spack/lib/spack/spack/config.py", line 395, in _method return method(self, *args, **kwargs) File "/home/apps/spack/lib/spack/spack/config.py", line 544, in update_config raise RuntimeError(msg) RuntimeError: The "config" section of the configuration needs to be written to disk, but is currently using a deprecated format. Please update it using:

spack config [--scope=<scope>] update config

Note that previous versions of Spack will not be able to use the updated configuration. You have mail in /var/spool/mail/root

[wdconinc]

Did you try spack config update config? Can you install aoflagger after doing that?

[pelesh]

I had a similar issue. In my case spack config update config didn't work. I got a message that my configuration does not need updating but the the problem with spack installation persisted. The workaround I found was to nuke .spack in my home directory.

[alalazo]

@pelesh We usually don't ensure compatibility across many minor versions of Spack, so it doesnt' surprise me that you could get issues updating from v0.17 to v0.22. What we do our best to ensure, is a nice transition from v0.X to v0.(X+1)