Installation of ESD/24.04 hangs when reading compilers.yaml

Summary


Summary	Spack package build failure
Package info
System	JUSUF
Related

Steps to reproduce the issue

$ spack spec -I <spec>
...
$ spack -d install --fresh --test root
==> [2024-11-27-14:34:13.817418] [BOOTSTRAP CONFIG SCOPE] name=bootstrap, path=/p/home/jusers/deepu1/jusuf/.spack/bootstrap/config
==> [2024-11-27-14:34:13.817439] [BOOTSTRAP CONFIG SCOPE] name=bootstrap/linux, path=/p/home/jusers/deepu1/jusuf/.spack/bootstrap/config/linux
==> [2024-11-27-14:34:13.818481] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/config.yaml
==> [2024-11-27-14:34:13.848604] Reading config from file /p/home/jusers/deepu1/jusuf/.spack/bootstrap/config/linux/config.yaml
==> [2024-11-27-14:34:13.866183] DATABASE LOCK TIMEOUT: 10s
==> [2024-11-27-14:34:13.866269] PACKAGE LOCK TIMEOUT: No timeout
==> [2024-11-27-14:34:13.869329] Reading config from file /p/home/jusers/deepu1/jusuf/.spack/bootstrap/config/linux/compilers.yaml
==> [2024-11-27-14:34:14.031815] [BOOTSTRAP ROOT SPEC] patchelf@0.13.1: %gcc target=x86_64
==> [2024-11-27-14:34:14.033574] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/bootstrap.yaml
==> [2024-11-27-14:34:14.058002] [BOOTSTRAP EXECUTABLES patchelf] Try installed specs with query 'patchelf@0.13.1: %gcc target=x86_64'
==> [2024-11-27-14:34:14.073459] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/modules.yaml
==> [2024-11-27-14:34:14.090182] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/linux/modules.yaml
==> [2024-11-27-14:34:14.375066] Adding env modifications for patchelf
==> [2024-11-27-14:34:14.582078] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/packages.yaml
==> [2024-11-27-14:34:14.641709] [BOOTSTRAP ROOT SPEC] gnupg@2.3: %gcc target=x86_64
==> [2024-11-27-14:34:14.657674] [BOOTSTRAP ROOT SPEC] clingo-bootstrap@spack+python %gcc target=x86_64
==> [2024-11-27-14:34:14.657762] [BOOTSTRAP MODULE clingo] Try importing from Python
==> [2024-11-27-14:34:38.390128] [BOOTSTRAP MODULE clingo] The installed spec "clingo-bootstrap@spack+python %gcc target=x86_64 ^python@3.9/bhqgwuvef354fwuxq7heeighavunpber" provides the "clingo" Python module
==> [2024-11-27-14:34:38.393413] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/config.yaml
==> [2024-11-27-14:34:38.438743] Creating ConfigScope env:/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jusuf/stage2025/ebrains-spack-builds:jusuf for '/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jusuf/stage2025/ebrains-spack-builds/site-config/jusuf'
==> [2024-11-27-14:34:38.439139] Reading config from file /p/usersoftware/ebrains-sw-stack/ebrains-24.04/jusuf/stage2025/ebrains-spack-builds/site-config/jusuf/config.yaml
==> [2024-11-27-14:34:38.443698] Reading config from file /p/usersoftware/ebrains-sw-stack/ebrains-24.04/jusuf/stage2025/ebrains-spack-builds/spack.yaml
==> [2024-11-27-14:34:38.473240] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/config.yaml
==> [2024-11-27-14:34:38.499043] Using environment '/p/usersoftware/ebrains-sw-stack/ebrains-24.04/jusuf/stage2025/ebrains-spack-builds'
==> [2024-11-27-14:34:38.499495] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/concretizer.yaml
==> [2024-11-27-14:34:38.508948] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/repos.yaml
==> [2024-11-27-14:34:38.511947] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/repos.yaml
==> [2024-11-27-14:34:39.272294] Reading config from file /p/usersoftware/swmanage/deepu1/easybuild/stage2025/Spack/easybuild/jusuf/software/Spack/0.21.1_ebrains-GCCcore-13.3.0/etc/spack/defaults/packages.yaml
==> [2024-11-27-14:34:39.310676] Reading config from file /p/usersoftware/ebrains-sw-stack/ebrains-24.04/jusuf/stage2025/ebrains-spack-builds/site-config/jusuf/packages.yaml
==> [2024-11-27-14:34:54.453824] Reading config from file /p/usersoftware/ebrains-sw-stack/ebrains-24.04/jusuf/stage2025/ebrains-spack-builds/site-config/jusuf/compilers.yaml


 Update: modified the compilers.yaml file. Using only GCC/13.3.0

$ spack install --fresh --test root 2>&1 | tee jusuf_install.log                                                                                                   
==> Error: concretization failed for the following reasons:

   1. vtk: '%gcc@13' conflicts with '@9.2'
   2. intel-tbb: '%gcc@13' conflicts with '@:2021.3'
   3. vtk: '%gcc@13' conflicts with '@9.2'
        required because conflict applies to spec @9.2 
          required because py-tvb-widgets depends on vtk@=9.2.6 
            required because py-tvb-widgets@2.0.3 requested explicitly 
          required because py-pyvista depends on vtk+python 
            required because py-tvb-widgets depends on py-pyvista@0.43.0: 
        required because conflict is triggered when %gcc@13 
          required because py-tvb-widgets depends on vtk@=9.2.6 
            required because py-tvb-widgets@2.0.3 requested explicitly 
          required because py-pyvista depends on vtk+python 
            required because py-tvb-widgets depends on py-pyvista@0.43.0: 
   4. intel-tbb: '%gcc@13' conflicts with '@:2021.3'
        required because conflict applies to spec @:2021.3 
          required because suite-sparse depends on intel-tbb@:2020 build_system=makefile when +tbb ^intel-tbb 
            required because apbs depends on suite-sparse+tbb 
        required because conflict is triggered when %gcc@13 
          required because suite-sparse depends on intel-tbb@:2020 build_system=makefile when +tbb ^intel-tbb 
            required because apbs depends on suite-sparse+tbb . You could consider setting `concretizer:unify` to `when_possible` or `false` to allow multiple versions of some packagessome packages.


Modified the compilers.yaml file by adding the system GCC too which is 11.4.1. Now the install command just hangs..

Added gcc11.4.1 to the packages.yaml file. Added the entries for vtk and intel-tbb to the packages.yaml file by explicitly specifying to use gcc11.4.1 for both packages. Also gcc13.3 for suitparse.

Error message


(add error logs here)

Information on your system

Additional information

compilers.yaml
packages.yaml
[modified_compilers.yaml] (compilers.yaml)
jusuf_install.log
[modified_compilers2.yaml] (compilers.yaml)
[modified_packages.yaml] (packages.yaml)

Edited 5 months ago

Designs

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Activity

Rajalekshmi Deepu changed title from Installation of esd24.04 hangs with reading compilers.yaml to Installation of ESD/24.04 hangs when reading compilers.yaml 5 months ago

changed title from Installation of esd24.04 hangs with reading compilers.yaml to Installation of ESD/24.04 hangs when reading compilers.yaml
Rajalekshmi Deepu changed the description 5 months ago

changed the description
Rajalekshmi Deepu changed the description 5 months ago

changed the description
Eleni Mathioulaki @elmath · 5 months ago

Owner

@deepu could you try using v0.21.1_ebrains24.11 from our fork of Spack?
Rajalekshmi Deepu changed the description 5 months ago

changed the description
Rajalekshmi Deepu @deepu · 5 months ago

Author Reporter

@elmath Am using the ebrains customised spack which was working fine for ESD/24.04 under Stages/2024 which uses GCC/12.3.0.

Spack/0.21.1_ebrains module in JUSUF. This is compiled for both Stages 2024 and 2025 each using a different version of GCC

Edited 5 months ago by Rajalekshmi Deepu
Rajalekshmi Deepu @deepu · 5 months ago

Author Reporter

@elmath I just checked the version of the module under Stages/2025:

$ spack --version 0.21.1 (01330d6328807175eda9504d02824fdd209e6c64)

On the other hand, for Stages/2024, hash is different.

$ spack --version 0.21.1 (6b3ed3d9a53ecffbb22f1a2c9ac4979089e39717)

The one under Stages/2025 is the second last commit :-(

Edited 5 months ago by Rajalekshmi Deepu
Eleni Mathioulaki @elmath · 5 months ago

Owner

yes, it's exactly that commit that would solve the issue with the hanging concretization
Eleni Mathioulaki @elmath · 3 weeks ago

Owner

For Spack v0.21.1, the issue was fixed by using the suggested workaround. In Spack v0.23.0, the issue still appears sometimes, but much less frequently, for complex/impossible to concretize environments. I am closing, and we can open a dedicated issue if it comes up again in a specific environment.
Eleni Mathioulaki closed 3 weeks ago

closed

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