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[CI] GROMACS installation uninstalls mdanalysis #252

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orbeckst opened this issue Jun 29, 2023 · 3 comments
Closed

[CI] GROMACS installation uninstalls mdanalysis #252

orbeckst opened this issue Jun 29, 2023 · 3 comments
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@orbeckst
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For GROMACS > 2018, our CI µmamba uninstall MDAnalysis (currently 2.5.0) which leads to failing tests.

Run micromamba install 'gromacs==2021.1' pocl
  micromamba install 'gromacs==2021.1' pocl
  shell: /bin/bash -l {0}
  env:
    MPLBACKEND: agg
    MSYS: winsymlinks:nativestrict
    MAMBA_ROOT_PREFIX: /Users/runner/micromamba-root
    MAMBA_EXE: /Users/runner/micromamba-bin/micromamba

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

conda-forge/osx-64                                          Using cache
conda-forge/noarch                                          Using cache
bioconda/osx-64                                             Using cache
bioconda/noarch                                             Using cache

Pinned packages:
  - python 3.10.*


Transaction

  Prefix: /Users/runner/micromamba-root/envs/test

  Updating specs:

   - gromacs==2021.1
   - pocl


  Package                         Version  Build                    Channel           Size
────────────────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────────────────

  + fftw                           3.3.10  nompi_h4fa670e_108       conda-forge        2MB
  + gromacs                        2021.1  nompi_h2eb4de6_102       bioconda          16MB
  + khronos-opencl-icd-loader  2023.04.17  hb7f2c08_0               conda-forge       74kB
  + ld64                              609  ha02d983_13              conda-forge       19kB
  + ld64_osx-64                       609  hbfe4790_13              conda-forge        1MB
  + libclang-cpp11.1               11.1.0  default_he082bbe_1       conda-forge       13MB
  + libhwloc                        2.5.0  h05ad0d7_0               conda-forge        3MB
  + libllvm11                      11.1.0  h8fb7429_5               conda-forge       23MB
  + libllvm16                      16.0.3  hf646ca0_1               conda-forge       25MB
  + ocl_icd_wrapper_apple           1.0.0  hbcb3906_0               conda-forge       18kB
  + pocl                              1.7  h25429ea_2               conda-forge       17MB
  + sigtool                         0.1.3  h88f4db0_0               conda-forge      214kB
  + tapi                        1100.0.11  h9ce4665_0               conda-forge      201kB

  Remove:
────────────────────────────────────────────────────────────────────────────────────────────

  - libnetcdf                       4.9.2  nompi_hfeda9e8_106       conda-forge     Cached
  - mdanalysis                      2.5.0  py310hd3c6219_1          conda-forge     Cached
  - netcdf4                         1.6.4  nompi_py310h845552d_101  conda-forge     Cached

  Downgrade:
────────────────────────────────────────────────────────────────────────────────────────────

  - libxml2                        2.11.4  hd95e348_0               conda-forge     Cached
  + libxml2                        2.10.4  h554bb67_0               conda-forge      636kB

  Summary:

  Install: 13 packages
  Remove: 3 packages
  Downgrade: 1 packages

  Total download: 102MB
@orbeckst
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orbeckst commented Jun 29, 2023

Trying to find the problem in a local environment and running

micromamba install --no-allow-uninstall -c conda-forge -c bioconda  'gromacs==2021.1' pocl

There's now an incompatibility:

error    libmamba Could not solve for environment specs
    The following packages are incompatible
    └─ gromacs 2021.1  is installable with the potential options
       ├─ gromacs 2021.1 would require
       │  └─ libhwloc >=2.4.1,<2.4.2.0a0 , which requires
       │     └─ libxml2 >=2.9.10,<2.11.0a0  with the potential options
       │        ├─ libxml2 [2.10.0|2.10.1|...|2.9.14] would require
       │        │  └─ icu >=70.1,<71.0a0 , which can be installed;
       │        ├─ libxml2 [2.9.10|2.9.11], which can be installed;
       │        ├─ libxml2 [2.9.12|2.9.14] would require
       │        │  └─ icu >=69.1,<70.0a0 , which can be installed;
       │        ├─ libxml2 2.9.12 would require
       │        │  └─ icu >=68.1,<69.0a0 , which can be installed;
       │        ├─ libxml2 [2.10.3|2.10.4], which can be installed;
       │        └─ libxml2 [2.10.3|2.9.12|2.9.14] would require
       │           └─ icu >=58.2,<59.0a0 , which can be installed;
       └─ gromacs 2021.1 would require
          └─ libhwloc >=2.5.0,<2.5.1.0a0 , which requires
             └─ libxml2 >=2.9.12,<2.11.0a0  with the potential options
                ├─ libxml2 [2.10.0|2.10.1|...|2.9.14], which can be installed (as previously explained);
                ├─ libxml2 [2.9.12|2.9.14], which can be installed (as previously explained);
                ├─ libxml2 2.9.12, which can be installed (as previously explained);
                ├─ libxml2 [2.10.3|2.10.4], which can be installed;
                └─ libxml2 [2.10.3|2.9.12|2.9.14], which can be installed (as previously explained).
critical libmamba Could not solve for environment specs

@orbeckst
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micromamba install -c conda-forge -c bioconda  'gromacs==2021.1' pocl mdanalysis

will keep mdanalysis and just downgrade hdf5 and libxml2 so I need to pin mdanalysis.

@orbeckst
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... no idea how to tell anaconda to keep mdanalysis so we'll just add it to the GROMACS installation line.

This seems to be a problem with gromacs packages on bioconda (up to gromacs 2021, 2021.1 nompi_h2eb4de6_102 bioconda). For gromacs>=2022 (on conda-forge, 2022 nompi_habda4e6_101 conda-forge) there don't seem to be problems:

micromamba install -c conda-forge   'gromacs==2022' pocl

installs everything.

Thus, once we drop tests for GROMACS < 2022, we can

  • drop bioconda channel
  • remove mdanalysis from the gromacs installation step installs

@orbeckst orbeckst self-assigned this Jun 29, 2023
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