Goal: Understand how to load modules, reset your environment by purging, and potential dependency issues.
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Will changing the version of Python affect R? In this case probably not. But if underlying versions of libraries are changing - then maybe - and that’s the best we can say… Remember: The more complicated your environments, the more dependencies there’ll be, the more potential for dependency hell. |
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Exercises:
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Try answers the following questions: What modules are available that relate to netcdf? What modules become available after loading nvhpc-sdk/24.3? How would you identify modules that have no dependencies?
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Exercises: Answers:
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| title | What modules are available that relate to netcdf? |
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Use the module spider command to search for modules. You will see something of the form: | Code Block |
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[]$ module spider netcdf
----------------------------------------------------------------------------
netcdf-c: netcdf-c/4.9.2-ompi
----------------------------------------------------------------------------
You will need to load all module(s) on any one of the lines below before the "netcdf-c/4.9.2-ompi" module is available to load.
arcc/1.0 gcc/13.2.0 openmpi/4.1.6
Help:
NetCDF (network Common Data Form) is a set of software libraries and
machine-independent data formats that support the creation, access, and
sharing of array-oriented scientific data. This is the C distribution.
----------------------------------------------------------------------------
netcdf-cxx4: netcdf-cxx4/4.3.1-ompi
----------------------------------------------------------------------------
You will need to load all module(s) on any one of the lines below before the "netcdf-cxx4/4.3.1-ompi" module is available to load.
arcc/1.0 gcc/13.2.0 openmpi/4.1.6
Help:
NetCDF (network Common Data Form) is a set of software libraries and
machine-independent data formats that support the creation, access, and
sharing of array-oriented scientific data. This is the C++ distribution.
----------------------------------------------------------------------------
parallel-netcdf: parallel-netcdf/1.12.3-ompi
----------------------------------------------------------------------------
You will need to load all module(s) on any one of the lines below before the "parallel-netcdf/1.12.3-ompi" module is available to load.
arcc/1.0 gcc/13.2.0 openmpi/4.1.6
Help:
PnetCDF (Parallel netCDF) is a high-performance parallel I/O library for
accessing files in format compatibility with Unidata's NetCDF,
specifically the formats of CDF-1, 2, and 5. |
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| title | What modules become available after loading nvhpc-sdk/24.3? |
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First, module load this compiler, and then use the module avail to see what additional modules are now available. | Code Block |
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[]$ module purge
[]$ module load nvhpc-sdk/24.3
[]$ module avail
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----------------- /apps/u/opt/compilers/nvhpc/24.3/modulefiles -----------------
nvhpc-byo-compiler/24.3 nvhpc-hpcx/24.3 nvhpc-openmpi3/24.3
nvhpc-hpcx-cuda12/24.3 nvhpc-nompi/24.3 nvhpc/24.3
... |
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| title | How would you identify modules that have no dependencies? |
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Modules that are available from the containers, conda-envs and linux trees are typically installed with no dependencies. | Code Block |
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[]$ module avail
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-------------- /apps/s/lmod/mf/opt/linux-rhel9-x86_64/containers ---------------
stress-ng/0.17.08
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-------------- /apps/s/lmod/mf/opt/linux-rhel9-x86_64/conda-envs ---------------
julia/1.10.3 python2/2.7.18
----------------- /apps/s/lmod/mf/opt/linux-rhel9-x86_64/linux -----------------
matlab/2024a nextflow/23.10.1 pycharm/2024.1.3
miniconda3/24.3.0 paraview/5.12.0 rstudio/2024.04.1
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Essentially, anything that hasn’t been built with a compiler. |
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