Aexus Answers

CIME Build Error On Perlmutter: Troubleshooting Guide

Alex Johnson
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CIME Build Error On Perlmutter: Troubleshooting Guide

Encountering build errors while working with CIME (Community Earth System Model) on the Perlmutter supercomputer can be a frustrating experience. This comprehensive guide breaks down a common build error, explores potential causes related to submodules and provides a systematic approach to troubleshooting and resolving such issues.

Understanding the Build Error

When working with complex software like the Earth System Model (E3SM), encountering build errors is not uncommon. Build errors can arise from various sources, including issues with the environment, dependencies, or the code itself. A clear understanding of the error message is crucial for effective troubleshooting. In this case, the error message indicates a TypeError: 'NoneType' object is not subscriptable, which occurs during the namelist generation phase of the build process. This error often points to a problem with how the model configuration is being set up, specifically with variables related to component interactions.

Error Message Breakdown

Let's dissect the provided error message:

Namelist default for variable lnd2iac_smapname refers to unknown XML variable LND2IAC_SMAPNAME.
Traceback (most recent call last):
  File "/global/u2/j/jaholm/Model_Runs/E3SM_runs/fates-symbiosis_p1.pm-cpu.E5fedc5648e-Ff6355b1b.2025-10-19/./case.build", line 269, in <module>
    _main_func(__doc__)
  ...
TypeError: 'NoneType' object is not subscriptable

The key part of this error message is the TypeError: 'NoneType' object is not subscriptable. This error typically arises when the code attempts to access an element (like a character in a string) of a variable that is None. In the context of CIME and E3SM, this often happens when a namelist variable is expected to have a value but is instead receiving a None value. The preceding line, "Namelist default for variable lnd2iac_smapname refers to unknown XML variable LND2IAC_SMAPNAME," gives a vital clue. It suggests that the variable lnd2iac_smapname, which is related to the interaction between the land (LND) and ice (IAC) components, is trying to use an XML variable LND2IAC_SMAPNAME that is not defined.

Potential Causes and Solutions

Given the error message and the context of building an E3SM case on Perlmutter, here are the most probable causes and how to address them:

1. Submodule Issues

Submodules are essentially repositories within a repository, often used in projects like E3SM to manage dependencies or modular components. If submodules aren't correctly updated or initialized, it can lead to inconsistencies in the codebase, causing build errors. In this case, outdated or incorrectly updated submodules are the most likely culprit.

  • How to Identify: The user suspects submodule issues, which is a good starting point. It's essential to verify this suspicion. This can be done by comparing the current state of the submodules with the expected state in the repository.
  • Solution:

    1. Ensure submodules are initialized and updated:

      git submodule init
git submodule update --recursive

      The --recursive flag is important to ensure that any nested submodules are also updated.

    2. If the problem persists, try a more forceful update:

      git submodule deinit --all --force
git submodule init
git submodule update --recursive

      This process removes the submodule information and re-initializes them, which can resolve issues caused by corrupted submodule states.

2. Incorrect CIME or E3SM Branch

Using an incompatible version of CIME or E3SM can lead to build errors. Version mismatches can cause inconsistencies in the expected variables and configurations.

  • How to Identify: The user has provided the CIME and E3SM branch versions. Verify that these versions are compatible and recommended for the specific case setup.
  • Solution:

    1. Consult the E3SM documentation or release notes to determine the correct CIME version for the E3SM version being used.

    2. Switch to the recommended branches:

      git checkout <CIME_branch>

git checkout <E3SM_branch> ```

    Replace `<CIME_branch>` and `<E3SM_branch>` with the appropriate branch names.
3.  After switching branches, ensure that submodules are updated again:

    ```bash

git submodule update --recursive ```

3. Case Configuration Issues

Errors in the case configuration can also lead to build failures. This includes incorrect settings in the env_*.xml files or inconsistencies in the namelist configurations. The error message specifically points to an issue with lnd2iac_smapname, suggesting a problem in the interaction setup between the land and ice components.

  • How to Identify: Review the case setup, particularly the env_*.xml files and namelist settings, for any misconfigurations related to component interactions.
  • Solution:
    1. Check the env_*.xml files for the case, especially those related to the land (LND) and ice (IAC) components.
    2. Look for the definition of LND2IAC_SMAPNAME. If it's missing, it needs to be added with the correct value.
    3. If the variable is present, ensure its value is appropriate for the chosen configuration.
    4. If unsure, compare the settings with a known working case or consult the E3SM documentation for recommended configurations.

4. Environment Issues on Perlmutter

The Perlmutter supercomputer has its own environment setup, and issues with loaded modules or environment variables can interfere with the build process. Incorrectly set environment variables or missing modules can cause the build to fail.

  • How to Identify: Ensure that all necessary modules are loaded and that the environment variables are correctly set for CIME and E3SM.
  • Solution:
    1. Load the required modules for CIME and E3SM. This usually involves modules for compilers, MPI libraries, and other dependencies.
    2. Check the environment variables used by CIME and E3SM to ensure they are correctly defined. This may include variables like CIME_MODEL, CIME_MACHINE, and others.
    3. Use the module list command on Perlmutter to see which modules are currently loaded. Compare this with the recommended module list for E3SM.

5. Namelist Generation Problems

The error occurs during namelist generation, which is a crucial step in the build process. Incorrect namelist settings or a failure to generate namelists can halt the build.

  • How to Identify: The traceback points to cime/CIME/nmlgen.py, indicating an issue with the namelist generation scripts. This suggests a problem in how the namelists are being created or processed.
  • Solution:

    1. Examine the namelist generation scripts (buildnml) for any errors or inconsistencies.

    2. Check the XML variable definitions to ensure that LND2IAC_SMAPNAME is correctly defined and accessible.

    3. Try regenerating the namelists manually to see if the error persists:

      ./case.build --clean
./case.build

      The --clean option removes the existing build artifacts and forces a fresh build.

Step-by-Step Troubleshooting Guide

To systematically address the build error, follow these steps:

  1. Verify Submodule Integrity:
    • Run git submodule init and git submodule update --recursive to ensure submodules are correctly initialized and updated.
    • If issues persist, try git submodule deinit --all --force followed by git submodule init and git submodule update --recursive.
  2. Check CIME and E3SM Branches:
    • Consult the E3SM documentation for recommended CIME and E3SM versions.
    • Use git checkout to switch to the appropriate branches.
    • Update submodules after switching branches.
  3. Examine Case Configuration:
    • Review env_*.xml files for any misconfigurations, particularly those related to land-ice interactions.
    • Ensure that LND2IAC_SMAPNAME is defined with a correct value.
  4. Assess Perlmutter Environment:
    • Load necessary modules for compilers, MPI libraries, and other dependencies.
    • Verify that environment variables like CIME_MODEL and CIME_MACHINE are correctly set.
  5. Investigate Namelist Generation:
    • Check namelist generation scripts for errors.
    • Ensure XML variable definitions are correct.
    • Try regenerating namelists manually using ./case.build --clean.
  6. Consult Documentation and Community:
    • Refer to the E3SM documentation for troubleshooting tips and recommended practices.
    • If the issue remains unresolved, seek assistance from the E3SM community forums or mailing lists. Providing detailed information about the error, the steps taken, and the system configuration will help others assist you effectively.

Conclusion

Troubleshooting build errors in complex models like E3SM requires a systematic approach. By understanding the error message, identifying potential causes, and following a step-by-step guide, you can effectively diagnose and resolve the issue. In this case, the TypeError: 'NoneType' object is not subscriptable likely stems from a misconfiguration related to the LND2IAC_SMAPNAME variable, which could be due to submodule issues, incorrect CIME/E3SM branches, or case configuration errors. By addressing these potential causes, you can successfully build your E3SM case on Perlmutter.

For more in-depth information on E3SM and CIME, refer to the official E3SM Project Website.

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