Software Tools Documentation Review

[Pereira-Luc]

General Improvements

• Add Small Example: Including a simple, easy-to-test example would make it easier to detect problems in different versions.
• Improve Documentation: Some of the documentation is minimal and doesn't provide much help. Expanding these sections would be beneficial.
• Use Default Loading Method: It would be better to use the default loading method for tools, such as load tool/name, without specifying versions. This avoids the need for updates. If a specific version is required, using load tool/name/version as an additional option should suffice.
• Remove Outdated Versions: Remove available versions since they are outdated anyway.

---

FEniCS

• Tutorial:
  • Needs to be updated to use micromamba. Other than that, it seems to work.

---

ANSYS

• INFO:
  • The modules in the tutorial are outdated.
• Interactive:
  • Doesn't seem to work on a Mac.
  • Version: ANSYS 21.1, intel/2020.
  • Error:

    Got a SIGABRT while executing native code. This usually indicates a fatal error in the mono runtime or one of the native libraries used by your application.
    /Framework/bin/Linux64/runwb2: line 22: 3010567 Aborted (core dumped) $MONO_PREFIX/bin/mono "$@"

• Sbatch:
  • There's no link to defFile=Benchmark.def. Providing a link would make it easier to test if it's working.

---

OpenFOAM

• INFO:
  • Listed modules are outdated.
  • swenv is not used anymore. Should we remove it or update it?
• Interactive:
  • Error when running paraFoam:

    QStandardPaths: error creating runtime directory /run/user/490151437 (Permission denied)

• Sbatch:
  • Missing source env.
  • Missing cd inside the directory before running blockMesh.
  • When following the tutorial after loading these, I get:

    FOAM FATAL IO ERROR:
    keyword n is undefined in dictionary "OpenFOAM/damBreak/system/decomposeParDict"

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Abaqus

• INFO:
  • Good documentation.
  • No info about the license server, so cannot test, but the documentation seems to be good and will probably work.
• Interactive:
  • Not tested.
• Sbatch:
  • Not tested.

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FDS

• INFO:
  • Listed modules are outdated.
  • swenv is not used anymore. Should we remove it or update it?
  • There is no example file to test. It would be nice to add one.
• Interactive:
  • Not tested.
• Sbatch:
  • Not tested.

---

GMSH

• INFO:
  • Listed modules are outdated.
  • swenv is not used anymore. Should we remove it or update it?
  • There is no example file to test. It would be nice to add one that is tested to work, but there is a link to Demos.
• Interactive:
  • After downloading the example from Git, GMSH seems to work, but it doesn't open any UI. Not sure if it should.
• Sbatch:
  • No sbatch in the documentation.

---

Salome

• INFO:
  • Listed modules are outdated.
  • swenv is not used anymore. Should we remove it or update it?
• Interactive:
  • Error:

    Fatal Python error: init_import_size: Failed to import the site module
    Python runtime state: initialized
    AttributeError: module 'importlib._bootstrap_external' has no attribute '_w_long'

• Sbatch:
  • No sbatch in the documentation.

---

ABINIT

• INFO:
  • Module doesn't exist.
• Interactive:
  • Not tested.
• Sbatch:
  • Not tested.

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ASE

• INFO:
  • Listed modules are outdated.
  • No example available. It would be nice to have a simple example to make testing easier.
• Interactive:
  • Not tested.
• Sbatch:
  • Not tested.

---

Meep

• INFO:
  • Module doesn't exist.
• Interactive:
  • Not tested.
• Sbatch:
  • Not tested.

---

Quantum Espresso

• INFO:
  • Listed modules are outdated.
  • No link for the test. It would be nice to have one to quickly check if it works correctly.
• Interactive:
  • Not tested.
• Sbatch:
  • Not tested.

---

VASP

• INFO:
  • Listed modules are outdated.
  • Not sure how to use since there isn't much information available.
• Interactive:
  • Error:

    No INCAR found, STOPPING

• Sbatch:
  • Not tested.

---

CP2K

• INFO:
  • Module doesn't exist.
• Interactive:
  • Not tested.
• Sbatch:
  • Not tested.

---

GROMACS

• INFO:
  • Listed modules are outdated.
• Interactive:
  • Add an example of something to run.
• Sbatch:
  • Not tested.

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MATLAB

• INFO:
  • Works.
• Interactive:
  • Works.
    • It starts, uses dark mode from my Mac, and is completely broken.
• Sbatch:
  • Works.

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Mathematica

• INFO:
  • Listed modules are outdated.
• Sbatch:
  • Some auth key is missing; no information about that in the documentation.

---

Stata

• INFO:
  • Mostly updated.
  • stata &:
    • Command starts and stops directly, not sure if that is expected.
• Interactive:
  • CLI + Parallel:
    • Works.
  • GUI:
    • Doesn't start.
• Sbatch:
  • No example available to test if it works.
  • Given that CLI works, I expect it to work.

---

Julia

• INFO:
  • Listed modules are outdated.
  • swenv is not used anymore. Should we remove it or update it?
• Interactive:
  • CLI:
    • Works.
  • GUI:
    • Not sure if there is one. No info about it.
• Sbatch:
  • Example is not working.
  • Error:

    LoadError: KeyError: key "SLURM_CPUS_PER_TASK" not found

[gkaf89]

• FEniCS
• ANSYS
  Updated documentation and installed latest available version.
• OpenFOAM
• Abaqus
• FDS
• GMSH
• Salome
• ABINIT
• ASE
• Meep
• Quantum Espresso
• VASP
• CP2K
  Installed latest version.
• GROMACS
  Installed latest version.
• MATLAB
  Installed latest version and updated documentation.
• Mathematica
• Stata
• Julia