### Example obsparam YAML File for pyuvsim Simulation

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/docs/parameter_files.rst

This YAML file defines core simulation parameters for pyuvsim, including output filing, frequency setup (Nfreqs, channel_width, start_freq, end_freq, freq_array, bandwidth), source catalog details (path, type, spectral_type), telescope configuration (array_layout, telescope_config_name), time parameters (Ntimes, integration_time, start_time, end_time, duration_hours), and baseline selection criteria (bls, ant_str, antenna_nums, redundant_threshold, conjugation_convention, blt_order). It serves as the primary input for `pyuvsim.simsetup.initialize_uvdata_from_params`.

```yaml
filing:
  outdir: '.'   #Output file directory
  outfile_prefix: 'sim' # Prefix for the output file name, separated by underscores
  outfile_suffix: 'results' # Suffix for output file name
  outfile_name: 'sim_results' # Alternatively, give the full name
  output_format: 'uvfits'  # Format for output. Default is 'uvh5', but 'uvfits', measurement sets ('ms'), and 'miriad' are also supported.
  clobber: False        # overwrite existing files. (Default False)
freq:
  Nfreqs: 10    # Number of frequencies
  channel_width: 80000.0    # Frequency channel width
  end_freq: 100800000.0     # Start and end frequencies (Hz)
  start_freq: 100000000.0
  freq_array : [1.0000e+08,   1.0008e+08,   1.0016e+08, 1.0024e+08,
      1.0032e+08,   1.0040e+08,   1.0048e+08, 1.0056e+08,
      1.0064e+08, 1.0072e+08]
  bandwidth: 800000.0
sources:
  catalog: '../pyuvsim/data/gleam_50srcs.vot' # Path to catalog file (txt, vot, skyh5, fhd, etc.) readable with pyradiosky.
  filetype : "gleam" # optionally specify the catalog filetype (skyh5, gleam, vot, text, fhd). If not specified, the code attempt to guess the type.
  spectral_type: flat # If using the GLEAM catalog, specify the spectral type (flat, subband or spectral_index). Defaults to flat.
  table_name: single  # Required for non-GLEAM VO table files
  id_column: name  # Required for non-GLEAM VO table files
  flux_columns: Si  # Required for non-GLEAM VO table files
  ra_column: RAJ2000  # Recommended for non-GLEAM VO table files
  dec_column: DEJ2000  # Recommended for non-GLEAM VO table files
  catalog: 'mock'       # Alternatively, use 'mock' to use a builtin catalog).
  mock_arrangement: 'zenith'    # If using the mock catalog, specify which one. Additional mock keywords are specified here.
telescope:
  array_layout: 'triangle_bl_layout.csv'    # Antenna layout csv file
  telescope_config_name: '28m_triangle_10time_10chan.yaml'  # Telescope metadata file.
time:
  Ntimes: 10        # Number of times.
  integration_time: 11.0  # Time step size  (seconds)
  start_time: 2457458.1738949567    # Start and end times (Julian date)
  end_time: 2457458.175168105
  duration_hours: 0.0276
select: # limit which baselines are simulated. Use any UVData.select keywords (except polarizations) and/or redundant_threshold
  bls: '[(1, 2), (3, 4), (5, 6)]'
  ant_str: 'cross'
  antenna_nums: [1, 7, 9, 15]
  redundant_threshold: 0.1 # redundancy threshold in meters. Only simulate one baseline per redundant group
ordering: # specify the baseline-time order and baseling conjugation convention
  conjugation_convention: ant1<ant2
  blt_order: [time, baseline]
```

--------------------------------

### Running Tests via Setup.py (Shell)

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/README.md

This command executes the tests defined in the `setup.py` file of the `pyuvsim` project. It's a traditional method for running tests in Python packages, often used during development or installation.

```Shell
python setup.py test
```

--------------------------------

### Installing pyuvsim in Developer Mode with Pip

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/benchmarking/README.md

Installs the `pyuvsim` repository in 'developer' mode using Pip. This enables local changes to be active immediately, which is a prerequisite for utilizing the benchmarking scripts.

```Bash
pip install -e
```

--------------------------------

### Running Single-Core Reference Simulation with pytest-benchmark (Shell)

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/docs/developers.rst

This command demonstrates how to execute a single-core regression test for a specific pyuvsim reference simulation using `mpiexec` and `pytest-benchmark`. It utilizes the `--refsim` flag to identify the target simulation (e.g., '1.1_uniform') and `--benchmark-only` to focus on performance metrics. This setup is primarily for linear operations and does not assess parallel performance.

```shell
# use mpiexec to run pytest specifying one core
> mpiexec -n 1 -np 1 pytest --refsim=1.1_uniform --benchmark-only
```

--------------------------------

### Running Pytest for pyuvsim Testing (Shell)

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/README.md

This command executes the `pytest` test suite from the current directory, typically `pyuvsim/`, to verify the installation and functionality of the `pyuvsim` package. It requires `pytest` to be installed and all `pyuvsim` dependencies to be met.

```Shell
pytest
```

--------------------------------

### Installing pyuvsim in Developer Mode with Conda

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/benchmarking/README.md

Installs the `pyuvsim` repository in 'developer' mode using Conda. This allows for local modifications to be reflected without reinstallation, which is necessary for effective use of the benchmarking tools.

```Bash
conda develop .
```

--------------------------------

### Running pyuvsim with MPI Parallelization (Python)

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/docs/usage.rst

This command demonstrates how to execute a pyuvsim simulation using MPI for parallel processing. It launches the `run_param_pyuvsim` script with a specified number of MPI processing units and an observation parameter file. This setup enables distributed computation to accelerate simulations, with further speedup from NumPy/SciPy internal threading.

```python
# Running with 50 MPI processing units
> mpirun -n 50 python run_param_pyuvsim obsparam_filename.yaml   # This will run a parameter file job with 10 processing units.
```

--------------------------------

### Initializing pyuvsim Benchmarking Configuration

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/benchmarking/README.md

Generates the necessary configuration files and SLURM job script for a `pyuvsim` benchmarking run based on the parameters defined in `settings.yaml`. By default, it creates a dated directory for output.

```Python
python run_benchmarking.py settings.yaml --init_config
```

--------------------------------

### Running pyuvsim Reference Simulations with SLURM (Bash)

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/reference_simulations/README.md

This Bash command initiates all `pyuvsim` reference simulations by launching SLURM jobs. It takes `obsparam_*` as arguments, which are observation parameter files, and delegates the job execution to `jobscript.sh`.

```bash
./run_ref_sims.sh obsparam_*
```

--------------------------------

### Running pyuvsim Simulation with MPI

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/README.md

This command demonstrates how to execute a pyuvsim simulation using `mpirun` for parallel processing. It specifies 4 MPI ranks and points to a YAML configuration file (`obsparam_ref_1.1.yaml`) which defines the simulation parameters, such as observation times, frequencies, and array configuration.

```Shell
mpirun -n 4 python scripts/run_param_pyuvsim.py reference_simulations/first_generation/obsparam_ref_1.1.yaml
```

--------------------------------

### Submitting pyuvsim Benchmarking Job to SLURM

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/benchmarking/README.md

Submits the `pyuvsim` benchmarking job to the SLURM workload manager. If the configuration files haven't been generated yet, this command will also initialize them before submission.

```Python
python run_benchmarking.py settings.yaml --submit
```

--------------------------------

### Running Pytest via Python Module (Shell)

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/README.md

This command runs the `pytest` test suite specifically for the `pyuvsim` package by invoking `pytest` as a Python module. It's an alternative to directly running `pytest` and ensures the correct Python environment is used.

```Shell
python -m pytest pyuvsim
```

--------------------------------

### Updating pyuvsim Benchmarking Log File

Source: https://github.com/radioastronomysoftwaregroup/pyuvsim/blob/main/benchmarking/README.md

Updates the `BENCHMARKS.log` file with the results from the latest `pyuvsim` benchmarking run. This log is tracked by Git and serves as a historical record of performance changes over time.

```Python
python run_benchmarking.py settings.yaml --update_log
```

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