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Clean up docs
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Andrew-S-Rosen committed Oct 13, 2023
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4 changes: 2 additions & 2 deletions docs/install/wflow_engines.md
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Expand Up @@ -6,7 +6,7 @@ Using a workflow engine is a crucial component for scaling up quacc calculations

For a comparison of the different compatible workflow engines, refer to the [Workflow Engines Overview](../user/basics/wflow_overview.md) section.

=== "Parsl"
=== "Parsl"

**Installation**

Expand All @@ -18,7 +18,7 @@ Using a workflow engine is a crucial component for scaling up quacc calculations

Parsl has [many configuration options](https://parsl.readthedocs.io/en/stable/userguide/configuring.html), which we will cover later in the documentation.

=== "Covalent"
=== "Covalent"

**Installation**

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4 changes: 2 additions & 2 deletions docs/user/basics/wflow_overview.md
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Expand Up @@ -8,7 +8,7 @@ Everyone's computing needs are different, so we ensured that quacc is interopera

If you are new to workflow engines, we recommend trying either **Parsl** or **Covalent**. If you have a need for speed and appreciate flexibility, Parsl is the choice for you. If you are looking for a visual dashboard with an emphasis on distributed compute resources, Covalent may be worth considering.

=== "Parsl"
=== "Parsl"

[Parsl](https://github.com/Parsl/parsl) is a workflow management solution out of Argonne National Laboratory, the University of Chicago, and the University of Illinois. It is well-adapted for running on virtually any HPC environment with a job scheduler.

Expand All @@ -28,7 +28,7 @@ Everyone's computing needs are different, so we ensured that quacc is interopera
- Monitoring job progress is more challenging and less detailed than other solutions
- The concept of always returning a "future" can be confusing for new users

=== "Covalent"
=== "Covalent"

[Covalent](https://github.com/AgnostiqHQ/covalent/) is a workflow management solution from the company [Agnostiq](https://agnostiq.ai/).

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12 changes: 6 additions & 6 deletions docs/user/basics/wflow_syntax.md
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Expand Up @@ -8,7 +8,7 @@ Here, we provide code snippets for several decorator-based workflow engines. For

To help enable interoperability between workflow engines, quacc offers a unified set of decorators: [`#!Python @job`](https://quantum-accelerators.github.io/quacc/reference/quacc/utils/wflows.html#quacc.wflow.job), [`#!Python @flow`](https://quantum-accelerators.github.io/quacc/reference/quacc/utils/wflows.html#quacc.wflow.flow), and [`#!Python @subflow`](https://quantum-accelerators.github.io/quacc/reference/quacc/utils/wflows.html#quacc.wflow.subflow).

=== "Parsl"
=== "Parsl"

Take a moment to read the Parsl documentation's ["Quick Start"](https://parsl.readthedocs.io/en/stable/quickstart.html) to get a sense of how Parsl works. Namely, you should understand the concept of a [`#!Python python_app`](https://parsl.readthedocs.io/en/stable/1-parsl-introduction.html#Python-Apps) and [`#!Python join_app`](https://parsl.readthedocs.io/en/stable/1-parsl-introduction.html?highlight=join_app#Dynamic-workflows-with-apps-that-generate-other-apps), which describe individual compute tasks and dynamic job tasks, respectively.

Expand All @@ -22,7 +22,7 @@ To help enable interoperability between workflow engines, quacc offers a unified

</center>

=== "Covalent"
=== "Covalent"

Take a moment to learn about the main [Covalent Concepts](https://docs.covalent.xyz/docs/user-documentation/concepts/concepts-index), namely the [`#!Python @ct.electron`](https://docs.covalent.xyz/docs/user-documentation/concepts/covalent-basics#electron) and [`#!Python @ct.lattice`](https://docs.covalent.xyz/docs/user-documentation/concepts/covalent-basics#lattice) decorators, which describe individual compute tasks and workflows, respectively.

Expand Down Expand Up @@ -84,7 +84,7 @@ graph LR
A[Input] --> B(add) --> C(mult) --> D[Output];
```

=== "Parsl"
=== "Parsl"

!!! Important

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2. The `#!Python @flow` decorator doesn't actually do anything when using Parsl, so we chose to not include it here for brevity.

=== "Covalent"
=== "Covalent"

!!! Important

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## Learn More

=== "Parsl"
=== "Parsl"

If you want to learn more about Parsl, you can read the [Parsl Documentation](https://parsl.readthedocs.io/en/stable/#). Please refer to the [Parsl Slack Channel](http://parsl-project.org/support.html) for any Parsl-specific questions.

=== "Covalent"
=== "Covalent"

If you want to learn more about Covalent, you can read the [Covalent Documentation](https://docs.covalent.xyz/docs/). Please refer to the Covalent [Discussion Board](https://github.com/AgnostiqHQ/covalent/discussions) for any Covalent-specific questions.

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4 changes: 2 additions & 2 deletions docs/user/wflow_engine/executors1.md
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Expand Up @@ -2,7 +2,7 @@

In the previous examples, we have been running calculations on our local machine. However, in practice, you will probably want to run your calculations on one or more HPC machines. This section will describe how to set up your workflows to run on HPC machines using your desired workflow engine to scale up your calculations.

=== "Parsl"
=== "Parsl"

Out-of-the-box, Parsl will run on your local machine. However, in practice you will probably want to run your Parsl workflows on HPC machines.

Expand Down Expand Up @@ -96,7 +96,7 @@ In the previous examples, we have been running calculations on our local machine

Parsl supports tying specific executors to a given `PythonApp`, as discussed in the [Multi-Executor section](https://parsl.readthedocs.io/en/stable/userguide/execution.html#multi-executor) of the Parsl documentation.

=== "Covalent"
=== "Covalent"

By default, Covalent will run all jobs on your local machine using the Dask backend. This is a parameter that you can control. For instance, Covalent offers many [executor plugins](https://docs.covalent.xyz/docs/plugin) that can be installed and used to interface with a wide range of HPC, cloud, and quantum devices.

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12 changes: 6 additions & 6 deletions docs/user/wflow_engine/executors2.md
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Expand Up @@ -17,7 +17,7 @@ conda activate quacc

Then install the necessary dependencies:

=== "Parsl"
=== "Parsl"

On both remote machine:

Expand All @@ -28,7 +28,7 @@ Then install the necessary dependencies:
quacc set CREATE_UNIQUE_WORKDIR True
```

=== "Covalent"
=== "Covalent"

On both the local and remote machines:

Expand Down Expand Up @@ -66,7 +66,7 @@ Then install the necessary dependencies:

When deploying calculations for the first time, it's important to start simple, which is why you should try to run a sample EMT workflow first.

=== "Parsl"
=== "Parsl"

**Starting Small**

Expand Down Expand Up @@ -203,7 +203,7 @@ When deploying calculations for the first time, it's important to start simple,
)
```

=== "Covalent"
=== "Covalent"

Run the following code on the local machine:

Expand Down Expand Up @@ -289,7 +289,7 @@ In this example, we will run a sample VASP recipe that will highlight the use of

First, prepare your `VASP_PP_PATH` environment variable in the `~/.bashrc` of your remote machine as described in the [ASE documentation](https://wiki.fysik.dtu.dk/ase/ase/calculators/vasp.html#pseudopotentials). When you're done, follow the steps below.

=== "Parsl"
=== "Parsl"

From an interactive resource like a Jupyter Notebook or IPython kernel on the remote machine:

Expand Down Expand Up @@ -347,7 +347,7 @@ First, prepare your `VASP_PP_PATH` environment variable in the `~/.bashrc` of yo
print(future1.result(), future2.result())
```

=== "Covalent"
=== "Covalent"

Run the following code on the local machine:

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8 changes: 4 additions & 4 deletions docs/user/wflow_engine/wflow_engines1.md
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Expand Up @@ -14,7 +14,7 @@ graph LR
A[Input] --> B(Relax) --> C[Output];
```

=== "Parsl"
=== "Parsl"

!!! Important

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2. The use of `.result()` serves to block any further calculations from running until it is resolved. Calling `.result()` also returns the function output as opposed to the `AppFuture` object.

=== "Covalent"
=== "Covalent"

!!! Important

Expand Down Expand Up @@ -168,7 +168,7 @@ graph LR
B --> F(Slab Relax) --> J(Slab Static) --> K[Output];
```

=== "Parsl"
=== "Parsl"

```python
from ase.build import bulk
Expand All @@ -184,7 +184,7 @@ graph LR
print(future.result())
```

=== "Covalent"
=== "Covalent"

```python
import covalent as ct
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12 changes: 6 additions & 6 deletions docs/user/wflow_engine/wflow_engines2.md
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Expand Up @@ -11,7 +11,7 @@ graph LR
A[Input] --> B(Relax) --> C(Static) --> D[Output];
```

=== "Parsl"
=== "Parsl"

!!! Important

Expand Down Expand Up @@ -62,7 +62,7 @@ graph LR

Parsl `PythonApp` objects will implicitly know to call `.result()` on any `AppFuture` it receives, and it is good to rely on this fact to avoid unecessary blocking.

=== "Covalent"
=== "Covalent"

!!! Important

Expand Down Expand Up @@ -209,7 +209,7 @@ graph LR
A[Input] --> C(Relax) --> D[Output];
```

=== "Parsl"
=== "Parsl"

```python
from ase.build import bulk, molecule
Expand Down Expand Up @@ -238,7 +238,7 @@ graph LR
print(result1, result2)
```

=== "Covalent"
=== "Covalent"

```python
from ase.build import bulk, molecule
Expand Down Expand Up @@ -338,7 +338,7 @@ graph LR
C(Make Slabs) --> G(Slab Relax) --> H[Output];
```

=== "Parsl"
=== "Parsl"

```python
from ase.build import bulk
Expand Down Expand Up @@ -367,7 +367,7 @@ graph LR

1. We chose to set `#!Python run_static=False` here to disable the static calculation that is normally carried out in this workflow.

=== "Covalent"
=== "Covalent"

```python
import covalent as ct
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