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Update Running_jobs_on_our_clusters.md
gwenwhite Jun 25, 2021
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Update Running_jobs_on_our_clusters.md
gwenwhite Jun 29, 2021
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61 changes: 61 additions & 0 deletions wiki/pages/Running_jobs_on_our_clusters.md
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Expand Up @@ -10,6 +10,67 @@ If you are unsure what 'TPS' stands for and why we want so many of them, you sho
Also, you'll need accounts on our supercomputing clusters - take a look at [Accounts for computer clusters](Accounts_for_computer_clusters.md) to get set up on Fry and Kestrel.


# Order of operations
### 1. Pull in the planckton image
In the home directory of your cluster, create an ```images``` directory
```
cd $HOME
mkdir images
```
Inside the images directory, pull in the [planckton](https://github.com/cmelab/planckton) image
```
cd images
singularity pull docker://cmelab/planckton_gpu_v0.4.0.sif
export PLANCKTON_SIMG=$(pwd)/planckton_gpu_v0.4.0.sif
```


### 2. Clone signac-flow
Inside of your project workspace clone [signac-flow](https://github.com/glotzerlab/signac-flow.git)
```
cd $PROJECT
git clone https://github.com/glotzerlab/signac-flow.git
```
Inside of the signac-flow clone directory, pull commit #441 then checkout the corresponding branch.
```
cd signac-flow
git fetch origin pull/441/head:pr441
git checkout pr441
pip install .
```


### 3. Clone planckton-flow
In the home of your project workspace, create a directory called ```jobs``` and clone [planckton-flow](https://github.com/cmelab/planckton-flow) into it.
```
cd $HOME
mkdir jobs
cd jobs
git clone https://github.com/cmelab/planckton-flow.git
```
Go into the planckton-flow clone directory, and set up the planckton-flow environment inside of it
```
cd planckton-flow
conda env create -f environment.yml
conda activate planckton-flow
```

### 4. Run a job
Edit the init.py file in the src directory to the variables you want to see ran. Use python to initialize the jobs and then submit the project.py file to run the jobs using the variables you set. Check the status of you job by running the squeue command.
```
vim src/init.py
python src/init.py
python src/project.py submit
squeue -u <your username>
```


### Celebrate the fact that you just ran a job!!!
```
echo "WOOHOO"
```


# What is a job scheduler and which one am I using? #


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