# Running Cellpose/napari on Janelia's Cluster
## 1) Login to [Janelia's NoMachine via a browser](https://login2.int.janelia.org)
You must be on the campus' secure network or the VPN to do this.

**Enter your Janelia login credentials to login**
**Then start a new virtual machine**


**IF this process fails, like it does here:**
Then you most likely need to have your user account added for cluster access.

## 2) Install napari/Cellpose
### a) Open a terminal instance

### *) If you don't already have micromamba installed, strongly consider doing so (If conda is already installed that will work instead, but is slower):
Run the following in the terminal (simply press enter anytime it asks for input):

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

Then close the terminal and open a new instance. Run the following commands:

micromamba config append channels conda-forge
micromamba config append channels nvidia
micromamba config append channels pytorch

### b) Initialize an interactive GPU bash session on the slurm cluster to install from:
In the terminal run the following:

bsub -n 4 -gpu "num=1" -q gpu_short -Is /bin/bash

Wait for the job to launch:

### The steps below are very similar for both Cellpose and napari, but I will split them up for clarity. First, napari:
### c.napari) Create and activate a new micromamba environment:
*If you're using conda instead, just replace ```micromamba``` in the following commands with ```conda```*

Run:

micromamba create -y -n napari-env python=3.10

Once that has completed, run:

micromamba activate napari-env

### d.napari) Install:
Run:

python -m pip install "napari[all]"

For more help, see [the napari installation instructions](https://napari.org/stable/tutorials/fundamentals/installation).

### Now for Cellpose:
### c.cellpose) Create and activate a new micromamba environment:
*If you're using conda instead, just replace ```micromamba``` in the following commands with ```conda```*

Run:

micromamba create -y -n cellpose-env python=3.10

Once that has completed, run:

micromamba activate cellpose-env

### d.cellpose)
run:

python -m pip install "cellpose[gui]"

For more help, see [the Cellpose installation instructions](https://github.com/mouseland/cellpose?tab=readme-ov-file#instructions).

### e) End the GPU session by running ```exit```

## 3) Run an interactive GPU session for napari/Cellpose:
### napari:
#### i) Activate the environment with ```micromamba activate napari-env```
#### ii*) Launch the job with ```bsub -n 12 -gpu "num=1" -q gpu_short -Is napari```

### cellpose:
#### i) Activate the environment with ```micromamba activate cellpose-env```
#### ii*) Launch the job with ```bsub -n 12 -gpu "num=1" -q gpu_short -Is cellpose```

### *) Options for the job can be configured as follows:
* include ```-B``` to receive email notifications associated with your jobs.
* ```-n 12``` corresponds to 12 CPUs for the job. Each CPU is generally allocated 15GB of RAM (memory).
* ```-gpu "num=1"``` corresponds to 1 GPU. Most GPU nodes offer up to 4 GPUs at once.
* ```-q gpu_short``` corresponds to the "gpu_short" queue. More information about the GPU queues is available on [the Scientific Computing Systems Confluence](https://wikis.janelia.org/display/SCS/Janelia+Compute+Cluster#JaneliaComputeCluster-GPUComputeCluster). But, in general, "gpu_short" will leverage just about any available gpus. gpu_tesla, gpu_a100, and gpu_h100 are also options (listed in increasing order of power).

## 4) If you run a big job, leave the remote virtual machine alive and/or make sure you have run the job in a ```tmux``` or ```screen``` persistent session (see more here ).
Before running :
* Create a [tmux](https://tmuxcheatsheet.com/) session using `tmux` or `tmux new -s napari` if you want to name it
* Run [part (3)](https://hackmd.io/S3YSFh-XRK2caW6w1rs_TA?both#3-Run-an-interactive-GPU-session-for-napariCellpose) code
* Detach from session using 

This give you the ability for a forever running ssh session. you can re attach to again again by:
* Getting the session name via `tmux ls`
* Attach to it using `tmux attach -t name` ( Will be named `0` if it is created via `tmux` only )

If you feel like you need to double check it's still running, you can see the space you're taking on the cluster here: https://cluster-status.int.janelia.org/cluster_status/