Connecting to Rstudio Server on Farm

Link to Titus's Github Instructions

Starting a Tmux session

I highly recommend starting a tmux session to run R (can also use screen ):

tmux new -s rstudio

To detach from your tmux session use Ctrl+B then D

To relogin or reattach to the session

tmux a -t rstudio

Connecting to Rstudio on Farm using without a Conda Environment

Rstudio can not run on the head node, must start a srun (example below)

srun -p bmm --time=12:00:00 --nodes=1 \
    --cpus-per-task 2 --mem 100GB --pty /bin/bash

If you have conda installed, you may need to run the following to use the system provided R module:

conda deactivate
unset CONDA_EXE

To use a system-installed R package:

module load R

Load and run rstudio server

module load rstudio-server
rstudio-launch

You should then see a message like this:

Run the following command in a new terminal on your computer:

    ssh -L52842:aa10:52842 [e-mail]

• Copy the newly generated ssh and paste it in a new terminal on your computer. Do not close your current terminal.

You should also see this message:

Then, on your computer, navigate your browser to:

    URL: http://localhost:12345
    Username: username
    Password: very-long-pass-word-copy-and-past-in-brower

• Copy and paste the url into your web browser of choice. When prompted for username and password, use the provided username and password.

You should then be able to use Rstudio on Farm.

Connecting to Rstudio on Farm using a Conda Environment

Recommend starting a tmux session to run R (can also use screen ):

tmux new -s rstudio

To relogin to the session

tmux a -t rstudio

Create a conda environemetn

conda create -n r-env

Activate the conda env:

conda activate r-env

Make sure your channels are in the correct order:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

• if this doesn't work may need to check Biocondato see if the recommended configuration has changed
  To created a new R environment with phyloseq use:

mamba create -n r-env2 bioconductor-phyloseq

Or you can name the conda environment, r-env if it is your first R environment

mamba create -n r-env bioconductor-phyloseq

Rstudio can not run on the head node, must start a srun (example below)

srun -p bmm --time=12:00:00 --nodes=1 \
    --cpus-per-task 2 --mem 100GB --pty /bin/bash

To activate the Rstudio and the conda environemnt use:

module load rstudio-server
conda activate r-env
rstudio-launch

You should then see a message like this:

Run the following command in a new terminal on your computer:

    ssh -L12345:aa10:12345 [e-mail]

• Copy the newly generated ssh and paste it in a new terminal on your computer. Do not close your current terminal.

You should also see a message like this:

Then, on your computer, navigate your browser to:

    URL: http://localhost:12345
    Username: username
    Password: very-long-pass-word-copy-and-past-in-brower

• Copy and paste the url into your web browser of choice. When prompted for username and password, use the provided username and password.

You should then be able to use Rstudio on Farm.