EMMA Docker Container

Instructions

Quickstart

docker run --rm -p 8787:8787 -e PASSWORD=yourpasswordhere adamwilsonlab/emma:latest

Visit localhost:8787 in your browser and log in with username rstudio and the password you set. NB: Setting a password is now REQUIRED. Container will error otherwise.

Local machine (no password)

If you are running on a local machine with other security mechanisms, you can use the following:

docker run --rm \
  -p 127.0.0.1:8787:8787 \
  -e DISABLE_AUTH=true \
  adamwilsonlab/emma:latest

HPC

To use this container in an HPC environment like UB's CCR, you need to use singularity (a wrapper for docker that keeps things secure in a networked environment).

You must be on campus or in the UB VPN to use this service.

Set up Apptainer (Singularity)

You only need to run this once (unless you want to update the container). Before building the container, you will need to set some temp/cache folders or the build will fail because the home directory doesn't have much room.

First, you can log into a compute node. For example:

ssh vortex.ccr.buffalo.edu

salloc --cluster=faculty --qos=adamw --partition=adamw  --job-name "InteractiveJob" --nodes=1 --ntasks=2 --mem=5G -C INTEL --time=05:20:00

Then set the following environment variables, create a few directories, and build the container.

# define groupname for paths
export GROUP="adamw"

# mount project folder inside container:
export PROJECT_FOLDER="/projects/academic/"$GROUP

# define local working folder to build the SIF file (this is faster than network storage)
export APPTAINER_CACHEDIR="/scratch/"$USER"/apptainer"
export APPTAINER_TMPDIR=$APPTAINER_CACHEDIR"/tmp"
export APPTAINER_LOCALCACHEDIR=$APPTAINER_CACHEDIR"/tmp"

# set singularity cache and tmp directories to the same as apptainer
# needed because CCR is still using singularity and it will use these directories
export SINGULARITY_CACHEDIR=$APPTAINER_CACHEDIR
export SINGULARITY_TMPDIR=$APPTAINER_TMPDIR
export SINGULARITY_LOCALCACHEDIR=$APPTAINER_LOCALCACHEDIR

# path to singularity container file.  If you want to use a different image, you'll need
# to update this line.
export DOCKER_PATH="docker://adamwilsonlab/emma:latest"
export SIF_FILE="AdamWilsonLab-emma_docker-latest.sif"
export SIF_PATH=$PROJECT_FOLDER"/users/"$USER"/apptainer/"

# Create the folders if they don't already exist
mkdir -p $PROJECT_FOLDER"/users/"$USER"/apptainer" # create project folder
mkdir -p $APPTAINER_CACHEDIR/tmp # create apptainer cache directory
mkdir -p $APPTAINER_CACHEDIR/run # create apptainer run directory
mkdir -p $APPTAINER_CACHEDIR/rstudio # create apptainer RStudio directory

# go to cachedir for faster build
cd $APPTAINER_CACHEDIR

## Build the singularity image (.SIF) directly from Docker image locally
### If it takes too long, you can use `nohup` first to allow it to keep running if the SSH connection is broken.
singularity build --force $SIF_FILE $DOCKER_PATH &

# Move it to its permanent home
mkdir -p $SIF_PATH # create SIF path if it doesn't exist
mv $SIF_FILE $SIF_PATH # move the SIF file to its permanent location

Now the container exists at $SIF_PATH and is ready to be used. You only need to repeat the above steps if you want to update the container.

Run the container for interactive computation

SSH to vortex.ccr.buffalo.edu and then request an interactive job with something like:

ssh vortex.ccr.buffalo.edu
salloc --cluster=faculty --qos=adamw --partition=adamw  --job-name "InteractiveJob" --nodes=1 --ntasks=2 --mem=5G -C INTEL --time=05:20:00

Then run the following to start using R from the container:

export PROJECT_FOLDER="/projects/academic/adamw/"
export APPTAINER_CACHEDIR="/scratch/"$USER"/apptainer"
export SIF_PATH=$PROJECT_FOLDER"/users/"$USER"/apptainer"
export SIF_FILE="AdamWilsonLab-emma_docker-latest.sif"

# set singularity cache and tmp directories to the same as apptainer
# needed because CCR is still using singularity and it will use these directories
export SINGULARITY_CACHEDIR=$APPTAINER_CACHEDIR
export SINGULARITY_TMPDIR=$APPTAINER_TMPDIR
export SINGULARITY_LOCALCACHEDIR=$APPTAINER_LOCALCACHEDIR


singularity run \
      --bind $PROJECT_FOLDER:$PROJECT_FOLDER \
      --bind $APPTAINER_CACHEDIR/tmp:/tmp \
      --bind $APPTAINER_CACHEDIR/run:/run \
      $SIF_PATH/$SIF_FILE R

Use CCR OnDemand

You can also use CCR OnDemand Use CCR's OnDemand portal