UMIACS Servers

Notes on using UMIACS servers

Modules

Use modules to load programs you need to run.

Notes

• You can load modules in your .bashrc file

# List loaded modules
module list

# Load a module
module load [my_module]

# List all available modules
module avail

Some useful modules in my .bashrc file

module load tmux
module load cuda/10.0.130
module load cudnn/v7.5.0
module load Python3/3.7.6
module load git

Python

Do not install anaconda. You will run out of space.
Load the Python 3 module adding the following to your .bashrc file

module load Python3/3.7.6
export PATH="${PATH}:$(python3 -c 'import site; print(site.USER_BASE)')/bin"

Then run the following to get pip installed

curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py --user

Notes

• You will need to install things with pip --user
• You may need to add your local site-packages to your PYTHONPATH environment variable
  • Add this to .bashrc:
  • export PYTHONPATH="${PYTHONPATH}:/nfshomes/$(whoami)/.local/lib/python3.7/site-packages/"
• You can also install using pip install --target=/my-libs-folder/

Install PyTorch

pip install --user torch===1.3.1 torchvision===0.4.2 -f https://download.pytorch.org/whl/torch_stable.html

pip install --user torch===1.3.1 torchvision===0.4.2 -f https://download.pytorch.org/whl/torch_stable.html -t /scratch0/davidli

MBRC Cluster

See UMIACS MBRC

SLURM Job Management

See https://docs.rc.fas.harvard.edu/kb/convenient-slurm-commands/

1 GPU

srun --pty --gres=gpu:1 --mem=16G --qos=high --time=47:59:00 bash

2 GPUS mbrc01

srun --pty --gres=gpu:2 --mem=16G --qos=default --time=23:59:00 -w mbrc01 bash

Notes

• You can add -w mbrc01 to pick mbrc01
• -c 4 for 4 cores

See Jobs

See my own jobs

squeue -u <user> -o "%8i %10P %8j %10u %10L %5b"

Formatting

• %L is remaining time
• %b is the number of GPUs

See all jobs

squeue

.bashrc

Expand

My .bashrc

#PS1='\w$ '
PS1='\[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$'

if test -f "/opt/rh/rh-php72/enable"; then
    source /opt/rh/rh-php72/enable
fi

export NVM_DIR="$HOME/.nvm"
[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"  # This loads nvm
[ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"  # This loads nvm bash_completion

command_exists() {
  type "$1" &> /dev/null ;
}


# Modules
if command_exists module ; then
  module load tmux
  module load cuda/10.0.130
  module load cudnn/v7.5.0
  module load Python3/3.7.6
  module load git/2.25.1
fi
if command_exists python3 ; then
  alias python=python3
fi

if command_exists python3 ; then
  export PATH="${PATH}:$(python3 -c 'import site; print(site.USER_BASE)')/bin"
fi
export PYTHONPATH="${PYTHONPATH}:/nfshomes/dli7319/.local/lib/python3.7/site-packages/"

export PATH="${HOME}/bin/:${PATH}"

Software

git

The MBRC cluster has an git available in the modules.
Then you can download git-lfs compiled and drop it in ~/bin/.
Make sure ${HOME}/bin is in your path and run git lfs install

Notes

• Make sure you have a recent version of git
  • E.g. module load git/2.25.1