Run Rstudio server with singularity on HPC

Background Please read the following before go ahead: what is docker? what is Rocker? what is singularity? from Harvard Research computing website: Odyssey has singularity installed. Why Singularity? There are some important differences between Docker and Singularity: Docker and Singularity have their own container formats. Docker containers may be imported to run via Singularity. Docker containers need root privileges for full functionality which is not suitable for a shared HPC environment.

open files on remote with sublime by ssh

I am still suck at vim or emacs. I use nano to edit files on remote machines. But for more complicated editing, I prefer to use sublime. use this https://github.com/randy3k/RemoteSubl for editing remote files. Steps: on remote machine, install rmate ssh bio1 curl -o ~/bin/rmate https://raw.githubusercontent.com/aurora/rmate/master/rmate chmod u+x bin/rmate on your local computer, install RemoteSubl on your local computer, open sublime, click tools –> Command Palette –> type Package control:Install Package –> type RemoteSubl to install.

set up odyssey HPC dot files

dot files Those files are originally got from Samir Amin, my labmate in Roel Verhaak’s lab. Thanks for sharing! .screenrc .bashrc .bash_profile and inside .profile.d folder, there is a file named 01_odyssey_config.sh. It was executed when you login the shell. You can grab my dot files in my github repo. Inside the .bash_profile: if [ -d $HOME/.profile.d ]; then for i in $HOME/.profile.d/*.sh; do if [ -r $i ]; then if [ "${-#*i}" !

set up ssh odyssey HPC

request an account following here. Harvard odyssey HPC requires a two-factor security login. First set up the VPN following here Then read about OpenAuth here. One can download mobile apps such as Duo and google-Authenticator on your phone, but then each time you will need to type the password to the terminal. Or you can download the java program for desktop, if you have a FAS research computing account, you should be able to download it from the link FASRC send you.