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.

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.

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}" !

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.