During this hands-on, all computations will be done on a remote linux (ubuntu 18) server that was rented on the cloud (Amazon Web Services, AWS) specifically for this summer course.
This means you will have to be able to:
connect/login to the remote server (to launch all computations there)
edit files on the remote server from you laptop
The instructions below will allow you to do that and to configure your account on the server to run jobs properly.
In order to edit remote files you have two possibilities:
install sshfs to mount the server file system on your laptop and use the editor of your choice on your laptop
install the atom editor with packages like platform-ide-terminal and remote-edit-ni (see Geert's page for more information)
You will receive an e-mail shortly before the workshop with a key, username and IP address to login on a cloud server. Login like this:
ssh -i path/to/key/key_[USERNAME].pem [USERNAME]@[AWS_IP]
Launch MobaXterm
Go to session and then ssh
enter the remote host (AWS_IP), the username and the key file
On your laptop, make an mnt/aws directory in your home where you the remote server file system will be mounted and make a symboli link to it in your home:
cd mkdir mnt mkdir mnt/aws ln -s mnt/aws
Enable mounting the remote server file system on your laptop by adding the following lines to your ~/.bashrc file:
alias maws='sshfs [USERNAME]@[AWS_IP]:/home/[AWS_IP] $HOME/mnt/aws -o IdentityFile=path/to/key/key_[USERNAME].pem,uid=1000,gid=1000,follow_symlinks,allow_other,workaround=rename'
If it does not work on your mac then type this on a terminal:
sshfs -o IdentityFile=path/to/key_[USERNAME].pem,defer_permissions,reconnect,ServerAliveInterval=15,ServerAliveCountMax=3 [USERNAME]@[AWS_IP]:/home/[USERNAME] $HOME/mnt/aws
You can also skip the above and use atom with the remote-edit-ni package (see Geert's page for more information or windows details provided below).
Use Notepad++ with NppFTP plugin with the following details:
protocol: sftp
username: your username
hostname: server IP
port: 22
authentication/logon type: path to private key file
Add these lines at the end of your ~/.bashrc file:
alias ll='ls -lhrt' alias c='~sdjebali/SIB_august2020/code/analysis.scripts/check_simple.sh' export PATH=~sdjebali/SIB_august2020/code/analysis.scripts/:/usr/local/bin:~sdjebali/bin/:$PATH
Once you have logged in for the first time on the remote server, initiate conda:
/opt/miniconda3/bin/conda init