JHU Economics August 24, Galaxy How To SSH and RDP

Transcription

1 Galaxy How To SSH and RDP The host name for the Econ Linux server is galaxy.econ.jhu.edu. It is running Ubuntu LTS. Please NOTE: you need to be connected to the Hopkins VPN before attempting a connection if you are off campus. Please refer to the Ubuntu LTS documentation for additional help: To connect to it you can use SSH, or RDP remote desktop. 1. SSH only: Any SSH client will work. Putty (SSH): To connect from a Windows machine, download putty from and install. Any other SSH application should work as well. Open putty and type in the Host Name for the Ubuntu machine -(galaxy.econ.jhu.edu). You can name and save your session. Type your user name and password and login. To exit type exit at the prompt $.

2 For Macs - in a terminal session enter: $ ssh user-name@galaxy.econ.jhu.edu To keep processes running after ending the ssh session: ssh into your remote box. Type screen, then start the process you want. Press Ctrl-A then Ctrl-D. This will "detach" your screen session but leave your processes running. You can now log out of the remote box. If you want to come back later, log on again and type "screen -r". This will "resume" your screen session, and you can see the output of your process. To stop a process kill processid Will attempt to kill the indicated process 'gently", giving it a chance to save and close files and perform other housekeeping. If a subsequent check, after a few seconds, with the ps command shows that the errant process is still running, you can give the much more definitive "hard" kill: kill -9 processid

3 2. RDP connections: Please use the regular RDC application for Windows, the Microsoft Remote Desktop app for Mac and Remmina Remote Desktop for Linux. Starting with Ubuntu the unity desktop is no longer accessible through VNC. RDP works over VNC and uses the MATE Desktop Environment instead When using the Mac or Linux remote desktop clients you may get an error immediately after connecting just press Ok and you will get to the regular login screen below. Please enter your User ID and password at the next screen. If this is the first time you are logging in, or after a server restart, leave the port as is (-1). Important: Please note the port number on the next screen 59XX. You will be using it at subsequent logins. Replace the -1 with this number. This is the only way in the moment that you can get back to your

4 original session. Please DO NOT use the log out option in the MATE desktop, just disconnect (X out) from your RDP connection when you are done. If you forgot, or are unsure of your port number, please open a terminal session (you can do this either within Ubuntu, or using SSH). Your port number is 59 followed by the number after the colon - in this case 5912.

5 3. Customizing the MATE menu and panel: To customize the Mate menu right click on Applications and choose Edit Menus. To add an application to the panel right click on it and choose add this launcher to panel. NOTE: Please do not use the Log out or Shut Down options under System.

6 4. Connecting and mounting network shares: Click on Places in the panel and then choose Connect to Server. Enter the appropriate server name, type, share and log on information. If you need the path to your network files the mount point for network shares is at /run/user/xxxx/gvfs/smbshare:domain=win.ad.jhu.edu,server=stella.win.ad.jhu.edu,share=share_name,user=user_id.

7 To unmount a share right click on it and choose unmount or click on eject. To locate the folder in Terminal type: $cd /run/user/xxxx/gvfs/smb-share:domain=win.ad.jhu.edu,server=stella.win.ad.jhu.edu,share=users2,user=user_name

8 You can mount and unmount network shares manually using the terminal as well: Note: You must be logged on through RDC or VNC before doing that. $ gvfs-mount smb://stella.win.ad.jhu.edu/share_name To unmount use: $ gvfs-mount u smb://stella.win.ad.jhu.edu/share_name 5. Transferring files using WinSCP [use SFTP]

9 For Macs: Cyberduck [ Launching applications: All applications are accessible through Dash Home Applications Refer to section 3: Customizing the MATE menu and panel. 1. Stata MP4 Stata can also be launched from the terminal using the command stata-mp or xstata-mp for the graphical interface. 2. Matlab Matlab can be launched from the terminal using the command matlab. 3. Mathematica use the command mathematica at the terminal. 4. R use the command R at the terminal.

10 7. Monitoring CPU Load Please be mindful of the resources you are taking while using Galaxy, especially when running Matlab. Depending on the computation you are running, the load gets distributed among all available CPUs. Running 1 Matlab process doesn't necessarily mean using 1 CPU, or using 4 workers - 4 CPUs. For the time being, since there are no restrictions or quotas in place, please keep an eye on the average load (run "top" - press 1 to see per CPU load) each time there is a need of using more than 4-6 cores. If you notice congestion or higher than average load, please reduce the number of cores used and/or communicate to the rest of the Galaxy users that have jobs running including me as well. Also to reduce I/O overhead, which adds to the average load, consider copying and running all scripts from within your home directory on Galaxy and not over the network. You can make backup copies of all results to your network shares as often as you like.