SCP: Moving a workspace to SSRDE
MOVING A WORKSPACE TO SSRDE WITH WINDOWS
The process for moving your workspace from your local computer is different depending on the operating system you use. If you're on a Mac or Linux machine, we'll show you how to do this in the next section.
For Windows, though, you'll need a program called WinSCP. SCP stands for "secure copy", WinSCP is a client that allows you to connect to remote machines securely so that you can drag and drop files to and from those remote machines.
Once you've installed and opened WinSCP, you'll be greeted by a login page. The hostname is the machine you want to connect to, in this case ssrde.ucsd.edu, and your login information is your AD username and password (the same credentials you use to connect to UCSD Protected). You don't have to change any of the other settings, although you can save the SSRDE hostname, as well as your credentials for later use if you choose:
If this is your first time connecting to WinSCP, you might see a prompt asking you about a "security certificate" or an "ssh key" or something along those lines. If you're sure you spelled the hostname right, and that prompt is coming up in a context you'd expect it to -- specifically, if it shows up the first time you're connecting to a server you want to connect to -- then it's OK to hit Yes. If it pops up when you don't mean to be connecting to a server, hit Cancel, and if it keeps happening contact SSCF:
Once you've logged in successfully, you'll see two panes that represent your local and remote machines. You can navigate through both of them to the locations you need and then drag and drop files or folders to transfer them from one location to the other. You may see an additional dialogue when transferring folders similar to the following image, but you can use the default settings and simply hit OK:
MOVING A WORKSPACE TO SSRDE WITH MAC/LINUX
Mac and Linux machines also use SCP to move files to and from remote machines. However, instead of a client these operating systems use scp as a Terminal command.
The basic syntax is: scp source:/path/to/file destination:/path/to/desired_directory
If we want to move our dataset to our personal storage on SSRDE, the command is scp /path/to/dataset <username>@ssrde.ucsd.edu:/home/<username>
We can copy entire folders over with the -r flag. If we want the destination to just be our home directory (the directory we start in when we connect to SSRDE), all we have to type for the destination path is ~
We can also copy data and code from SSRDE to our local computers, we just provide the command with a source location on SSRDE and a destination on our personal machine:
Note that the destination requires login information -- <username>@ssrde.ucsd.edu -- and the source does not. This is because you're initiating the transfer from your local computer. It's very important that you use scp either before you connect to SSRDE through ssh or after you've ended your connection.
If you do so during an SSRDE session, SSRDE becomes the local computer and your personal device becomes the remote; it's much harder for the network to find your device than it is for it to find SSRDE, which means you likely won't be able to establish a connection and your transfer commands will fail.
A good workflow template is something like the following:
Develop your code locally using resources like RStudio, SublimeText, or the IDE of your choice
Transfer your finished code and data to SSRDE with scp
Run your code on your data as an SSRDE job, then end your SSRDE session
Transfer any finished results you need on your local machine from SSRDE using scp
SSCF representatives are not programmers and will not be able to provide substantial help with your code itself, but we can assist with the transfer and organization of files, navigating the server, and using the job submission program Slurm.
If you need additional help setting up your environment, please don't hesitate to contact SSCF at firstname.lastname@example.org (or reach out to your department SSCF representative, ex. email@example.com) and we'll be happy to assist!