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Copy file name to clipboardExpand all lines: docs/hpc/02_connecting_to_hpc/01_connecting_to_hpc.md
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@@ -16,7 +16,7 @@ The following sections will outline basic ways to connect to the Greene cluster.
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To connect to HPC systems, you have to configure the SSH client on your machine. We recommend the following configuration:
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```sh
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Host torch.hpc.nyu.edu dtn.hpc.nyu.edu
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Host dtn.hpc.nyu.edu
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User <NetID>
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StrictHostKeyChecking no
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ServerAliveInterval 60
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Someone could be eavesdropping on you right now (man-in-the-middle attack)!
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It is also possible that a host key has just been changed.
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```
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Do not be alarmed - this is an issue that occurs because the Greene and Torch clusters have multiple login nodes. For instance, `torch.hpc.nyu.edu` resolves to one of three possible login nodes (`log-1`, `log-2`, and `log-3`). The configuration directive `StrictHostKeyChecking no` referenced in the recommended config above will prevent this error. Ensure that you have not missed adding it.
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Do not be alarmed - this is an issue that occurs because the Greene and Torch clusters have multiple login nodes. For instance, `login.torch.hpc.nyu.edu` resolves to one of three possible login nodes (`log-1`, `log-2`, and `log-3`). The configuration directive `StrictHostKeyChecking no` referenced in the recommended config above will prevent this error. Ensure that you have not missed adding it.
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:::
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:::info SSH Timeout errors
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Once you're on the VPN or the main NYU network on campus you can SSH directly to torch like so:
Copy file name to clipboardExpand all lines: docs/hpc/02_connecting_to_hpc/02_x11_forwarding.md
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In rare cases when you need to interact with GUI applications on HPC clusters, you need to enable X11 forwarding for your SSH connection. Mac and Linux users will need to run the ssh commands described above with an additional flag:
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```sh
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ssh -Y <NYU_NetID>@torch.hpc.nyu.edu
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ssh -Y <NYU_NetID>@login.torch.hpc.nyu.edu
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```
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However, Mac users need to install [XQuartz][xquartz], since X-server is no longer shipped with the macOS.
You'll need to log in with your password at least once even if you plan to use SSH keys in the future because we'll need to set up your keys.
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Once you are on the NYU WiFi or VPN you can connect with:
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```bash
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ssh <NetID>@torch.hpc.nyu.edu
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ssh <NetID>@login.torch.hpc.nyu.edu
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```
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When you are logged in you will see information about your last login, the host you've connected to, and your storage quota. It should look something like this:
in which `@` and `:` are field separators and `remote_destination` is a path relative to your remote home directory, or a new filename if you wish to change it, or both a relative path *and* a new filename. If you don’t have a specific folder in mind you can omit the `remote_destination` and the file will be copied to your home directory on the remote computer (with its original name). If you include a `remote_destination`, note that `scp` interprets this the same way `cp` does when making local copies: if it exists and is a folder, the file is copied inside the folder; if it exists and is a file, the file is overwritten with the contents of `local_file`; if it does not exist, it is assumed to be a destination filename for `local_file`.
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Upload the lesson material to your remote home directory like so:
To transfer an entire directory, we add the `-r` flag for “recursive”: copy the item specified, and every item below it, and every item below those… until it reaches the bottom of the directory tree rooted at the folder name you provided.
As written, this will place the local directory and its contents under your home directory on the remote system. If a trailing slash is added to the source, a new directory corresponding to the transferred directory will not be created, and the contents of the source directory will be copied directly into the destination directory.
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To download a file, we simply change the source and destination:
This command will fail, as the correct port in this case is the default: 22.
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To connect to the cluster, we’ll just need to enter our credentials at the top of the screen:
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- Host: `sftp://torch.hpc.nyu.edu`
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- Host: `sftp://login.torch.hpc.nyu.edu`
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- User: Your NetID
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- Password: Your NetID password
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- Port: (leave blank to use the default port)
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Say you have a “data” folder containing 10,000 or so files, a healthy mix of small and large ASCII and binary data. Which of the following would be the best way to transfer them to Greene?
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```bash
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[user@laptop ~]$ scp -r data NYUNetID@torch.hpc.nyu.edu:~/
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[user@laptop ~]$ scp -r data NYUNetID@login.torch.hpc.nyu.edu:~/
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```
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```bash
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[user@laptop ~]$ rsync -ra data NYUNetID@torch.hpc.nyu.edu:~/
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[user@laptop ~]$ rsync -ra data NYUNetID@login.torch.hpc.nyu.edu:~/
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```
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```bash
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[user@laptop ~]$ rsync -raz data NYUNetID@torch.hpc.nyu.edu:~/
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[user@laptop ~]$ rsync -raz data NYUNetID@login.torch.hpc.nyu.edu:~/
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