You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
run `ssh -i ~/.ssh/key_for_remote_computer <NetID>@greene.hpc.nyu.edu`.
16
16
---
17
17
18
+
## Prerequisites
19
+
To access the Greene HPC cluster, you must be connected to the NYU network. If you are physically on campus and connected via a wired connection in your office or through NYU's WiFi, you can directly SSH into the clusters without any additional steps. However, if you are off-campus or working remotely, connecting through the NYU VPN or using the gateway servers is required to establish a secure connection to the HPC systems.
20
+
21
+
### Remote Connections with the NYU VPN & HPC Gateway Server
22
+
If you are connecting from a remote location that is not on the NYU network (your home for example), you have two options:
23
+
24
+
1. VPN Option: set up your computer to use the NYU VPN. Once you've created a VPN connection, you can proceed as if you were connected to the NYU net.
25
+
26
+
2. Gateway Option: go through our gateway servers (example below). Gateways are designed to support only a very minimal set of commands and their only purpose is to let users connect HPC systems without needing to first connect to the VPN.
27
+
28
+
### Log into the Greene Cluster
29
+
NYU Campus: From within the NYU network, that is, from an on-campus location, or after you VPN inside NYU's network, you can login to the HPC clusters directly.
30
+
31
+
Off-campus: The host name of Greene is 'greene.hpc.nyu.edu'. Logging in to Greene is the two-stage process. The HPC clusters (Greene) are not directly visible to the internet (outside the NYU Network). If you are outside NYU's Network (off-campus) you must first login to a bastion host named gw.hpc.nyu.edu.
32
+
33
+
From within the NYU network, that is, from an on-campus location, or after you VPN inside NYU's network, you can log in to the HPC clusters directly. You do not need to log in to the bastion host.
34
+
35
+
To log in to the HPC cluster (Greene), simply use:
36
+
37
+
```bash
38
+
ssh <NYUNetID>@greene.hpc.nyu.edu
39
+
```
40
+
41
+
For access from Windows stations using PuTTY, please [click here](#).
42
+
43
+
To connect to VPN from Linux/MAC, please [click here](#).
44
+
45
+
From an off-campus location (outside NYU-NET), logging in to the HPC clusters is a two-step process:
46
+
47
+
1. First, log in to the bastion host, `gw.hpc.nyu.edu`. From a Mac or Linux workstation, this is a simple terminal command (replace `<NYUNetID>` with your NetID). Your password is the same password you use for NYU Home:
48
+
49
+
```bash
50
+
ssh <NYUNetID>@gw.hpc.nyu.edu
51
+
```
52
+
53
+
Windows users will need to use PuTTY, see [here](#) for instructions.
54
+
55
+
2. Next, log in to the cluster. For Greene, this is done with:
56
+
57
+
```bash
58
+
ssh <NYUNetID>@greene.hpc.nyu.edu
59
+
```
60
+
61
+
18
62
## Opening a Terminal
63
+
Accessing the Greene HPC cluster is primarily done through the Command Line Interface (CLI). A CLI provides a text-based environment that allows users to manage files, run programs, and navigate directories via command input. On macOS, the built-in CLI tool is Terminal, while Windows 10 users can leverage the Windows Subsystem for Linux (WSL) for similar functionality. Additionally, a popular tool for connecting to Linux servers from Windows is PuTTY, a free SSH client.
19
64
20
65
Connecting to an HPC system is most often done through a tool known as "SSH"
21
66
(Secure SHell) and usually SSH is run through a terminal. So, to begin using an
@@ -37,6 +82,17 @@ then a quick search on the Internet for "how to open a terminal window in" with
37
82
your particular Linux flavour appended to the end should quickly give you the
38
83
directions you need.
39
84
85
+
To connect to the gateway servers, simply open a terminal application and enter the following command:
86
+
```bash
87
+
ssh <NetID>@gw.hpc.nyu.edu
88
+
```
89
+
90
+
After typing in your password you will be logged in to the cluster. Once this connection is established, you can make one more hop and connect to one of the HPC clusters:
91
+
```bash
92
+
# this will connect you to Greene HPC cluster
93
+
ssh <NetID>@greene.hpc.nyu.edu
94
+
```
95
+
40
96
### Mac
41
97
42
98
Macs have had a terminal built in since the first version of OS X since it is
@@ -48,6 +104,19 @@ of results (it will look like a tiny, black computer screen) and you will be
48
104
presented with a terminal window. Alternatively, you can find Terminal under
49
105
"Utilities" in the Applications menu.
50
106
107
+
To connect to the gateway servers, simply open a terminal application and enter the following command:
108
+
109
+
```bash
110
+
ssh <NetID>@gw.hpc.nyu.edu
111
+
```
112
+
113
+
After typing in your password you will be logged in to the cluster. Once this connection is established, you can make one more hop and connect to one of the HPC clusters:
114
+
115
+
```bash
116
+
# this will connect you to Greene HPC cluster
117
+
ssh <NetID>@greene.hpc.nyu.edu
118
+
```
119
+
51
120
### Windows
52
121
53
122
While Windows does have a command-line interface known as the "Command Prompt"
@@ -80,6 +149,8 @@ it is easy to add plug-ins or remove the software. The installer edition adds
80
149
MobaXterm to your Windows installation and menu as any other program you might
81
150
install. If you are not sure that you will continue to use MobaXterm in the
82
151
future, the portable edition is likely the best choice for you.
Running PuTTY will not initially produce a terminal but instead a window full
112
185
of connection options. Putting the address of the remote system in the "Host
@@ -128,6 +201,47 @@ For those logging in with PuTTY it would likely be best to cover the terminal
128
201
basics already mentioned above before moving on to navigating the remote
129
202
system.
130
203
204
+
### Open OnDemand (Web-based Graphical User Interface)
205
+
Open OnDemand is an open source project funded by the National Science Foundation (NSF). Open OnDemand is designed to create easier access to users to interface with HPC systems. Originally developed by Ohio Supercomputer Center (OSC), used by many universities around the world, and now servicing the NYU Greene HPC cluster.
206
+
207
+
Open OnDemand has a variety of convenient tools to manage files, access the command line, manage and monitor jobs, and launch interactive applications, such as Jupyter Notebooks, RStudio sessions, and even full Linux Desktops.
208
+
209
+
Features Include:
210
+
211
+
Easy file management - upload and download files, view HTML and pictures without downloading
212
+
213
+
Command-line shell access without any SSH client locally installed
214
+
215
+
Job management and monitoring
216
+
217
+
Full Linux desktop experience without X11
218
+
219
+
Interactive Apps such as JupyterHub and RStudio without the need for port forwarding
220
+
221
+
Open OnDemand (OOD) is accessible to all users with a valid NYU HPC account while on-campus network or through a VPN.
222
+
223
+
To access OOD visit: https://ood.hpc.nyu.edu (VPN Required)
224
+
225
+
#### Access the Shell
226
+
227
+
Under the clusters menu you can select the Greene Shell Access option to access the Linux shell. No local SSH client is required.
228
+
229
+
#### Interactive Applications
230
+
231
+
GUI based applications are accessible without the need for port or X11 forwarding. Select the Interactive Apps menu, select the desired application, and submit the job based on required resources and options.
232
+
233
+
#### Troubleshooting Connections to Open OnDemand
234
+
235
+
A common issue that can occur is receiving an error that the Open OnDemand page cannot be reached. Sometimes this can indicate that the service is down, but often this is an issue with the the local browser cache. You can test this by opening a private browser window and seeing if https://ood.hpc.nyu.edu will load. If it does, try deleting the cache for https://ood.hpc.nyu.edu in your browser history to resolve this issue.
236
+
237
+
In Chrome, this can be done by navigating to this page in your settings:
The link above will automatically search for the Open OnDemand site data and cookies. You can then simply click on the trashcan icon to delete the site cache.
242
+
243
+
Once done, try navigating again to https://ood.hpc.nyu.edu and the site should load. For other issues please email [email protected].
244
+
131
245
## Creating an SSH key
132
246
133
247
SSH keys are an alternative method for authentication to obtain access to
| /home | $HOME | Program development space; storing small files you want to keep long term, e.g. source code, scripts. | NO | 20 GB |
35
+
| /scratch | $SCRATCH | Computational workspace. Best suited to large, infrequent reads and writes. | YES. Files not accessed for 60 days are deleted. | 5 TB |
| cp test_file1.txt test_file2.txt | Copies a duplicate copy of `test_file1.txt` with the new name `test_file2.txt`. |
233
+
| cp -r subdir subdir2 | Recursively copies the directory "subdir" to a new directory "subdir2". That is, a new directory "subdir2" is created, and each file and directory under "subdir" is replicated in "subdir2". |
0 commit comments