Biowulf High Performance Computing at the NIH
Connecting to the NIH HPC systems

Quick Links

There are several secure options for connecting to the NIH HPC Systems from a Windows, Mac or Linux desktop. The hostnames for the systems are:

HostHostnameAccessible by
Helixhelix.nih.govAll HPC users
Biowulfbiowulf.nih.govAll HPC users
Felixfelix.nimh.nih.govNIMH Users only

To connnect to any of the three HPC systems listed above you will need one of the following options:

If you try to connect to one of the systems and see a message saying your account is locked due to inactivity: if you are on the NIH network or the VPN, you can unlock it yourself by going to the User Dashboard. If you are not on the NIH network, send email to staff@hpc.nih.gov.

Detailed setup & usage instructions for each method are below.

Connecting from Windows

Windows: SSH

Secure Shell or SSH is an encrypted network protocol that provides secure communication between two computers. PuTTY is a free implementation of Telnet and SSH for Win32 and Unix platforms, along with an xterm terminal emulator. It is written and maintained primarily by Simon Tatham.

Installing PuTTY

Installation of PuTTY may require administrative privileges. Please consult with your local system administrators regarding installation policies.

Because PuTTY is continuously updated, you should download the latest version of the installer from http:// www.chiark.greenend.org.uk/~sgtatham/putty/download.html (filename will be something like putty-<version>-installer.exe) and install it on your machine. We currently recommend you select the latest development snapshot rather than the beta release version, as the snapshot supports GSSAPI authentication.

Once PuTTY is installed, start PuTTY by double-clicking the icon created on your desktop or go to
Start -> All Programs -> PuTTY > PuTTY.

Setting up sessions in PuTTY

When starting PuTTY, you will see a dialog box. This dialog box allows you to control everything PuTTY can do. In the 'Host Name' box, enter helix.nih.gov or biowulf.nih.gov.

Enter host name

You don't need to change most of the configuration options, but here are a few suggestions for Helix systems' use:

The Backspace Key

Set backspace key to Control H

The Window Title

Set Window Title

Enable X11 Forwarding (for running X-Windows applications)

Enable X11 Forwarding

After making your configuration changes, be sure to save the session so you will not have to reconfigure PuTTY each time.

Save session

Creating icons on your Windows desktop

Right-click the PuTTY icon on your desktop, then left-click "Properties".

Change PuTTY Properties

In the "Target" box under the Shortcut tab, type -load "helix" or -load "helix.nih.gov" after putty.exe:

Edit properties

Click on the 'General' tab and change the name from PuTTY to helix, then click the OK button.

Changing icon name

Double-click on the helix icon to login to helix

Helix icon

To create an icon for any of the other systems, be sure to make a copy of the helix or PuTTY icon, then change the properties of the copy.

Copy icon

Paste copy

Documentation

For more in-depth knowledge of PuTTY, see the PuTTY Documentation Page

Windows: X11

Windows users should use NX as their X11 graphical terminal. See below.

Connecting from Macs

Macs: SSH

Mac OS X automatically includes ssh software. In a terminal window, type ssh hostname to start an ssh session to a host. If your username on your local system is different from your NIH domain username, you will need to type ssh username@hostname or ssh -l username hostname

The first time you connect to a host, you will be asked about the RSA key fingerprint. After this, you will not be asked this question in future sessions. Sample session (user input in bold):

[mymac:~] macuser% ssh -X user@helix.nih.gov
The authenticity of host 'helix.nih.gov (128.231.2.3)' can't be established.
RSA key fingerprint is e9:87:ba:5b:4b:fd:ca:82:04:79:c1:60:b3:99:95:75.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'helix.nih.gov,128.231.2.3' (RSA) to the
list of known hosts.
                             ***WARNING***

You are accessing a U.S. Government information system, which includes
(1) this computer, (2) this computer network, (3) all computers
connected to this network, and (4) all devices and storage media
attached to this network or to a computer on this network. This
information system is provided for U.S.  Government-authorized use only.

Unauthorized or improper use of this system may result in disciplinary
action, as well as civil and criminal penalties.

By using this information system, you understand and consent to the
following:

* You have no reasonable expectation of privacy regarding any
communications or data transiting or stored on this information system.
At any time, and for any lawful Government purpose, the government may
monitor, intercept, record, and search and seize any communication or
data transiting or stored on this information system.

* Any communication or data transiting or stored on this information
system may be disclosed or used for any lawful Government purpose.

--

NOTE: This system is rebooted for patches and maintenance on the first
Monday of every month at 7:00 AM unless Monday is a holiday, in which
case it is rebooted the following Tuesday.  A detailed schedule is
available at    http://helix.nih.gov/Documentation/reboots.html

Last login: Wed Jul  8 11:34:37 2015 from hostname
[username@host ~]$

Macs: X11

X-windows software allows users the ability to run graphics applications remotely & display their graphics locally. As of OS X 10.6, X11 is no longer included with the OS. The X11 server and client libraries for OS X are available from the XQuartz project: http://xquartz.macosforge.org. You should use the latest available version of XQuartz.

Making an Xwindows Connection

Once you have X-windows software installed on your machine, click on the XQuartz icon in the Applications or Utilities menu to start up X11. You should see an xterm window appear. (This window will look much like the Terminal window shown above, but it has some additional capabilities needed for running remote X11 applications.)

In the xterm window, type

ssh -Y username@hostname

Sample session:

bash-3.2$ ssh -Y username@hostname
                             ***WARNING***

You are accessing a U.S. Government information system, which includes
(1) this computer, (2) this computer network, (3) all computers
connected to this network, and (4) all devices and storage media
attached to this network or to a computer on this network. This
information system is provided for U.S.  Government-authorized use only.

Unauthorized or improper use of this system may result in disciplinary
action, as well as civil and criminal penalties.

By using this information system, you understand and consent to the
following:

* You have no reasonable expectation of privacy regarding any
communications or data transiting or stored on this information system.
At any time, and for any lawful Government purpose, the government may
monitor, intercept, record, and search and seize any communication or
data transiting or stored on this information system.

* Any communication or data transiting or stored on this information
system may be disclosed or used for any lawful Government purpose.

--

NOTE: This system is rebooted for patches and maintenance on the first
Monday of every month at 7:00 AM unless Monday is a holiday, in which
case it is rebooted the following Tuesday.  A detailed schedule is
available at    http://helix.nih.gov/Documentation/reboots.html

Last login: Wed Jul  8 11:34:37 2015 from hostname
[username@host ~]$

At this point you are logged on to Helix and can run Xwindows programs. To test, type 'xclock' at the Helix prompt. You should see a clock window appear on your desktop, as below:

xclock

Connecting from Linux

Linux: SSH

Linux automatically includes SSH software. In a terminal window, type ssh username@hostname to start an ssh session to a host, where username is your NIH domain username. A sample session will be exactly like the Mac session displayed above.

Linux: X11

Your Linux distribution automatically installs X11. In a terminal window, type ssh -X to start an ssh session to a host, where username is your NIH domain username. A sample session will be exactly like the Mac session displayed above.

Persistent Connections to the NIH HPC Systems

NX

About NX

NoMachine's NX Terminal Server is available on all systems listed above. If you haven't already, download the latest client from nomachine.com.

Configuration for Helix/Biowulf/Felix

To set up a new connection:

  • Click 'New' from the top menu.
  • Protocol: Set the Protocol to SSH.
  • Host: Set the Host to either helix.nih.gov, biowulf.nih.gov or felix.nimh.nih.gov. The port must be 22.
  • Authentication: Choose Use the system login.
  • Authentication: Choose Password.
  • Proxy: Choose Don't use a proxy.
  • Save as: Any choice is a good choice.

Once the connection is set, double click on the connection and enter your username and password. NOTE: Never check the "Save Your Password" button.

Once the login is successful and a connection has been established, a session must be chosen or created. If this is the first time, or no previous sessions are available, click "Create a new virtual desktop". Save the setting in the connection file. Otherwise, choose the previous session to open.

NOTE: If your client asks you to upgrade NX, you can safely ignore it. That notification is for the server.

For more information about using NX, see https://www.nomachine.com/getting-started-with-nomachine

Additional Authentication Information

GSSAPI (Kerberos) Access

Connecting with ssh keys