High-Performance Computing at the NIH

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Helix (helix.nih.gov)

Helix (helix.nih.gov) is the primary login machine for the Helix Systems. It provides a full set of scientific applications and is intended for interactive use. Helix is a 64 core, 128-thread, (8 X 2.27 GHz 8-core Xeon™ X7560) Fujitsu RX900 S1 with 1033GB of main memory running RedHat Enterprise Linux 6.

Connecting to Helix

Users connect via ssh to helix.nih.gov. X-windows connection software will usually provide better terminal emulation, and is necessary to run any X-windows graphics applications. Unix workstations (including Macs with OS X) can handle X-windows by default. We provide free X-windows emulation software for Macs and PCs users of the Helix Systems.

Transferring Files

Users will not be able to use FTP to transfer files between their desktop machines and Helix. Instead, users should use one of the secure file transfer alternatives to transfer files to their /home/<username> or /scratch/<username> directories on Helix.

General Information

Accounts: To obtain a Helix Systems account, see the Accounts page. Accounts not accessed within a 60 day period are automatically locked as a security precaution.

Passwords: You will use your NIH Active Directory (AD) account password when logging into Helix and/or Biowulf.

If you forget your password, have trouble changing it, or your account gets locked for repeated failed logins, you will need to contact the NIH Service Desk or use iforgotmypassword.nih.gov to reset or unlock your account. Use the passwd command on Helix/Biowulf to change your NIH password. This will have the same effect as changing it via a Windows workstation or at password.nih.gov.

Shells: The Bourne shell ('bash') is the default shell. Other available shells, including csh and tcsh, are listed in /etc/shells.

Mail: Helix users may read and send mail while either directly logged into Helix or remotely, by means of an IMAP (Internet message access protocol) client, or via the Squirrelmail web interface. Details about email on Helix.
Users who do not read Helix e-mail are required to forward mail to their alternative e-mail address. (Directions for forwarding Helix mail)

Disk Storage: Storage options are the same as on the Helix Systems. In addition to their /home/<username> directory, all users can access the /scratch area which is also accessible from Helix and Biowulf. Files in /scratch which have not been accessed for 14 days are automatically deleted. More information about storage.

Programming Tools/Libraries: The Helix systems run the RedHat Operating System. A full complement of programming tools and libraries is available. The compilers available are the same as on the Biowulf cluster. Details are available in the Biowulf user guide.

Questions? Problems? Contact the Helix staff at staff@helix.nih.gov.