Working with NOAA HPC Hera

Authors

Nicholas Ducharme-Barth

Megumi Oshima

Last updated

2024-11-06

1 Hera

Hera is one of NOAA’s high performance computing resources available to NMFS scientists where jobs are run and scheduled with SLURM. In order to access the system, you must first have a RDHPCS user account and request access to a project. For all of the examples in this documentation, we will be working in the htc4sa project. For complete documentation about Hera and other RDHPCS resources, see the NOAA RDHPCS website.

Coding alert!

In the following code you will need to, where necessary:

  1. Replace User.Name with your RDHPCS user name.

  2. Replace bastion with either boulder or princeton depending on which bastion you wish to login in through.

  3. Replace project_name with your RDHPCS project name.

2 Connecting to Hera via ssh

Open a terminal window (.e.g, command prompt or PowerShell), then open an ssh tunnel to Hera by using the following command:

ssh -m hmac-sha2-256-etm@openssh.com User.Name@hera-rsa.bastion.rdhpcs.noaa.gov -p22

Note that the flag -p22 specifies opening port 22 and is optional. When prompted, put in your password followed by the RSA authentication code:

XXXXXXXXRSACODE

If you see the following then you have connected successfully:

________________________________________________________
|                                                        |
|                                                        |
|  Welcome to the Hera High Performance Computing system |
|                                                        |
|        This system is located in Fairmont, WV          |
|                                                        |
|          Please Submit Helpdesk Requests to:           |
|               rdhpcs.hera.help@noaa.gov                |
|                                                        |
|________________________________________________________|

Note that you will also see the following terminal output upon connecting:

Local port XXXXX forwarded to remote host.
Remote port YYYYY forwarded to local host.

Where XXXXX and YYYYY are your 4-5 digit port forwarding numbers. Make note of what your local port number (XXXXX) is since this will be used for scp file transfer using an ssh tunnel.

3 Transferring files to/from Hera

3.1 via scp using data transfer node (DTN)

Information in this section is largely based on this wiki. File transfer using a DTN is only possible from machines within the noaa.gov domain (VPN ok), and can only transfer files to the scratch directory. However, this is ok since it is recommended that input/output data files are stored in the scratch directory. Using a DTN is faster than using the ssh tunnel.

Note

The scratch1/NMFS/project_name/ directory is a shared space (shared access and shared disk space) for all users of a project. Rather than dumping files into the root project directory (e.g., project_name/) it is better to place them in your own sub-directory. Since this sub-directory structure does not already exist you will need to log into Hera and create it:

mkdir scratch1/NMFS/project_name/User.Name/

This will avoid over-writing other users’ work.

File transfer takes place via scp and you need to specify the source file (and path to the file if your terminal is not in that directory) and destination path as shown:

## format is scp <source> <destination> 
scp /path/to/local/file User.Name@dtn-hera.fairmont.rdhpcs.noaa.gov:/scratch1/NMFS/project_name/User.Name/

If trying to transfer from a machine not within the NOAA domain (or on the VPN) you can use scp with an untrusted DTN:

scp /path/to/local/file User.Name@udtn-hera.fairmont.rdhpcs.noaa.gov:/scratch1/data_untrusted/User.Name/

Note that dtn-hera was changed to udtn-hera. Since files cannot stay in the data_untrusted directory we will need to log in to Hera and move it to the correct project directory on scratch. Once logged in, moving the files can be done with rsync, and then they can be deleted from data_untrusted by:

rsync -axv /scratch1/data_untrusted/User.Name/file /scratch1/NMFS/project_name/User.Name/
rm /scratch1/data_untrusted/User.Name/file

Files can be downloaded back to your local machine using scp from either the trusted (dtn) or untrusted (udtn) DTN:

scp User.Name@dtn-hera.fairmont.rdhpcs.noaa.gov:/scratch1/NMFS/project_name/User.Name/file /path/to/local/file

3.2 via scp using an ssh tunnel

Information in this section is largely based on this wiki. File transfer using an ssh tunnel is possible from all locations. Using the ssh tunnel for file transfer requires a two-step process with two active terminal windows (we suggest using PowerShell):

  1. In the first terminal window, open an ssh connection to Hera with port forwarding:
ssh -m hmac-sha2-256-etm@openssh.com -LXXXXX:localhost:XXXXX User.Name@hera-rsa.bastion.rdhpcs.noaa.gov

Replace XXXXX with your local port number.

  1. In the second terminal window you can check to see if the tunnel was properly created:
ssh -p XXXXX User.Name@localhost

if you get prompted for your password then success! Press CONTROL+C to ignore this prompt. Staying within this 2nd terminal window use scp to transfer your file:

scp -P XXXXX /path/to/local/file User.Name@localhost:/home/User.Name/

This will copy your file from your local machine into your home directory on Hera. Simply append additional directory structure to /home/User.Name/ to copy it into a sub-directory that you have created on Hera (e.g., /home/User.Name/sub/dir/). To transfer files into your scratch directory, specify the proper destination path (e.g., /scratch1/NMFS/project_name/User.Name/).

To download a file from Hera using scp and the ssh tunnel use the following:

scp -P XXXXX User.Name@localhost:/home/User.Name/file_name /path/to/local/file
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