Humus

Humus is a pair of computers located at Dalhousie University managed by ACENET on behalf of researchers who purchased the equipment. Humus is integrated with the Nefelibata cluster, but Humus and the balance of Nefelibata are owned by two different research groups.

Access

You may only access Humus with the permission of the contributing Principal Investigator. If you don't have access to Humus and believe you should, please write to support@ace-net.ca and say so. Copy the PI, and mention in the email your Digital Research Alliance of Canada username.

We strongly recommend creating and installing an SSH key pair and using that for access.

• For more on key pairs, see https://docs.alliancecan.ca/wiki/SSH_Keys.
• For more on SSH in general, see https://docs.alliancecan.ca/wiki/SSH.
• Step-by-step instructions for setting up key-pair authentication from Windows using MobaXterm

The two machines are named humus216 and humus217. (The numbers are in relation to the node numbering of Nefelibata.) Choose one to log into, like so:

 ssh -J username@nefelibata.ace-net.ca -A username@humus216

or

 ssh -J username@nefelibata.ace-net.ca -A username@humus217

The -J parameter above stands for "jump"; you are "jumping" through nefelibata.ace-net.ca to get to humus21[6,7]. The -A turns on "agent forwarding", which allows you (for example) to then log from 216 to 217 or vice versa using the same SSH key pair that you used to authenticate to the first machine.

Storage system

When you log in to Humus your default working directory will be /home/username on the shared Nefelibata filesystem. But there is very little space on it for Humus users.

For primary storage please use /scratch/username on each Humus node. Each node has approximately 58 TB of (unshared, node-local) storage space in /scratch.

Data transfer

sftp can be used for interactive command-line data transfer, following the pattern shown above for ssh:

sftp -J username@nefelibata.ace-net.ca username@humus216
> cd /scratch/username
> put somefile.txt
> get some-other-file
> exit

scp can be used similarly for wild-card or script-driven data transfers:

scp -J username@nefelibata.ace-net.ca somefiles.* username@humus216:/scratch/username/

Graphical (drag-and-drop) file transfer applications can be used if they implement the scp or sftp protocols. WinSCP has been tested successfully; use username@humus216.nefelibata.ace-net.ca etc.

rsync is a good choice for large-scale data transfers. For example, to back up a directory from 217 to 216

rsync -r humus217:/scratch/username/back_me_up_here /scratch/username/back_me_up_here

For more on rsync see Transferring_data at the Alliance wiki.

Software

Humus uses the same modules system as Alliance clusters, providing access to the same list of available software.

For software which requires a graphical user interface (e.g. RStudio), you can connect to Humus using VNC. Here is a step-by-step guide to creating a VNC session.

Job scheduling

There is currently no job scheduler running on Nefe or Humus.