Math HPC

Resources available

Requesting access

• Email math-helpdesk@umd.edu to request access.
• If you aren't listed as having a Math affiliation in the campus directory, include who you are working with in Math.

Connecting to the servers

If you aren't familiar with Linux, start with this introduction.

• If you are off campus, connect to the UMD GlobalProtect VPN first.
• Use Secure shell access to connect to your preferred server from the table above.
• Use SFTP to transfer files to and from the servers:
  • Windows - SCP/SFTP using Winscp
  • [Link for document 98260 is unavailable at this time]
  • Linux — SFTP using the command line in a terminal

Errors about running out of processes

If you see errors related to running out of processes, you may have been enrolled in a CS or ECE class that instructed you to add a process limitation to your profile. This will cause problems with VS Code and other remote editors.

Go to your home space and check .cshrc.mine (most likely) and .bashrc.mine (less likely, but worth checking):

cd ~
vi .cshrc.mine

Look for a line containing ulimit, limit maxproc, limit process, or something similar. Comment it out by adding a # at the beginning of that line, then save and exit. Log back in and the issue should be resolved.

Storage

On mathhpavw1202a, b, and c there is a significant amount of local storage available to each user under /export/<username>. This storage is local to each server, meaning you can't see the storage on one server from any of the others. This local storage is not backed up and should be used as temporary space during your computations.

These servers also connect to a file server that provides a small amount of home space accessible from any TerpConnect server, so it can be seen from all three of these servers as well as glue.umd.edu and login.math.umd.edu.

You can see how much space is left with:

df -h

You should see something like the output below. Look for the / entry — the last one here — which has 1.7 TB free.

mathhpavw1202a:~$ df -h
Filesystem                           Size  Used Avail Use% Mounted on
devtmpfs                             377G     0  377G   0% /dev
tmpfs                                377G  512K  377G   1% /dev/shm
tmpfs                                377G  1.8G  376G   1% /run
tmpfs                                377G     0  377G   0% /sys/fs/cgroup
/dev/mapper/rhel_mathhpavw1202a-root 7.0T  5.4T  1.7T  77% /

Quota management

If you run out of quota in your home space on the file server, leverage the local space described above.

Check your quota. The -human flag prints it in an easier-to-read format:

fs lq -human

Check what is using the quota:

du -h ~<username> > /tmp/<username>.usage

Then look at the /tmp/<username>.usage file to see where the storage is being used. It's typically in .cache or other dot-file locations, and these can be moved to /export/<username>.

Note that /tmp is temporary space that can and will be cleared out by the operating system on reboots or when needed. Don't use it for anything important. The size of this partition is also small relative to the other local storage mounted on /export.

Redirecting large directories to /export

For example, if you are trying to install something like miniconda3, you can create a symbolic link so that anything written to ~<username>/miniconda3 is redirected to /export/<username>/miniconda3:

ln -s /export/<username>/miniconda3 ~/miniconda3

To move .cache, so all future data written to ~/.cache is redirected to /export/<username>/.cache:

mv ~/.cache /export/<username>
ln -s /export/<username>/.cache ~/.cache

See Issues below if you need assistance with this.

Long running jobs

• For jobs that you think will run over 24 hours, don't use your home space. Use the temporary /export/<username> directory to store input and output files — the file server where your home space is located expires access every 24 hours for security reasons.
• If you end your SSH session, anything you have running will terminate as well. There are multiple ways to handle this, but we recommend using screen or tmux:
  • Guide for using screen
  • Guide for using tmux

Accessing software

If you run a command to execute a piece of software and the command isn't found, you can use the module command to see if the software is available that way.

Issues

Contact math-helpdesk@umd.edu, call 301-405-1634, or stop by Martin Hall 0123 for assistance, including requests for any software installations.

UMD HPC

Zaratan is available, but Math has not made any investments. There are some free allocation options available. See hpcc.umd.edu.