HPE DSI

HPE DSI#

This page describes the basics of using the HPE Data Science Institute clusters at UH.

Getting an account#

If you have never used HPE DSI clusters, first request an account at https://uh.edu/rcdc/getting-started/request-account.php. The below information may be needed:

  • Principal Investigator (PI): Mingjian Wen

  • PI Email address: mjwen@uh.edu

  • Grant information: N/A

  • Please select the Resource (Cluster): Carya or Sabine # Check with Mingjian on which cluster to use

  • Please select your login shell: Bash

You will receive an email shortly after submitting your request, which contains the login information such as your username (called Login name in the email).

Tip

For all the below sections, replace <username> by your username. And replace <clustername> by either carya or sabine depending on which cluster you are using.

Logging into the system#

You need to use ssh to log into the cluster. In any terminal on Linux or Mac (Linux subsystem can be installed on Windows), type

ssh <username>@<clustername>.rcdc.uh.edu

Replace <username> by yours and replace <clustername> by the corresponding cluster name. press Enter and then provide your CougarNet credentials to login.

Tip

The clusters can be accessed via the UHSecure not the UHGuest network. If you cannot log in and see error message like ssh: connect to host carya.rcdc.uh.edu port 22: Operation timed out, check your Wi-Fi connection.

If you are off campus, use UH VPN to get access.

Transferring data#

Transfer a file from your laptop to the cluster:

scp </local/path/my_file.txt> <username>@<clustername>.rcdc.uh.edu:</remote/path/>

Replace </local/path/my_file.txt> by the path to your file on your laptop, and </remote/path/> by the path to a directory on Carya where you want to place your file.

Transfer a file from Carya to your laptop:

scp <username>@<clustername>.rcdc.uh.edu:/remote/path/my_file.txt /local/path

Again, replace </local/path> by the path to a directory on your laptop where you want to place your file, and </remote/path/my_file.txt> by the path to your file on Carya.

Alternatively, if you prefer a graphical user interface or want to transfer a large amount of data, globus is a good option. See HPE DSI User Guide for instructions. [TODO: add instructions here].

Submitting jobs#

  • Do not submit jobs from your home directory /home/<username>, which is not configured for I/O and has a limited storage space of 10GB.

  • Do not submit jobs on the login node; it can affect other users.

Instead, submit jobs to the compute node from the project directory and using Slurm script.

First, create a directory with your username:

$ cd /project/wen
$ mkdir <username>      # change <username> to yours
$ chmod g-w <username>  # remove write access for others

All your jobs should be submitted in the project/wen/<username> directory and its subdirectories.

Next, let’s submit a job. Suppose you want to run a python script example.py placed in project/wen/<username>. A Slurm script for it can be:

#!/bin/bash -l

#SBATCH --job-name=my_1st_job
#SBATCH --account=wen           # account of our group
#SBATCH --time=00:10:00         # run for a max of 10 mins
#SBATCH --nodes=1               # run on 1 node

python example.py

scontrol show job $SLURM_JOBID  # show job details, for later reference

Copy the above content into a file named, e.g., submit.sh, and place it in the same directory as example.py. Then you can submit the job using sbatch:

$ sbatch submit.sh

Using GPU#

#!/bin/bash -l

#SBATCH --job-name=my_1st_job
#SBATCH --account=wen
#SBATCH --time=00:10:00
#SBATCH --nodes=1
#SBATCH --mem=10GB  # don't forget this; otherwise, it can throw out-of-memory error
#SBATCH --gpus=1    # run on 1 gpu

python example.py

scontrol show job $SLURM_JOBID  # show job details, for later reference

Checking balance#

To check the group allocations and accounts, use

$ sbalance

Authentication via ssh (optional)#

You need to enter the CougarNet password every time you log in or use scp. You can avoid this by using ssh authentication.

  1. Generate SSH keys if you have not done so. See SSH for instructions.

  2. Copy you public key (replace <username> by yours):

    $ cat ~/.ssh/id_rsa.pub | ssh <username>@<clustername>.rcdc.uh.edu "mkdir -p ~/.ssh && cat >> ~/.ssh/authorized_keys"

    This copies your public key in ~/.ssh/id_rsa.pub to the cluster, and appends it to ~/.ssh/authorized_keys on the cluster. You will be asked for your password.

After doing this, you can log in without entering your CougarNet password. If you have a passphrase for your private key, you will be asked for it. But you can avoid this by adding your private key to the ssh-agent. See SSH for instructions.

More information#

HPE DSI User Guide: https://uh.edu/rcdc/support-services/user-guide/getting-started-clusters

Open a ticket at the HPE DSI Support Center: https://support.hpedsi.uh.edu

Policies and data management: https://hpedsi.uh.edu/about/policies

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