This guide will help you log in to CWRU's High Performance Computing (HPC) cluster and run a test job. Please visit the links - Job Scheduling, Guides and Training for details.
For new users, it is recommended to get familiarized with the information in HPC Site where you can do keyword search for most of the topics of your interest. If you are seeking for an HPC account, please check the Faculty Guide.
You need to have an HPC account to log in to the cluster. If you don't have an account, please go through the Access Policy.
Except Ondemand that just need DUO, you need to use VPN (e.g. Forticlient) outside of the case network.
There are separate login nodes for research group members, and academic course group members. You will have the same view of your files in all these clusters as they all use network mounted file systems i.e. when you make changes in the file, you are changing the same file irrespective of in which cluster you logged on.
pioneer.case.edu # Pioneer Cluster for research
markov.case.edu # For Coursework
to get the compute nodes using in batch submission,
please specify "-p markov_cpu" flag i.e. sbatch -p markov_cpu <job-script>
Try to keep a separate directory for each job
If everything is on a single directory, the same files might be accessed over and over again at similar timescale, thereby confusing the storage access. It would become worse if the jobs write to the same files at the same time, creating file contention.
With interactive job submission, you may encounter a termination of connection to HPC after several hours. We recommend you to use batch submission but if you still want to use interactive session , please use "ServerAliveInterval flag" as showed:
ssh -o ServerAliveInterval=60 <caseID>@pioneer.case.edu
Pioneer: https://ondemand-pioneer.case.edu
Markov: https://ondemand-markov.case.edu
X2Go client :
requires a client installation that is available for Windows, Mac, and Linux.
probably provides the best performance for Graphical Interface applications.
Click here to download putty executable or install X2Go (recommended - supported in Linux, Windows, Mac) or MobaXterm (supported in Windows only) for visual access. Also, consider Windows Subsystem for linux.
Putty's instructions:
Open the executable.
In the putty configuration window, enter pioneer.case.edu under "Host Name (or IP address)"
Click open. You will be prompted for a login and password. Enter your CaseID (e.g. xxx125) and Case Password. You may not see the password being entered, that's fine. Just click Enter after you entered your password.
You should get a compute node prompt similar to the one shown below. Now you are ready to run your jobs.
[<caseID>@hpc8 ~]$
Open the Terminal Application.
You will get a prompt similar to the one shown:
bash-3.2$
At the prompt, type the following and press the Enter key (-X for X-forwarding for Visual access). Make sure that XQuartz is running.
ssh -X <CaseID>@pioneer.case.edu
Enter your Case Password when prompted.
You should get a compute node prompt similar to the one shown below. Now you are ready to run your jobs.
[<caseID>@hpc8 ~]$
Go to Applications->System Tools and choose Terminal
At the prompt, Type the following and press the Enter key (-X for X-forwarding for Visual).
ssh -X <CaseID>@pioneer.case.edu
Enter your Case Password when prompted.
You should get a login node prompt similar to the one shown below. Now you are ready to run your jobs.
[<caseID>@hpc8 ~]
Request a compute node to run your job by typing the "srun" command at the prompt as shown (--x11 for X-forwarding for visual access). Note that Matlab is memory intensive and it requires more than the default 1gb memory. So, 4gb is requested with --mem flag. Get more information in Graphical Access.
[<caseID>@hpc8 ~]$ srun --x11 --mem=4gb --pty /bin/bash
You will get the compute node prompt similar to the one below:
[<caseID>@compt335 ~]$
Load the appropriate module. For the MATLAB application, type "module load matlab" at the prompt, as shown below, and press the Enter key:
[<caseID>@compt335 ~]$ module load matlab
Run MATLAB and get the value of pi by typing pi at the prompt and pressing the Enter key (if you do not want GUI, use -nodisplay flag e.g matlab -nodisplay &).
matlab &
>>pi
Congratulations!!! You ran a job in the HPC.
To quit MATLAB:
>>quit
To exit the HPC cluster, type the logout command, as shown below (or press control-d).
[<caseID>@compt335 ~]$ logout