Intro to Accessing the Cluster

Introduction: This workshop will introduce users on how to remotely access the clusters and how to set up and personalize their environment for their computational needs. After the workshop, participants will understand:

How to (remotely) access the cluster.

Participants will require an intro level of experience of using Linux, as well as the ability to use a text editor from the command line.

Course Goals:

Introduce a number of ways to access an ARCC HPC Cluster.

Sections

Methods for HPC Cluster Access

There are a number of different ways to access the cluster, but all consist of 2 main methods for access:

OnDemand (web based):

SSH (secure shell CLI):

Link to main workshops page

OnDemand

Download Slides:

Opening Screen:

Message of the day
Storage usage - across project spaces

General Format:[<username>@<server/node-name> <folder>]$ 

[<username>@blog2 ~]$ arccquota

# ‘man’ is only available on the login nodes.
# It is not available on the compute nodes.
[<username>@blog2 ~]$ man id
[<username>@blog2 ~]$ id –-version
[<username>@blog2 ~]$ id

[<username>@blog2 ~]$ groups

Which groups?

[arcc-t05@blog1 ~]$ id
uid=10339923(arcc-t05) gid=10339923(arcc-t05) groups=10339923(arcc-t05),89997(beartooth),446824(uwit-research-arccanetraining),5735503(teton_backup),6000211(arccanetrain)

[arcc-t05@blog1 ~]$ groups
arcc-t05 beartooth uwit-research-arccanetraining teton_backup arccanetrain

Beartooth: FileSystem

Type	Location	Description
home	/home/<username>	Space for configuration files and software installations.
project	/project/<project-name>/[username]	Space to collaborate among project members. Data here is persistent and is exempt from purge policy.
gscratch	/gscratch/<username>	Space to perform computing for individual users. Data here is subject to a purge policy defined below.
node local scratch	/lscratch	Only on compute.
memory filesystem	/dev/shm	RAM-based tmpfs available as part of RAM for very rapid I/O operations; small capacity.

Home and Project Folders:

# Home folder:
[]$ cd ~
[]$ pwd
/home/arcc-t05

[]$ cd /gscratch/arcc-t05

# Shared project space
[]$ cd /project/arccanetrain/
[arcc-t05@blog1 arccanetrain]$ ls
arcc-t01  arcc-t06  arcc-t11  arcc-t16  arcc-t21  arcc-t26  brewer       mkillean
arcc-t02  arcc-t07  arcc-t12  arcc-t17  arcc-t22  arcc-t27  excotest     salexan5
arcc-t03  arcc-t08  arcc-t13  arcc-t18  arcc-t23  arcc-t28  intro_to_hpc
arcc-t04  arcc-t09  arcc-t14  arcc-t19  arcc-t24  arcc-t29  lmainzer
arcc-t05  arcc-t10  arcc-t15  arcc-t20  arcc-t25  arcc-t30  lreilly

Copy files:

[]$ cd 

[~]$ cp -r /project/arccanetrain/intro_to_hpc/ .

[~]$ cd intro_to_hpc/

[intro_to_hpc]$ ls
Intro_to_hpc.pdf  python01.py  python01.py.fixed  run_gpu.sh  run.sh

Let's run a python script:

# If you have NOT already copied the files.
# Navigate back to your home folder.
[]$ cd
[~]$ mkdir intro_to_hpc
[~]$ cd intro_to_hpc/
[intro_to_hpc]$ ls
[intro_to_hpc]$ pwd
/home/<username>/intro_to_hpc


[intro_to_hpc]$ vim python01.py
"python01.py" [New File] 

# Using vim: Press ESC followed by ‘i’ to INSERT: Start typing:
import sys
print("Python version: " + sys.version)
print("Version info: " + sys.version_info)
# Using vim: ESC followed by ‘:wq’, then Return

Let's run a python script: Fixed:

[]$ python python01.py
Python version: 3.8.16 (default, May 31 2023, 12:44:21)
[GCC 8.5.0 20210514 (Red Hat 8.5.0-18)]
Traceback (most recent call last):
  File "python01.py", line 3, in <module>
    print("Version info: " + sys.version_info)
TypeError: can only concatenate str (not "sys.version_info") to str

# Let's update the code:
From: print("Version info: " + sys.version_info)
To:   print("Version info: " + str(sys.version_info))

[]$ python python01.py
Python version: 3.8.17 (default, Aug 10 2023, 12:50:17)
[GCC 8.5.0 20210514 (Red Hat 8.5.0-20)]
Version info: sys.version_info(major=3, minor=8, micro=17, releaselevel='final', serial=0)
[]$ python --version
Python 3.8.17

Exercises: Log on, and create and run a python script

(SSH onto a login node – if using an existing ARCC account.)
Access via SouthPass and start a shell terminal tab.
Commands: man, id, groups
Commands: arccquota
Create and run a Python script.