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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.
This training is available for download as a PDF here.
Course Goals:
Introduce a number of ways to access an ARCC HPC Cluster.
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Sections
Setting up SSH-Keys for HPC Login
Directory Navigation
Basic HPC System ExplorationRevoking and/or Replacing SSH Keys
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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):
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Download Slides:
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Opening Screen:
Message of the day
Storage usage - across project spaces
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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?
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[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:
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# 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:
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[]$ 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:
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# 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:
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[]$ 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
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(SSH onto a login node – if using an existing ARCC account.)
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Access via SouthPass and start a shell terminal tab.
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Commands: man, id, groups
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Commands: arccquota
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