In order to successfully complete this assignment you must do the required reading, watch the provided videos and complete all instructions. The embedded survey form must be entirely filled out and submitted on or before 11:59pm on January 23rd. Students must come to class the next day prepared to discuss the material covered in this assignment.
Goals for today’s pre-class assignment#
1. Create XSEDE Account#
The National Science Foundation invests quite a bit of money into providing computing resources to researchers. The Extreme Science and Engineering Discovery Environment (XSEDE) is a single virtual system that scientists can use to interactively share computing resources and expertise. Here is a short video that describes XSEDE.
from IPython.display import YouTubeVideo
YouTubeVideo("PBUIBJHZzD4",width=640,height=360)
This XSEDE resource has not been replaced by ACCESS. The old resource is the first link below. You can learn more about the new ACCESS resource in the second link below.
https://portal.xsede.org/#/guest
2. Finding software on the HPCC#
The following video describes the PATH environment variable and shows you how it can be changed to add software installed in a new location.
from IPython.display import YouTubeVideo
YouTubeVideo("2OXvoXejZcw",width=640,height=360)
Commands used in the above video#
ls
clear
which python
cd
env
echo $PATH
echo $PATH | sec -r "s/:/\\n/g"
export PATH=~/anaconda3/bin:$PATH
ssh dev-intel16
nano ~/.bashrc
✅ QUESTION: What is the which command used for?
Put your answer to the above question here.
✅ QUESTION: The PATH environment variable is a set of system folders separated by a colon (:). What command would you use to add the /mnt/research/mygroup/bin folder to the end of your path?
Put your answer to the above question here.
The following video shows some basics on how to use the module command that is available on the HPCC.
from IPython.display import YouTubeVideo
YouTubeVideo("lXYpQeU3j-0",width=640,height=360)
Commands used in the above video#
ssh dev-intel16
clear
who | wc -l
module list
module spider MATLAB
module unload MATLAB
module load MATLAB/2018b
which matlab
module swap MATLAB/2018b MATLAB/2018a
module avail
module unload gnu
module load intel
module show intel
module purge
✅ QUESTION: Use the module spider command to search modules. What versions of the libpng are available on the HPCC? (Note: if the modules have changed since the last time you used the module spider command it may need to rebuild it’s database which can take a few seconds).
Put the answer to the above question here.
3. Assignment wrap up#
Please fill out the form that appears when you run the code below. You must completely fill this out in order to receive credits for the assignment!
✅ Assignment-Specific QUESTION: Why do you think MSU’s HPCC has the module system to load in specific modules rather than just having everything loaded in by default?
Put your answer to the above question here
from IPython.display import HTML
HTML(
"""
<iframe
src="https://cmse.msu.edu/cmse401-pc-survey"
width="100%"
height="500px"
frameborder="0"
marginheight="0"
marginwidth="0">
Loading...
</iframe>
"""
)
Congratulations, we’re done!#
To get credit for this assignment you must fill out and submit the above survey from on or before the assignment due date.
Written by Dr. Dirk Colbry, Michigan State University. Updated by Dr. Nathan Haut in Spring 2025.
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.