CHE 330; Lab 1; Due Date: Feb.
4; 1:00 PM
Lab 1 Assignment:
General Instructions and Key Setups
Alexey Akimov *
Department of Chemistry, University at Buffalo, Buffalo, NY, USA
Keywords: Syllabus, writing guidelines, IQmol3, VESTA, Avogadro, VMD, Open OnDemand,
MobaXterm, vi, nano, Far3, Jupyter/JupyterLab, visualization nodes, terminal, command line,
Linux commands, sbatch.
Assignment Objectives
In this Lab, we will overview the key setups needed for your successful participation in this
course. You are expected to take notes and summarize the key information discussed in this class
and reflect those in your first Lab report. As you proceed to complete the objectives, please use
suitable ways (e.g. screenshots) to prove the completion of the objectives. The “Methodology”
section of your report should contain any relevant notes about the topic – these notes are not only
a part of the assignment, but also something meant to be useful to yourself. In fact, focus on doing
it for yourself. Their presence and meaningful content would mean you follow the topic. The
“Results and Discussion” section would contain the “proofs” of completions – e.g. screenshots of
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CHE 330; Lab 1; Due Date: Feb. 4; 1:00 PM
your work regarding the corresponding topics. The “discussion” part should contain your analysis
or reflection on the tools’ pros and cons regarding different tasks, as well as a comparison of their
capabilities for various application scenarios. In the “Conclusions”, please summarize your
preferred mode of operation after you’ve learned about all the tools covered.
The report should contain the notes/results in the following categories:
1.1. Course syllabus: learn and understand the course syllabus and key expectations
(https://ublearns.buffalo.edu/d2l/le/content/165057/Home in the “Overview” tab);
1.2. Writing guidelines: learn about the writing/presentation expectations, start using document
template (https://ublearns.buffalo.edu/d2l/le/content/165057/Home in the “Guidelines and
Rubric” tab);
1.3. Molecular editing software: install and/or try using the following packages: IQMol3
(http://iqmol.org/), Avogadro (https://avogadro.cc/), VESTA (https://jp-minerals.org/vesta/en/),
VMD (https://www.ks.uiuc.edu/Research/vmd/); For most of these packages, just proceed to the
“Download” page, download the code and install it to the place where you will be using it (either
your local account on UB machines in class) or on your personal laptop. For VMD, you’d need to
also go through the registration step before you can access the download page.
1.4. Accessing the cluster via Open OnDemand: set up your CCR account, two-factor
authentication (2FA) via the identity management (IDM) portal
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CHE 330; Lab 1; Due Date: Feb. 4; 1:00 PM
(https://docs.ccr.buffalo.edu/en/latest/portals/idm/); be able to use OnDemand
(https://docs.ccr.buffalo.edu/en/latest/portals/ood/) interfaces such as Terminal and File Transfer
tools, The following link can be useful: https://akimovlab.github.io/soft_and_tuts/4.4-
UBCCR_OnDemand.html
1.5. Accessing the cluster via MobaXterm: install MobaXtem (https://mobaxterm.mobatek.net/),
generate the private-public keys and add them to your CCR IDM account, be able to access CCR
using MobaXterm, use MobaXterm terminal and file transfer panel for the corresponding tasks;
1.6. Working with text editors: install on/and try using the following text editing software: Far3
(https://www.farmanager.com/; only Windows users); “vim” (https://www.vim.org/) or “nano”
(https://www.nano-editor.org/) – probably for Linux/Mac and Windows users (choose any of the
two) – you don’t need to install them, they usually just come with Linux system. Using “vim” or
“nano”, create (if not present) and edit a “.bashrc” file in your home directory to prepare it for
using “NWchem” or “VMD” software.
1.7. Working with Jupyter notebooks/JupyterLab: be able to start Jupyter or JupyterLab job on
CCR OnDemand portal. Use it to generate a plot of a simple function. More about Jupyter can be
found here (https://jupyter.org/)
1.8. Working with the visualization nodes on CCR: be able to start a Desktop job on CCR
OnDemand portal using the visualization node, execute the VMD package there and use it to
visualize molecular structure you create using one of the molecular editing software.
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CHE 330; Lab 1; Due Date: Feb. 4; 1:00 PM
1.9. Using Linux command line: learn the basic commands to get around on Linux system (e.g.
) and use them to create a hierarchical file system in your home directory to mimic a file
organization of a potential project. More details will be given in class. Also, these sources could
be useful:
* https://docs.alliancecan.ca/wiki/Linux_introduction
* https://buffalo.app.box.com/s/nqj3neyt2w1dtb3gix6zxqx5gcc9x30n
1.10. Submitting jobs on CCR: create a submit file for running a simple “NWChem” job and
submit it to be run on a cluster.
* https://docs.ccr.buffalo.edu/en/latest/hpc/jobs/
* https://akimovlab.github.io/soft_and_tuts/4.1-slurm.html
Please see the provided document for the prompts/rough examples on how the report should be
prepared.
