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Lab1 Assignment

The document provides instructions for students to complete the objectives of Lab 1, which include learning about the course syllabus and writing guidelines, installing molecular editing and visualization software, accessing the computing cluster, using text editors and Jupyter notebooks, and learning basic Linux commands and job submission.

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bhaveshdesireddy
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14 views

Lab1 Assignment

The document provides instructions for students to complete the objectives of Lab 1, which include learning about the course syllabus and writing guidelines, installing molecular editing and visualization software, accessing the computing cluster, using text editors and Jupyter notebooks, and learning basic Linux commands and job submission.

Uploaded by

bhaveshdesireddy
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© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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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.

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