Welcome to the lab!

Doing research is not a linear endeavor. However, we will try to make it as smooth as possible for you, yet maintaining the challenging nature of what creating new knowledge is about. 

For started please read the Getting Started codes that we use in the group: 

https://sites.google.com/site/mendozacortesgroup/home/getting-started

After, this please read the other guidelines:

https://sites.google.com/site/mendozacortesgroup/home/advice/criteria-for-authorship-in-papers

In general, I will give you a project in which I have worked for several years on. This will allow you to get started with some results and this will allow me to train you. Active notebooks and recent materials are in the care of a current researcher and are typically kept at the researcher’s desk or workspace. All notebooks and digital data are surrendered to the PI when the researcher exits the group.

If you do not agree with any of the terms above, please let me know otherwise, please print this page and send the PDF to me over email or Slack.

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Name here 

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Date

Beginner tutorials:

In order to have the general tools to use our codes and supercomputers, you must complete all the courses in ICER-D2L (it should not take more than a 1 week):  https://icer.msu.edu/education-events/desire2learn

Writing  papers, manuals  and proposals:
We now have access to the professional Overleaf account at MSU, follow these steps: https://www.overleaf.com/edu/msu  
Tutorials and additional information about LaTeX/Overleaf can be found in the LaTeX wiki subgpage. 

General tutorials (python, HPCC, Jupyter notebooks):

https://icer.msu.edu/education-events/desire2learn

Literature Search:
literature-search-with-google-scholar

Funding Search:

a-funding-advisers-guide-to-writing-a-great-grant-application 

Unix beginner:

To learn Unix commands: https://www.codecademy.com/learn/learn-the-command-line

https://linuxjourney.com/lesson/the-shell

Python beginner: 

To learn a bit of Python Programming language: https://www.codecademy.com/learn/python

https://developers.google.com/edu/python/

Mendeley beginner:

To organize your papers/literature: https://www.mendeley.com/

Inkscape beginner:

To manipulate images: https://inkscape.org/en/

vi editor beginner: 

Text editor for everything "Vi editor": this is the editor we use for manipulating most of the files

https://www.washington.edu/computing/unix/vi.html

https://www.cs.colostate.edu/helpdocs/vi.html

http://vim.rtorr.com/

Apps to connect to the supercomputer:

When using Linux or Mac, you can use the terminal, when using Windows  you can use: 

http://mobaxterm.mobatek.net/
https://termius.com/

Beginner Supercomputer/cluster:

Connecting to the supercomputer/cluster:

https://docs.icer.msu.edu/Connect_to_HPCC_System

Managing Files in the supercomputer/cluster:
https://docs.icer.msu.edu/Managing_File_Permissions_on_HPCC

https://docs.icer.msu.edu/Change_Primary_Group

Connecting to the supercomputer/cluster (Cheat Sheet):

Need a quick reference for submitting jobs to the HPC?

https://wiki.hpcc.msu.edu/display/ITH/Connect+to+HPCC+System

Connecting to the supercomputer/cluster when outside college campus:

If you are outside MSU campus, you can use ssh as usual, but you can also connect to the cluster via the web:

https://wiki.hpcc.msu.edu/display/ITH/Web+Site+Access+to+HPCC

For the HPCC/ICER, you can start with:

https://wiki.hpcc.msu.edu/display/TEAC/Introduction+to+HPCC

https://docs.icer.msu.edu/attachments/hpcc.pdf

Partition names:
https://docs.icer.msu.edu/filesystem_overview/

https://wiki.hpcc.msu.edu/pages/viewpage.action?pageId=18972892

How to submit jobs (SLURM scheduler):

https://docs.icer.msu.edu/Job_Script_and_Job_Submission/

https://docs.icer.msu.edu/SLURM_Check_Modify_and_Cancel_a_Job_by_scontrol_scancel_Command/

https://docs.icer.msu.edu/SLURM_commands/

Vesta:

This a program to visualize solids, molecules, and make images. 

http://jp-minerals.org/vesta/en/download.html

For more instructions about VESTA you can use: https://www.youtube.com/channel/UCmOHJtv6B2IFqzGpJakANeg/videos

Avogadro:

To visualize and manipulate solids and molecules, visualize trajectories and edit bonds,structures and so on.

http://avogadro.cc/wiki/Get_Avogadro

Installing LaTeX in your Computer (your reports will be in LaTeX):

Check our own guide. 

Editor for LaTeX online (Overleaf):

If you want to use LaTeX online and work with others like a google document, you can use Overleaf (see above to get your professional account!). Tutorials and additional information regarding LaTeX/Overleaf can be found in the LaTeX wiki subgpage. 

Dropbox:

for sharing reports, files, papers, If you want to start writing your reports/presentation you should open an account in:

Dropbox

Feedly: 

to get scientific paper updates on your phone/computer

http://feedly.com/

Matlab: 

To start, you should watch this introductory sets of videos:

https://learntocode.mathworks.com/portal.html

Intermediate tutorials:

Accessing our Archival Storage (for large files, long term): ~50 TB available. 

https://rcc.fsu.edu/doc/globus

Using our 3D-printer to create a physical model of your structures. 

https://sites.google.com/site/mendozacortesgroup/home/getting-started/3dprinting

Connecting interactively (with graphics) to the supercomputer/cluster:

Using software interactively (Matlab, VMD, GaussView) on hpc-cluster, you can use Spear: spear-login.rcc.fsu.edu

https://rcc.fsu.edu/docs/connecting-spear

ssh -X [YOUR-USERNAME]@spear-login.rcc.fsu.edu

#Once logged in with the -X flag, you can invoke graphical programs, such as MATLAB:

bash-4.1 $ matlab

#Or VMD

bash-4.1 $ vmd

Connecting to GPU-enabled Spear nodes in the supercomputer/cluster:

If you want to connect to a Spear node that has a GPU, simply use the spear-gpu.rcc.fsu.edu DNS name:

ssh -X [YOUR-USERNAME]@spear-gpu.rcc.fsu.edu

#Once logged in with the -X flag, you can invoke graphical programs, such as MATLAB:

bash-4.1 $ matlab

#Or VMD

bash-4.1 $ vmd

Use this instead of spear-login.rcc.fsu.edu in order to ensure that you are connected to one of our Spear nodes that has a GPU.

Sublime/Python

A good way to start coding Python is to use a standard editor, with python integrated. A good one that developers use is:

https://www.sublimetext.com/

You can run your python script there, using Ctrl+B, and you can do other things like C++, Make, Ruby, JAVA and things that.

Python

For more advanced tutorials (python 3.0):

https://docs.python.org/3/tutorial/

http://www.learnpython.org/

Python (installation) for numerical calculations (Anaconda):

https://www.continuum.io/downloads

http://conda.pydata.org/docs/test-drive.html

Vi editor advance option:

http://www.lagmonster.org/docs/vi2.html

SLURM: Submission script language

https://rcc.fsu.edu/docs/slurm-job-submission-and-management-reference

Good introductory papers to Quantum Chemistry-Physics

https://www.ch.ic.ac.uk/harrison/Group/Mallia/3year_lab_elec_str/hoffmann.pdf

Advanced tutorials:

SSH keys (SSH automatic connection)

For those in the lab that use Linux (hopefully at least something with KDE), this is a quick tutorial for adding keypair for automatic ssh login.

1. In ~/.ssh , open terminal and run ssh-keygen -t rsa -b 4096 Note: This will make a private (no file extension) and public key (.pub file extension) pair. You essentially want to add the public key onto the hpcc, and setup a way to use your private key as your login credential. You can chose to either make the private key password protected or not, but if you do, when you log in to HPCC, it will prompt for the private key password instead of HPCC password

2. Remote onto the HPCC like normal, go to (or make) ~/.ssh/ and ~/.ssh/authorized_keys  Add/append the pub key data to the authorized_keys file

3. Ensure proper permissions chmod 755 ~ or chmod 750 ~ , chmod 700 ~/.ssh , chmod 600 ~/.ssh/authorized_keys

4. Update key info on HPCC end by running restorecon -R -v ~/.ssh

5. Now on locally on your pc, if you are running something with KDE your default terminal should be Konsole. Navigate to plugins > SSH Manager , and click the + at the bottom to add the ssh info:

Identifier: [pick a name]

SSH Hostname: gateway.hpcc.msu.edu

Port: 22

SSH Key: [navigate to the id_rsa private key you made in step 1] 

Username: [Username]

Folder: [SSH Config]

Profile: Don't Change

or simply add something like ssh -i /home/marcus/.ssh/id_rsa -p 22 djokicma@gateway.hpcc.msu.edu as an alias in your bashrc/zshrc

Now you should just be able to press CTRL + ALT + H, it will pop up each ssh option you made. Once selected, it will log you into hpcc. Now you can repeat this same process on all your computers/laptops For more info/windows instructions

Lab Notebooks 

https://docs.icer.msu.edu/Lab_Notebooks/

Lab notebook documentation describes how to solve a specific problem at a particular time. It is not regularly maintained in the way ICER maintains general documentation. These pages can be casual, trial-and-error tutorials that are relevant for a period of time before becoming outdated. 

Recent Lab Notebooks:
How to use LLMs on the HPCC

Load Custom Models in Ollama 

Other olders ones (@Marcus Djokicand @Austin R, please see if they are missing in our Wiki, for now I put them under Adv. tutorials):

https://docs.icer.msu.edu/2024-09-05_LabNotebook_VSCode_Terminal_login/ 

https://docs.icer.msu.edu/2024-09-04_cuQuantum_Installation_and_Usage/ 

https://docs.icer.msu.edu/2023-11-09_LabNotebook_Molpro_Parallel/

Data Science Masters

http://datasciencemasters.org/

"The Open-Source Data Science Masters

The open-source curriculum for learning Data Science. Foundational in both theory and technologies, the OSDSM breaks down the core competencies necessary to making use of data.

The Internet is Your Oyster

With Coursera, ebooks, Stack Overflow, and GitHub -- all free and open -- how can you afford not to take advantage of an open source education?"

GitHub

Once you start writing your own codes/scripts and specially that you want to collaborate with colleagues about the different versions of your codes and scripts, we recommend to use GitHub. To get a nice introduction, please follow:

http://karthik.github.io/git_intro/#/slide-title

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004668

To make Covers for Journals:

https://www.blender.org/download/

Other  manuals:
https://sites.google.com/site/mendozacortesgroup/home/advice/lab-manual-well-being