ORCA---Computational-Chemistry/C2/Installation-of-ORCA-on-Linux/English

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Title of the script: Installation of ORCA on Linux

Author: Madhuri Ganapathi and Snehalatha Kaliappan

Keywords: orca, Linux, orca Forum, register, login, download, extract compressed archives, set up path, terminal, run a file, video tutorial.


Visual Cue Narration
Slide Number 1

Title slide

Welcome to the Spoken Tutorial on Installation of ORCA on Linux.
Slide Number 2

Learning Objectives


In this tutorial, we will learn to,
  • Download orca 5.0.2 compressed archive packages for Linux OS.
  • Extract the compressed packages.
  • Set up alias path to run orca executable.
  • Run an orca input file to check the installation.


Slide Number 3

System Requirements


This tutorial is recorded using,

Ubuntu Linux OS version 20.04

Orca version 5.0.2

Gedit Text Editor version 3.36.2

Firefox Web browser version 95.0.1


Before you begin, please make sure that you have working internet connection.

Slide Number 4

Pre-requisites

To follow this tutorial,
  • Learner must be familiar with basic computer and Internet skills.
Slide Number 5

Code Files

  • The input file to check the installation is provided in the Code files link.
  • Please download and extract the file.
  • Make a copy and then use it for practising.
Open a web browser and type orca forum in the Google search the web.

https://orcaforum.kofo.mpg.de/app.php/portal


Point to the ORCA Forum page.

Open your web browser and type orca forum and press Enter.

You can see the first instance as ORCA Forum - Portal.

Click on the link.

ORCA Forum page opens.

On the top right side of the page, we have links for Register and Login.

Point to the Register and Login links.

On the top right side of the page, we have links for Register and Login.
Cursor on the page.

Point to the Register link.

If you are a first time user, you have to register on the ORCA Forum.
Click on the Register link.

Point to ORCA Forum Registration page.

Scroll down the page.

Click on the Register link.

ORCA Forum - Registration page opens.

Scroll down the page.

Click on I agree to these terms button.

Point to ORCA Forum – Registration page.

Click on I agree to these terms button.

The Registration page refreshes with the details.

Point to the registration details part.


Point to the Email Address text box.

Point to the message.

Here you have to type your details to register on the ORCA Forum.

Please enter your valid email address in the Email Address text box.

Click on the Submit button. Click on the Submit button to complete the registration.


The ORCA team will send an activation link to the given email address.

You need to click on the link sent in the email to get the registration activated.

Point to login. I have already registered on the ORCA Forum.

So I will login now.

Fill in the details to login.


Click on the Login button.

I will log in using my Username and password.
Point to the page.

Click on the Downloads link on the top left side.

A new page opens.

On the top left side, click the Downloads link.

Point to Downloads – Categories page.

Point to the various versions on the page.

Downloads – Categories page opens.

The page shows various versions of ORCA.

Click on the ORCA 5.0.2 folder link. Click the ORCA 5.0.2 folder link.

A new page ORCA 5.0.2 opens.

A new version of ORCA might be available at the time of your download.

Point to the 3 files. The page has the required files for Linux as 3 compressed tarball files.

We need to download all 3 parts one at a time.

Click on ORCA 5.0.2, Linux, x86-64, .tar.xz Archive, Part ⅓.

Point to the file size.

Click on ORCA 5.0.2 part 1 of the tar.xz file link.

The page refreshes.

Here are the details of this file.

You can see the file size here.

Point to the file size Make sure that at least 35 GB of hard disk space is available on your system.
Point to the green Download button.

Click on the Download button.

Click the large green Download button at the bottom-right to start downloading.
Point to the dialog box.

Click on Save File option to download.

Click the OK button to download the file.

A dialog box opens, which prompts you to save the part 1 file.


Select the Save File option.

Then click the OK button to download the file.


The file takes some time to download due to its large file size.

Point to the tar.xz file. Here, the file downloads to the Downloads directory.


Go back to the previous page, where all the files are listed.

Click the part 2 tarball file link.

Show the downloading files.

Now download part 2 tarball file.
Click the part 3 tarball file link. Similarly, download part 3 tarball file for Linux.
In the left panel select Downloads. Open the File manager and go to Downloads directory.

Notice the three downloaded tarball files.

Enlarge the folder orca using Ctrl ++


Right-click in the Downloads folder.


From the context menu select the New Folder option.

Let us create a new directory and move these files to this directory.


Right-click in the Downloads directory .

From the context menu select the New Folder option.

Type the name as orca in the Folder Name text box.

>> Click Rename button.

Rename the folder as orca.
Point to the orca directory.


Press and hold the Ctrl key and click on all 3 files to select them.

Let’s move the 3 downloaded files to this newly created orca directory.


Press and hold the Ctrl key and click on all 3 files to select them.

Right-click on any one of the files.


Select the Move to option from the context menu.


Select the Downloads directory tab in the left panel.

Right-click on any one of the files.


Select the Move to option from the context menu.


Select the Downloads directory tab.

Select the newly created orca directory.


Click on the Select button at the top-right corner.

Select the newly created orca directory.


Click on the Select button at the top-right corner.

Double-Click on the orca folder to open it.


Point to the 3 tarball files.

Double-Click to open the orca directory.


You can see the 3 files here.

Press Ctrl, Alt and T keys together.

Open a terminal.

We will use terminal commands to extract the files.


Open the terminal by pressing Ctrl, Alt and T keys together.


All the commands typed on the terminal are provided in the Code files link.


Please download and use them as required.

cd Downloads

>> Press Enter.


cd orca

>> Press Enter.

Let's change the path to where we have saved the files.

Type cd space Downloads and press Enter.

Then type cd orca and Press Enter.

tar -xvf orca_5_0_2_linux_x86-64_openmpi411_part1.tar.xz

Point to the created folder.


Double-click on the folder to show the extracted files.

Extract the files one by one as seen with the tar hyphen(-) xvf command.


At the prompt type


tar space -xvf followed by filename as seen here for part 1.


Press Enter to execute the command.


A directory with the same name as the tarball file is created.


All the files are extracted to this directory.

Point to the extraction process.


Show the extracted files.


Point to the prompt

Please wait for the extraction to complete.

This may take some time.

Here are the extracted files.

After the first part is extracted the prompt is seen on the terminal.


Now press the up-arrow key to retrieve the last used command.

tar -xvf orca_5_0_2_linux_x86-64_openmpi411_part1.tar.xz

>> Press Enter.


tar -xvf orca_5_0_2_linux_x86-64_openmpi411_part2.tar.xz

>> Press Enter.


tar -xvf orca_5_0_2_linux_x86-64_openmpi411_part3.tar.xz

>> Press Enter.

Edit the part number in the file name as shown.

Press the Enter key.


Again a directory with the same name as the tarball file is created.

Wait for the extraction to complete.


All the files are extracted to this directory.

Repeat this process until you have extracted the files from 3 tarballs.

Point to the directories.


Double click to open them.

We have completed the extraction of all the parts.


We now have three directories with the extracted files.

Double click to open the folder.


Ctrl + A Select the files

Ctrl + X to cut the files

Ctrl + V to paste the files.

We have to put all the extracted files in the orca directory.


Open the first directory and cut all the files.

Then paste the files in the orca directory.


Similarly cut all the files from other two directories.

And then paste them in the orca directory.

Select the tarball files and empty directores.

Press the Delete key on the keyboard.

You may delete the empty directories.


You may also delete the tarball files to save the disk space.

Press Ctrl + L keys. Press control and L keys together to clear the terminal.
Type ls to list the files.

Scroll and show the files on the terminal.

At the prompt type ls and press Enter to list the files.


For me, the file list is colour coded by file types on the terminal.


The green colour indicates executable files and blue are directories.


Users may place the parent orca folder and all of its contents, in their desired location.


I will leave it as it is for now.

Point to the compiled files in the folder.


Point to the orca file.

Here, all the files are already compiled and are in executable format.


If you do not see them in executable format, you must change the file permissions.

All the files must be placed together for the program to function.


All calculations will run using the orca executable file.

Press Ctrl + L keys. Press control and L keys together to clear the terminal.
Type pwd on the terminal.

/home/spoken/Downloads/orca

Type pwd and press Enter to find the path of this file.

Note down the file path.


Let’s create an alias for the program.

Alias is a temporary, short, and legible command which users can define.


This increases clarity at the command prompt.

Type cd ~ and go to the Home directory.


Type gedit .bashrc

>> press Enter.

Type cd space tilda(~) and press Enter to go to the user Home directory.


Type gedit space .bashrc and press Enter to edit the bash file.


The file opens.

Go to the last line

alias orca ‘filepath’


alias orca='/home/spoken/Downloads/orca/orca'


Click on Save button

>> click on X button.

Scroll down, go to the last line in the file.

Type alias space orca equal to ‘filepath’ in single quotes.

Users must type their file path here, which was noted down earlier.

Save and exit the file.

Type source .bashrc at the prompt.


Press Enter.

Go back to the terminal, to source the file.


At the prompt type, source .bashrc and Press Enter.


From now on, instead of typing the full path just type orca at the prompt.

Point the parent orca file in the Downloads directory. We have created the alias for the ORCA executable file.

If you move the orca folder, be sure to change the path in the alias command.

Type orca at the prompt and press enter.


Read the message,

This program requires the name of a parameter file as argument

For example ORCA TEST.INP

Type orca at the prompt and press Enter.


You will see a message.


This program requires the name of a parameter file as argument

For example ORCA TEST.INP

Cursor on the terminal. Let us now check the installation with an input file.
Show file in Home folder.

Open and show carbonmonoxide.inp file.

I have created an orca input file for carbonmonoxide molecule.

The input file is saved in a separate directory named carbonmonoxide.

It is provided in the Code files link for learners to download and use it.

Open the input file in a text editor.

Notice that it is in text file format.


Let’s run it to check the installation.

Press Ctrl+Alt + T keys together to open the terminal.

orca /home/spoken/carbonmonoxide/carbonmonoxide.inp

Go to the terminal.

At the prompt type,

orca space, type the path for the input file.

Here I am typing the path for my input file.


Users must type their specific path for the input file location.


Press Enter to run the file.

Point to the processing.


Point to the output file.

Open and show the output files in the directory after orca terminates normally.

Observe that the input file is being processed.


You can see the output on the terminal.

You will see a message

ORCA TERMINATED NORMALLY


The generated output files are saved in the input file directory.

Here are the generated output files.


This shows that we have successfully installed orca.

Only Narration With this, we come to the end of this tutorial.

Let us summarise.

Slide Number 6

Summary

In this tutorial, we have learnt to,
  • Download orca 5.0.2 compressed archive packages for Linux OS.
  • Extract the compressed packages.
  • Set up alias path to run orca executable.
  • Run an orca input file to check the installation


Slide Number 7

Assignment


https://sites.google.com/site/orcainputlibrary/home


As an assignment


Users can go through ORCA Input Library and check the updates for input files.

Slide Number 8

Spoken Tutorial Project

This video summarises the Spoken Tutorial Project.

Please download and watch it.

Slide Number 9

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Slide Number 10

Answers for This Spoken Tutorial

  • Do you have questions in THIS Spoken Tutorial?
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Slide Number 11

Forum for specific Questions

  • The Spoken Tutorial forum is for specific questions on this tutorial.
  • Please do not post unrelated and general questions on them.
  • This will help reduce the clutter.
  • With less clutter, we can use this discussion as instructional material.
Slide Number 13

Acknowledgements

Spoken Tutorial project is funded by the Ministry of Education (MoE), Govt. Of India
This is Madhuri Ganapathi from IIT, Bombay signing off.

Thank you for watching.

Contributors and Content Editors

Madhurig, Snehalathak

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