orca setup

.gitignore

@@ -127,3 +127,4 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+.vscode/

docs/.vscode/settings.json

@@ -1,4 +1,7 @@
 {
 	"python.pythonPath": "/home/saikat/venv/documentation/bin/python3",
-	"restructuredtext.confPath": "${workspaceFolder}"
+	"restructuredtext.confPath": "${workspaceFolder}",
+	"cSpell.words": [
+		"supercomputuing"
+	]
 }

docs/basic_slurm.rst

@@ -0,0 +1,20 @@
+.. _basic_slurm:
+
+SLURM Queuing system
+====================
+
+The Slurm is a Workload Manager, formerly known as Simple Linux Utility for Resource Management (SLURM),
+or simply Slurm.
+
+If you are not familiar with this please read about this first before proceed to the tutorials.
+There are plenty of resource available in the web. Go ahead. 
+
+Here are some links
+
+`<https://slurm.schedmd.com/overview.html>`_
+
+You should also follow the IIT Kgp hpc website specially for the paramshakti configuration and quick start
+guide.
+
+`<http://www.hpc.iitkgp.ac.in>`_
+

docs/credits.rst

@@ -0,0 +1,9 @@
+.. _credits:
+
+
+---------
+Credits
+---------
+
+AnoopLab Research group
+

docs/index.rst

@@ -3,8 +3,26 @@
 Welcome to AnoopLab's Wiki !!
 ==================================
 
-This is a preleminary guide to set up different softwares in the `IIT Kgp <http://www.iitkgp.ac.in/>`_ supercomputuing
-facility.  
+Hello there !! 
+
+.. image:: figures/anooplablogo.png
+   :alt: anooplablogo
+
+We are a theoretical and computational chemistry research group at the 
+Indian Institute of Technology Kharagpur, India.
+
+**Want to know more about our research ?** `Click here <http://www.chemistry.iitkgp.ac.in/~anoop/>`_
+
+
+This preliminary guide is created for the following reasons
+
+- Help  beginners to quick start computational chemistry
+- Set up different softwares in the `IIT Kgp <http://www.iitkgp.ac.in/>`_ supercomputuing facility.  
+- Some essential tutorials about linux and programming 
+
+**Want to help?**
+
+Please feel free to contribute. Send PR to our github repo.
 
 Quantum Chemistry Packages
 ==========================
@@ -18,17 +36,20 @@ Currently we can offer help for these softwares
 - `PyAR <https://github.com/anooplab/pyar>`_
 - Psi4
 - CFour 
+- Mopac
 
-
-
-
+.. toctree::
+   :maxdepth: 3
+   :caption: SLURM 
+
+   basic_slurm
 
 
 .. toctree::
    :maxdepth: 3
-   :caption: Quickstart
+   :caption: Installation Guides
 
-   ORCAsetup
+   orca/ORCAsetup
 
 
 
@@ -41,6 +62,7 @@ Currently we can offer help for these softwares
    :caption: Misc
 
    license
+   credits
 
 ..
   * :ref:`genindex`

docs/orca/ORCAsetup.rst

@@ -0,0 +1,144 @@
+.. _ORCAsetup:
+
+-----
+ORCA
+-----
+
+This guide deal with setup ORCA package in 
+paramshakti supercomputing facility in user's
+own account
+
+
+.. contents::
+
+Getting the Program
+===================
+
+Goto the `orca <https://orcaforum.kofo.mpg.de/app.php/portal>`_
+forum website. Register yourself if you are new or login.
+Download the preffered version for Linux x86 and copy it 
+to your account. Now create a ``apps/`` directory inside your ``home``
+and move the tar file there and untar it.
+
+.. code-block:: bash
+	
+	mkdir -p ~/apps
+	mv orca_4_2_1_linux_x86-64_shared_openmpi411.tar.xz ~/apps
+	cd ~/apps
+	tar -xvf orca_4_2_1_linux_x86-64_shared_openmpi411.tar.xz
+
+
+Installation
+============
+
+ORCA is distributed as  precompiled binary files. So there is nothing to install other than the 
+environment paths.
+
+To run ORCA in parallel it requires OpenMPI package library. So either you have
+to load OpenMPI by ``module`` system in paramshakti (easy way!!) or you have to install OpenMPI. 
+Please visit the OpenMPI installtion for building it from source. In this tutorial we will use the pre-installed
+OpenMPI library in paramshakti for ORCA.  The supported MPI version are usually mentioned in the orca folder name
+when you extract it
+e.g ``orca_4_2_1_linux_x86-64_shared_openmpi314`` means ORCA version is 4.2.1 and supported OpenMPI version is 3.1.4
+
+Module File setup
+-----------------
+
+Packages in paramshakti are usually maintained by using the ``module`` system. You can easily maintain multiple version
+of same/different packages with this system.
+First create a ``modulefiles`` directory inside your ``\home``
+
+.. code-block:: bash
+	
+	mkdir -p ~/modulefiles/orca
+	cd ~/modulefiles/orca
+
+create a file with your preferred name e.g ``421`` (usually same with the orca version)
+
+Here is a sample modulefile(``421``)
+
+.. code-block:: bash
+
+	#%Module1_0
+	## ORCA modulefile
+	##
+	proc ModulesHelp { } {
+
+	        puts stderr "\tAdds ORCA to your environment"
+	}
+
+	module-whatis   "Adds ORCA to your environment"
+	module try-add compiler/gcc/8.3.0
+	module try-add openmpi3/3.1.4
+
+	setenv ORCAPATH /home/<username>/apps/orca_4_2_1_linux_x86-64_shared_openmpi314
+
+	prepend-path    PATH    /home/<username>/apps/orca_4_2_1_linux_x86-64_shared_openmpi314
+	prepend-path    LD_LIBRARY_PATH /home/<username>/apps/orca_4_2_1_linux_x86-64_shared_openmpi314
+
+Important points to remember:
+
+- ``module-tryadd`` will load the gcc (version 8.3.0) and openmpi (version 3.1.4) these two are pre-installed.
+- ``setenv ORCAPATH`` path to your orca directory. In this case it is located  under ``apps`` subdirectory inside the ``\home``
+- ``prepend-path`` usually the same directory required for ORCA
+
+Modify these variables according to your account 
+
+Now modulefile for ORCA is created and module path needs to be set in the environment ``~/.bashrc``
+
+open ``~/.bashrc`` file with an editor and paste this 
+
+.. code-block:: bash
+
+	export MODULEPATH=$MODULEPATH:/home/<username>/modulefiles
+
+save it and ``source`` it
+
+.. code-block:: bash
+
+	source ~/.bashrc
+
+try this in command line  
+
+.. code-block:: bash
+
+	module load module load orca/421
+
+if no error is coming out try 
+
+.. code:: bash
+
+	$ which orca
+
+it should print out
+
+.. code-block:: bash
+
+	$ /home/<username>/apps/orca_4_2_1_linux_x86-64_shared_openmpi314/orca
+
+
+Congratulation !! You have successfully installed ORCA in your account.
+
+Submit Script for SLURM in paramshakti
+--------------------------------------
+
+It's time to test the ORCA Program.
+
+Go to your ``scratch`` directory and submit a test job. Here is a sample submit script.
+
+.. code-block:: bash
+
+	#!/bin/bash
+	#SBATCH -J orca-testjob     # name of the job
+	#SBATCH -p standard-low     # name of the partition: available options "standard, standard-low, gpu, hm"
+	#SBATCH -n 16   	        # no of processes or tasks
+	#SBATCH -t 1:00:00          # walltime in HH:MM:SS, Max value 72:00:00
+	
+	#list of modules you want to use, for example
+	module load orca/421
+	#name of the executable
+	exe=$ORCAPATH/orca
+	#run the application
+	$exe opt.inp >& result.out
+
+