Welcome to AnoopLab’s Wiki !!

Hello there !!

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

This preliminary guide is created for the following reasons

  • Help beginners to quick start computational chemistry

  • Set up different softwares in the IIT KGP supercomputing 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

Currently we can offer help for these softwares

  • Gaussian

  • ORCA

  • Turbomole

  • xtb

  • PyAR

  • Psi4

  • CFour

  • Mopac

External Libraries/Packages

  • Conda Python

  • OpenMPI

  • OpenBLAS

  • Scalapack

  • Lapack

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

Note

You should also follow the IIT Kgp hpc website specially for the paramshakti configuration and quick start guide.

http://www.hpc.iitkgp.ac.in

Date

18.01.2021

Authors

  • saikat R

ORCA

This guide deal with setup ORCA package in paramshakti supercomputing facility in user’s own account

Getting the Program

Goto the orca forum website. Register yourself if you are new or login. Download the preferred 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.

mkdir -p ~/apps
mv orca_4_2_1_linux_x86-64_shared_openmpi314.tar.xz ~/apps
cd ~/apps
tar -xvf orca_4_2_1_linux_x86-64_shared_openmpi314.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

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)

#%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

Note

  • module try-add 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

export MODULEPATH=$MODULEPATH:/home/<username>/modulefiles

save it and source it

source ~/.bashrc

try this in command line

module load orca/421

if no error is coming out try

$ which orca

it should print out

$ /home/<username>/apps/orca_4_2_1_linux_x86-64_shared_openmpi314/orca

Congratulation !! You have successfully installed ORCA in your account.

Follow the same steps if you want to install a different version Create a new module file in the same location and add the paths accordingly. Also, don’t forget to load the new version in the submit script.

Still having problem ? Don’t worry, create an issue with proper error output here.

We are happy to help!!

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.

#!/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
Date

17.12.2021

Authors

  • saikat R

xtb

This guide deal with setup XTB package in paramshakti supercomputing facility in user’s own account

Getting the Program

Date

18.01.2021

Authors

  • AnoopLab

Conda Python

Anaconda is a python distribution. It also has its own package manger conda. You can install python and other softwares/packages through conda. Main advantage is that it comes with most of the necessary packages. Here we will tell you how to install anaconda python in paramshakti.

Installation

Goto the download page for anaconda individual edition. Download the Anaconda3-20XX.XX-Linux-x86_64.sh file and copy it to your paramshakti \home directory.

Run it

bash Anaconda3-20XX.XX-Linux-x86_64.sh

Accept the terms and condition by typing yes You can set up your custom install directory or default location is also fine. It will take some time to install

At the end it will ask you

Do you wish the installer to initialize Anaconda3
by running conda init? [yes|no]

Although the default is no type yes.

Now logout and login again. You will find there is (base) in front of login prompt. you can disable it by

conda config --set auto_activate_base false

Don’t worry it will go away next time you login

you can also notice there are some config in your ~/.bashrc file written by conda installer don’t remove it. If you install it in your home directory it will be something like this

# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/username/anaconda3/bin/conda' 'shell.zsh' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/username/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/home/username/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/username/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

Now you can activate base environment by

conda activate base

and deactivate it by

conda deactivate

You can also install different environment with required package. Details documentation is here.

Tip

We strongly recommend to create new environment each time when you work on a different projects.

You can read more documentation here

https://docs.anaconda.com/anaconda/user-guide/getting-started/

Date

18.01.2021

Authors

  • saikat R

Openmpi

This guide leads to the setup openmpi in paramshakti supercomputing facility in user’s own account

Requirement

gcc, g++, and gfortran compiler

In paramshakti try this

module avail | grep gcc

This will output all the available gcc versions. Load the latest (preferably) version or any other depending on your requirement. I loaded gcc 10.2.0

module load compiler/gcc/10.2.0

Getting the Program

Goto the openmpi website. Register yourself if you are new or login. Download the required 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. I am writing this tutorial for openmpi v 4.1.1.

mkdir -p ~/apps
mv  ~/apps
cd ~/apps
tar -xzvf openmpi-4.1.1.tar.gz

This will create a directory openmpi-4.1.1. It amy be different depending upon the version. Now create an installation directory. I created with the name openmpi411 and copy the path to this directory. For my case the path will be /home/<username>/apps/openmpi411

Now go to the openmpi-4.1.1 directory and follow the code below

cd openmpi-4.1.1
./configure --prefix=/home/<username>/apps/openmpi411 CC=gcc CXX=g++ F77=gfortran FC=gfortran
make -j10
make install

This will take some time. If it’s finished then the installation is successfully, otherwise check the error log for details. After finishing this go to openmpi411 directory. You wil find several directories, bin, lib, etc, include, share.

Next step is to create a modulefile for openmpi 4.1.1.

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

mkdir -p ~/modulefiles/openmpi
cd ~/modulefiles/openmpi

create a file with your preferred name e.g 411 (usually same with the openmpi version)

Here is a sample modulefile(411)

#%Module1_0
## ORCA modulefile
##
proc ModulesHelp { } {

puts stderr "\tAdds OPENMPI to your environment"
}

module-whatis   "Adds OPNMPI to your environment"

module try-add compiler/gcc/10.2.0

set openmpiversion  4.1.1
set MPI_HOME    /home/17cy91r04/apps/openmpi411

prepend-path    LD_LIBRARY_PATH /home/<username>/apps/openmpi411/lib
prepend-path    PATH /home/<username>/apps/openmpi411/bin

Modify these variables according to your account

Now modulefile for openmpi is created and module path needs to be set in the environment ~/.bashrc

open ~/.bashrc file with an editor and paste this

export MODULEPATH=$MODULEPATH:/home/<username>/modulefiles

save it and source it

source ~/.bashrc

try this in command line

module load openmpi/411

if no error is coming out try

$ which mpirun

it should print out

$ ~/apps/openmpi411/bin/mpirun

Congratulation !! You have successfully installed ORCA in your account.

Tip

If anything goes wrong, you have find what is the problem and after fixing the issue you have to follow all the steps from configure step. Before configuring do make clean first, otherwise it will take the old configuration setup.

Still having problem ? Don’t worry, create an issue with proper error output here.

We are happy to help!!

Date

14.05.2022

Authors

  • saikat R

How to Contribute

This website is build with the help of readthedocs.org and Sphinx with sphinx_rtd_theme

You can read their documentation for details.

Installation

Clone the github repo

$ git clone https://github.com/Saikat248/anooplab-docs.git

and install this two packages

$ pip install sphinx
$ pip install sphinx_rtd_theme

Navigate to anooplab-docs/docs directory

there is a Makefile and start

$ make html

It will create a _build directory and the html files

$ firefox _build/html/index.html

The whole website will run locally. Go ahead start editing the documents and before pushing make sure the build is successful.

Enjoy !!

License

This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0). To view a copy of this license, visit creative commons or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.

Credits

AnoopLab Research group