Basic Introduction to Git (Part 2)

Initialising a Repository in an Existing Directory

If you wish to have a project directory under version control with GIt, do the following

$ cd /home/user/my_project
$ git init

If you wish to add existing files into the version control

$ git add *.sh
$ git add LICENSE
$ git commit --m "Gekko Menu Help Application"
[master (root-commit) c98ae91] Gekko Menu Help Application
 1 file changed, 73 insertions(+)
 create mode 100755 mymenu.sh

You have an initial commit and tracked files. Hooray.

Checking the status of your Files

[user1@node1 menu]$ git status
# On branch master
nothing to commit, working directory clean

This means you have a clean working directory; in other words, none of your tracked files are modified.

Adding new files to your Git Directory

Let’s say you added a new file called check_license_abaqus.sh into the Project Directory, you will have something like

# On branch master
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       check_license_abaqus.sh
nothing added to commit but untracked files present (use "git add" to track)

To add files

[user1@node1 menu]$ git add check_license_abaqus.sh
[user1@node1 menu]$ git status
# On branch master
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#       new file:   check_license_abaqus.sh
#

To remove file

[user1@node1 menu]$ git rm check_license_abaqus.sh -f
rm 'check_license_abaqus.sh'
[user1@node1 menu]$ git status
# On branch master
nothing to commit, working directory clean

To see log, you want to use the command

[user1@node1 menu]$ git log
commit xxxxxxxxx
Author: user1 <kmyemail_used_in_Github@hotmail.com>
Date:   Sun Sep 25 23:50:33 2022 +0800

    Gekko Menu Help Application

There are many more usage. For more information, do take a look at 2.3 Git Basics – Viewing the Commit History

References:

  1. 2.2 Git Basics – Recording Changes to the Repository
  2. 2.3 Git Basics – Viewing the Commit History
  3. 2.4 Git Basics – Undoing Things

Basic Introduction to GitHub (Part 1)

GitHub is the largest code-hosting platform in the world. It uses Git as version control and the repository is based on GitHub. Features such as Pull Requests, Project Boards and GitHub are central and found in one place.

Sign up for a Free Account

To start using GitHub, please go to https://github.com/join and follow the instruction

Creating a PAT of SSH Key

A PAT is a string of characters that can be used in place of a password against the GitHub API and on command lone.

You may need to understand the various scopes on GitHub such as repo, admin: repo_hook, users etc. For more information, do take a look at https://docs.github.com/en/developers/apps/building-oauth-apps/scopes-for-oauth-apps#available-scopes

For starters, you may want to go to https://github.com/settings/tokens and click on Generate new token

On Linux, you can generate your SSH key using the email that you have created in your GitHub User Account

[user1@node1 ~]$ ssh-keygen -t rsa -C "myemail_used_in_Github@hotmail.com"
Generating public/private rsa key pair.
Enter file in which to save the key (/home/user1/.ssh/id_rsa):
/home/user1/.ssh/id_rsa already exists.
Overwrite (y/n)? y
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/user1/.ssh/id_rsa.
Your public key has been saved in /home/user1/.ssh/id_rsa.pub.
The key fingerprint is:
........
........

Adding the SSH Key to the ssh-agent

Although this is not mandatory, adding the SSH Key to the SSH Agent is a good practice that will keep the SSH Key safe. The SSH-agent is an SSH Key Manager that helps to keep the SSH key safe because it protects your SSH keys from being exported. The SSH Agent also saves you from having to type the passphrase you create. every time your SSH key is used.

Before you check, you want to check your ~/.ssh/config first

$ vim ~/.ssh/config
Host * 
AddKeysToAgent yes

At the Terminal,

$ ssh-add ~/.ssh/id_rsa

Copy your SSH Public Key to the field. In your ~/.ssh/config, it should have a .pub extension like id_rsa.pub

Configuring Git

To intialise the Git. Do the following. You may want to take a look at

[user1@node1 ~]$ git config --global user.name "Melvin Soh"
[user1@node1 ~]$ git config --global user.email "kittycool@hotmail.sg"
[user1@node1 ~]$ git config --global init.defaultBranch main
[user1@node1 ~]$ git config --list
credential.helper=netrc -f ~/.netrc.gpg -v
user.name=user1
user.email=myemail_used_in_Github@hotmail.com
init.defaultbranch=main

To continue, See Basic Introduction to GitHub (Part 2)

References:

  1. 1.5 Getting Started – Installing Git
  2. 1.6 Getting Started – First-Time Git Setup

Installing CP2K with Nvidia HPCX on Rocky Linux 8.5

What is HPCX?

NVIDIA® HPC-X® is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. For more information, do take a look at https://developer.nvidia.com/networking/hpc-x

What is CP2K?

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. CP2K provides a general framework for different modeling methods such as DFT using the mixed Gaussian and plane waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi-empirical methods (AM1, PM3, PM6, RM1, MNDO, …), and classical force fields (AMBER, CHARMM, …). CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimisation, and transition state optimization using NEB or dimer method. (Detailed overview of features.). For more information, do take a look at https://www.cp2k.org/

Getting the CP2K

git clone --recursive https://github.com/cp2k/cp2k.git cp2k

Unpack hpcx and Optimised OpenMPI Libraries. For more information on installation, do take a look at Installing and Loading HPC-X

Extract hpcx.tbz into your current working directory.

% tar -xvf hpcx.tbz
% cd hpcx
% export HPCX_HOME=$PWD
% module use $HPCX_HOME/modulefiles
% module load hpcx

Use the CP2K Toolchain to Compile for the easiest

% cd cp2k
% cd /usr/local/software/cp2k/tools/toolchain
% ./install_cp2k_toolchain.sh --no-check-certificate --with-openmpi

Compiling the CP2K

.....
.....
==================== generating arch files ====================
arch files can be found in the /usr/local/software/cp2k/tools/toolchain/install/arch subdirectory
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.ssmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_static.ssmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.sdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_coverage.sdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local.pdbg
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_static.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_warn.psmp
Wrote /usr/local/software/cp2k/tools/toolchain/install/arch/local_coverage.pdbg
========================== usage =========================
Done!
Now copy:
  cp /usr/local/software/cp2k/tools/toolchain/install/arch/* to the cp2k/arch/ directory
To use the installed tools and libraries and cp2k version
compiled with it you will first need to execute at the prompt:
  source /usr/local/software/cp2k/tools/toolchain/install/setup
To build CP2K you should change directory:
  cd cp2k/
  make -j 80 ARCH=local VERSION="ssmp sdbg psmp pdbg"

Do exactly on the ending instruction

% cp /usr/local/software/cp2k/tools/toolchain/install/arch/* /usr/local/cp2k/arch
% source /usr/local/software/cp2k/tools/toolchain/install/setup
% cd /usr/local/software/cp2k
% make -j 32 ARCH=local VERSION="ssmp sdbg psmp pdbg"

If you encounter an error during making like the one below, just do an install for liblsan

% /usr/bin/ld: cannot find /usr/lib64/liblsan.so.0.0.0
% dnf install liblsan -y

If you encounter error like the ones below for fftw libraries,

/usr/bin/ld: cannot find -lfftw3_mpi
collect2: error: ld returned 1 exit status

You have to go to the supporting package libraries and do some editing.

% cd /usr/local/software/cp2k/tools/toolchain/install/fftw-3.3.10/lib
% ln -s libfftw3.a libfftw3_mpi.a
% ln -s libfftw3.la libfftw3_mpi.la

Try again

% cd /usr/local/software/cp2k
% make -j 32 ARCH=local VERSION="ssmp sdbg psmp pdbg"

If successful, you should see binaries at /usr/local/software/cp2k/exe/local

Compiling VASP.6.3.0 with GPGPU Capability using Nvidia HPC-SDK on Rocky Linux 8.5

To Compile VASP with GPGPU Capability using Nvidia HPC-SDK. For more information, do take a look at VASP – Install VASP.6.X.X

VASP support several compilers. But we will be focusing on Nvidia HPC-SDK only for this blog. To download the NVIDIA HPC-SDK

To compile Nvidia HPC SDK, do take a look at HPC SDK Documentation

% tar -xpfz <tarfile>.tar.gz

You may want to use modulefiles provided at hpc-sdk if you are using Module Environment

% module use /usr/local/nvidia/hpc_sdk/modulefiles

You should be able to see something like

------------------- /usr/local/nvidia/hpc_sdk/modulefiles ---------------
nvhpc-byo-compiler/22.5  nvhpc-nompi/22.5  nvhpc/22.5

You can untar the VASP.6.3.3. and potpaw_PBE.54

% tar -xvf vasp.6.3.0.tar
% tar -xvf potpaw_PBE.54.tar 

At the installation base of vasp.6.3.0 base

% cp arch/makefile.include.nvhpc_ompi_mkl_omp_acc ./makefile.include

Load the Nvidia GPGPU SDK and compile. If you are using OneAPI Intel Compilers, you can use module use after compilation. It will not be covered in this write-up.

% module use /usr/local/intel/oneapi-2022/modulefiles
% module load nvhpc/22.5
% module load mkl/latest
% make veryclean
% make DEPS=1 -j

If during the make, you encounter the error

/usr/local/nvidia/hpc_sdk/Linux_x86_64/22.5/comm_libs/openmpi/openmpi-3.1.5/bin/.bin/mpif90: error while loading shared libraries: libatomic.so.1: cannot open shared object file: No such file or directory

You can dnf install libatomic

% dnf install libatomic -y

Try Compiling again

References:

  1. Installing VASP.6.X.X

Failover feature “HFSS SBR+Solve” is not available. Request name hfssbr_solve does not exist in the licensing pool.

During usage of ANSYS EM, you may encounter issues like the one below.

Fail to enable feature using current license setting. Note that pro, premium, enterprise licenses are available on your server. To use these licenses check the corresponding UI option. For more information, search "PPE" in the help documentation. Failover feature "HFSS SBR+Solve" is not available. Request name hfssbr_solve does not exist in the licensing pool. No such feature exists. Feature: hfssbr_solveLicensepath: 1055@kangkong.hpc.ntu.edu.sg: FlexNet Licensing error:-5,147

The resolution is to activate the correct product licensing which are not activated by default. See the Pix on how to activate the licensingsee less.

Compiling cmake-3.21.3 on Rocky Linux 8.5

If you are compiling the cmake-3.21.3 on Rocky Linux 8.5, and encounter the issues

-- Could NOT find OpenSSL, try to set the path to OpenSSL root folder in the system variable OPENSSL_ROOT_DIR (missing: OPENSSL_CRYPTO_LIBRARY OPENSSL_INCLUDE_DIR)

The problem is easy to resolve, you just need to install the openssl and openssl-devel libraries

# dnf install openssl openssl-devel

You should be able to bootrap easily.

Alternatively, instead of using ./boostrap, you can use the traditional configure command

#./configure --prefix=/usr/local/cmake-3.21.3
# make
# make install

Compiling ORCA-4.2.1 with OpenMPI-3.1.4

ORCA is a general-purpose quantum chemistry package that is free of charge for academic users. The Project and Download Website can be found at ORCA Forum

You have to register yourself before you can participate in the forum or download ORCA-4.2.1. The current latest version for ORCA is 5.0.3. The package you might want to consider is ORCA 4.2.1, Linux, x86-64, .tar.xz Archive

Prerequisites that I use.

Unpacking ORCA-4.2.1

% tar -xvf orca_4_2_1_linux_x86-64_openmpi314.tar.xz
.....
.....
orca_4_2_1_linux_x86-64_openmpi314/autoci_rhf_poly1_sigma
orca_4_2_1_linux_x86-64_openmpi314/orca_eprnmr_mpi
orca_4_2_1_linux_x86-64_openmpi314/autoci_uhf_poly1_sigma
orca_4_2_1_linux_x86-64_openmpi314/orca_casscf
orca_4_2_1_linux_x86-64_openmpi314/autoci_iprocisd_sigma_alpha_doublet_mpi
orca_4_2_1_linux_x86-64_openmpi314/autoci_rohf_cisd_product
orca_4_2_1_linux_x86-64_openmpi314/orca_gstep
orca_4_2_1_linux_x86-64_openmpi314/contrib/
orca_4_2_1_linux_x86-64_openmpi314/contrib/G2_MP2.cmp
orca_4_2_1_linux_x86-64_openmpi314/contrib/W2_2.cmp
orca_4_2_1_linux_x86-64_openmpi314/contrib/G2_MP2_SV.cmp
orca_4_2_1_linux_x86-64_openmpi314/contrib/G2_MP2_SVP.cmp
orca_4_2_1_linux_x86-64_openmpi314/orca4.2-eula.pdf
orca_4_2_1_linux_x86-64_openmpi314/Third_Party_Licenses_ORCA_4.2.pdf

Running ORCA. If your environment has Module Environment

% module load openmpi/3.1.4/gcc-6.5.0

If not, you have to pacify PATH and LD_LIBRARY_PATH, MANPATH

export PATH=$PATH:$OPENMPI_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$OPENMPI_HOME/lib:$OPENMPI_HOME/lib64
export MANPATH=$MANPATH:$OPENMPI_HOME/share

Typical Input file

Calling ORCA requires full pathing

/usr/local/orca_4_2_1_linux_x86-64_openmpi314/orca $INPUT > $OUTPUT "--bind-to core --verbose"

For Input File usage, you may want to take a look at the ORCA 4.2.1 Manual found when you unpack or you can look at it online at orca_manual_4_2_1.pdf (enea.it) .

For example…….

! B3LYP def2-SVP SP
%tddft
tda false
nroots 50
triplets true
end
%pal
nprocs 32
end

* xyz 0 1 fac_irppy3.xyz
  Ir        0.00000        0.00000        0.03016
   N       -1.05797        1.55546       -1.09121
   N        1.87606        0.13850       -1.09121
.....
.....

Compiling pybind11 with GNU-6.5

The Project Website can be found at https://github.com/pybind/pybind11

pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. Its goals and syntax are similar to the excellent Boost.Python library by David Abrahams: to minimize boilerplate code in traditional extension modules by inferring type information using compile-time introspection.

The Compiling Steps can be found at https://pybind11.readthedocs.io/en/stable/basics.html

mkdir build
cd build
cmake .. -DDOWNLOAD_EIGEN=ON -DDOWNLOAD_CATCH=ON
make check -j 4

Licensing Errors for ANSYS IcePak Solver

If you are encountering issues like the one below.

"If you have this error "Failed to enable features using current license settings. Note that Pro, Premium, Enterprise licenses are available on your server. To use these licenses check the corresponding option. For more information, search "PPE" in the help documentation. Failover feature "ANSYS IcePak Solver" is not available. Request name aice_solv does not exist in the....."