Computational Science

Skills Checklist

General technical skills
Computer Science Skills
Essential skills for software development
Essential skills for HPC
Essential skills for coding GPU
Essential skills for machine learning (bonus)

General technical skills

For Windows:
- Install programs and modify system variables
- Install Nvidia CUDA toolkit and driver
- Setup VPN and local network
- Setup dual boost for Linux, or install WSL for Ubuntu
For Linux and macOS:
- Basic/intermediate commands
- Know some important files/folders
- Understand some environmen variables
Scripting programming language
- Bash, awk, perl, Python + Jupyter notebook
Cluster / HPC
- Understand terminology: master node, compute node, scheduler, CPU cores, processes, memory
- Scheduler: Slurm, PBS, SGE
- Software manager: module
Software
- Commercial: Gaussian, Q-Chem, ADF, MOLPRO, MOLCAS, TURBOMOLE and many more
- Non-commercial: PySCF, Psi4, OpenMOLCAS, GAMESS, ORCA, NWChem, DIRAC, DALTON, CP2K, LAMMPS, VASP, QE and many more
- Full list is here
Graphic visualization
- JMol, Molden, Gaussview, Avogadro, UCSF Chimera, VMD, Ovito, PyMol
- 2D and 3D plots
Other useful tools
- ASE, MDTraj, Pymatgen, RDKit, OpenBabel
Writing
- Microsoft Word
- LaTeX
  - Compiler: pdflatex, xelatex, lualatex
  - Distribution: TeX Live, MikTeX
  - Editor: OverLeaf, TeXstudio, Texmaker
Presentation
- Powerpoint
- LaTeX Beamer

Computer Science Skills

Programming (Python, C++, etc.)
Scientific Computing
Scientific Programming in Python
High Performance Computing
Computer Applications in Chemistry, Biology, and Physics
Programming in C++
Algorithm in Software Development
Interdisciplinary Research Methods In Computational Biology
Data Analysis in Biology
Introduction to Machine Learning
Introduction to Deep Learning
Neural Network and Computer Vision

Essential skills for software development

Tex editor
- Vi/Vim, Nano
- VS Code, Atom, Eclipse, Sublime
File format
- XML, JSON
General programming skills
- Type of variables
- Loops and conditional statement
- Input/output
High-level programming
- Python
  - Pip and conda: Python helper
  - NumPy: Array (vector, matrix) computation
  - Numba: JIT compiler for NumPy
  - Jax: autograd of NumPy array
  - SciPy: a collection of math functions/routines
  - Scikit-learn: statistics routines, optimization, curve fitting
    - Intel Scikit-learn is 10x faster than the standard one
  - Matplotlib / Plotly for plotting graph
  - Theano: numerical computation
  - SCOOP: distributed modules for parallel programming
  - NetworkX: Graph library
Low-level programming
- C
  - Function, pointer, storage class
  - Enum, struct, union
  - Preprocessor
  - Operator, memory management, array
  - File handling
- C++
  - C++ 11 or newer
  - Type of variable: signed, unsigned, long, double, etc.
  - Loops, conditional statement
  - Standard libraries: vector, rand
  - Understanding header and source file
  - Preprocessor
  - Function, class, struct, template
  - Declaration
    - namespace, const, attribute, pointer, pass by reference, static_assert
  - Initialization
  - Misc: casting, lambda expression, encapsulation, file handling, exception handling
- Fortran
  - Learn either F77 or F90 or modern fortran (2003, 2008, 2018)
  - Module, subroutine, function
  - Array (allocatable and multidimentional) and string
  - Operator overloading
  - Flow control
  - Derived type
  - Callback
  - Interfacing to other language e.g. Python or C++
- GNU library
  - GSL
  - Many more libraries here
Memory allocation
- Stack, heap, global memory
Math libraries
- BLAS (OpenBLAS)
- LAPACK for linear algebra
- ScaLAPACK - a higher level LAPACK
- Intel MKL (Intel oneAPI)
- FFTW: for computing the discrete Fourier transform in one or more dimensions, real and complex data
- Eigen: linear algebra library
- Boost: a collection of C++ functions
QM libraries
- libxc: XC function library
- libint: For computing Gaussian integral
- libcint: general GTO integrals
Code optimization
- Benchaming/scaling
- Complexity (Big O)
GNU
- Static and dynamic libraries
- Archive
- Compiling (g++, gcc) and linking (ld)
- Useful flags for compiler and linker
Compilng tools
- autoconf
- configure
- Make, cmake, automake
Debugging
- gdb for general debugging
- Valgrind for memory leak analysis
Git (source code control)
- Basic/intermediate commands
- GitHub & GitLab
Documentation
- Sphinx (for markdown and reStructuredText)
- Doxygen

Essential skills for HPC

Architecture
- Memory management
- Threading, multithreading
- Block
Parallel computing (SPMD)
- Shared memory: OpenMP
- Distributed memory: MPI
  - Implementations: OpenMPI, Intel MPI, MVAPICH
Intel ecosystem
- OpenMP compiler: icc, ifort
- MPI compiler: mpicc, mpiicc (for Intel C compiler), mpicxx (for C++), mpiifort (for Fortran)
Cloud computing (bonus)
Server and database
Networking

Essential skills for coding GPU

Intermediate/advanced C or C++ skills
Programming model: Kernels, thread hierarchy, memory hierarchy, heterogeneous hierarchy, asynchronous SIMT
CUDA
- Understand CUDA operation:
  1. Declare and allocate host and device memory.
  2. Initialize host data.
  3. Transfer data from the host to the device.
  4. Execute one or more kernels.
  5. Transfer results from the device to the host.
- CUDA C and CUDA C++ API
- Compiler: nvcc

Essential skills for machine learning (bonus)

Basic math: linear algebra and calculus
Programming
- Python, R, Julia, Matlab
- TensorFlow, PyTorch, Scikit-learn
Python lib
- NumPy
- Pandas
Terminology: regression, classification, descriptor, feature, kernel, activation function
Data analysis/engineering: EDA, ETL
Graphical representation
- Histogram, bar plot, heatmaps
ML algorithms
- Decision tree
- Random forest
- Support vector machine
- Principal component analysis
- Kernel-ridge method
- Neural network
  - Feedforward NN
    - Autoencoder
  - CNN
  - RNN (LSTM)
  - GNN
  - Adversarial NN
    - GAN
Model training and optimization
- Hyperparameter optimization
Techniques to prevent overfittingTechniques
- Data augmentation, early stopping, regularization, dropout, batch normalization
Deploying model