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Introduction to module Software

Enter the command on mgmt-3 or mgmt-4 nodes: module ava

Below is a detailed introduction to the listed software and its basic usage:

3v and 3v_v2​

  • Introduction: These might be custom modules or specific versions of software packages, and their specific use needs to be understood from documentation or environment configuration.
  • Usage: Consult specific documentation or ask the administrator.

Anaconda3​

  • Introduction: A distribution of Python that includes numerous scientific computing, data analysis, and machine learning libraries.
  • Usage: Use the conda command to install, manage packages, and create virtual environments. For example: conda create --name myenv python=3.9 creates a Python 3.9 environment named myenv.

Biological Tools​

crisprcasfinder​

  • Introduction: Used for identifying CRISPR-Cas systems in genomes.
  • Usage: crisprcasfinder -i input.fasta -o output.txt

mmseqs​

  • Introduction: A tool for fast sequence similarity searches.
  • Usage: mmseqs easy-search queryDB targetDB resultDB tmpDir

prodigal​

  • Introduction: Gene prediction tool, especially for prokaryotes.
  • Usage: prodigal -i genome.fna -a proteins.faa -d nucleotides.fna

sratoolkit​

  • Introduction: Used for processing data from the NCBI SRA database.
  • Usage: fastq-dump --outdir . --gzip --skip-technical --readids --read-filter pass --dumpbase --split-files --clip SRR000001

CUDA​

  • Introduction: NVIDIA's parallel computing platform and programming model, allowing developers to accelerate applications using GPUs.
  • Usage: Write CUDA C/C++ code and compile using the nvcc compiler. For example: nvcc my_program.cu -o my_program

GROMACS, LAMMPS​

GROMACS​

  • Introduction: Molecular dynamics simulation software.
  • Usage: Prepare input files (such as topology and coordinate files) and then run the simulation program. For example: gmx mdrun -deffnm my_simulation

LAMMPS​

  • Introduction: Another molecular dynamics simulation software.
  • Usage: Prepare input scripts and then run. For example: lmp_serial -in in.script

HDF5​

  • Introduction: A data storage format that supports efficient management and access to large datasets.
  • Usage: Read and write HDF5 files through APIs (C, C++, Fortran, etc.). For example: h5copy or use HDF5 library functions in code.

ImageMagick​

  • Introduction: An image processing library capable of converting, editing, and composing images.
  • Usage: Operate image files via command-line tools or programming interfaces. For example: convert input.png output.jpg

MPI Libraries​

mpich, mvapich, openmpi​

  • Introduction: For parallel computing on distributed memory systems.
  • Usage: Write MPI programs and use mpirun or mpiexec to start. For example: mpirun -np 4 ./mpi_program

VASP​

  • Introduction: First-principles electronic structure calculation software.
  • Usage: Set input parameter files (such as INCAR, POSCAR, KPOINTS, etc.) and then run the VASP program. For example: mpirun vasp_std

Compilers and Libraries​

compilers/gcc-13.1.0​

  • Introduction: GNU Compiler Collection, including C, C++, Fortran compilers.
  • Usage: Compile source code using gcc, g++, gfortran commands.

compilers/icc-2023.1.0​

  • Introduction: Intel C++ Compiler.
  • Usage: Compile C/C++ code using the icc command.

compilers/mkl-2023.1.0​

  • Introduction: Intel Math Kernel Library, providing highly optimized mathematical functions.
  • Usage: Specify the MKL library path during the linking stage, for example: icc -mkl program.o

Other Software​

cmake​

  • Introduction: A cross-platform build system generator.
  • Usage: Use the cmake command to generate Makefile or other build files. For example: cmake ..

dot​

  • Introduction: Part of Graphviz, used for describing graphs.
  • Usage: Generate graphics files using the dot command. For example: dot -Tpng input.dot -o output.png

genesis-2.1.2​

  • Introduction: Molecular dynamics simulation software.
  • Usage: Similar to GROMACS, prepare input files and then run simulations.

git-lfs​

  • Introduction: Git Large File Storage, used for version control of large files.
  • Usage: After installing Git LFS, track large files using git lfs track.

matlab/2023b​

  • Introduction: Commercial software for numerical computation and algorithm development.
  • Usage: Launch the MATLAB interface or execute scripts using matlab -nodisplay -r "script".

nvhpc​

  • Introduction: NVIDIA HPC SDK, including compilers and libraries, supporting high-performance computing.
  • Usage: Compile code using the nvc or nvc++ command.

pdsh-2.29​

  • Introduction: Parallel remote command execution tool.
  • Usage: Execute remote commands using the pdsh command. For example: pdsh -w node[1-10] 'hostname'

plumed_2.9.0​

  • Introduction: A plugin for extending molecular dynamics simulations.
  • Usage: Use in conjunction with GROMACS or LAMMPS. For example: gmx mdrun -plumed plumed.dat

Modules System​

modules​

  • Introduction: Environment module system for loading and unloading software environments.
  • Usage: Manage modules using module load/unload/list commands. For example: module load anaconda3

singularity-ce-4.1.3​

  • Introduction: Container solution, particularly suitable for HPC environments.
  • Usage: Create containers using singularity build, run commands using singularity exec.

slurm​

  • Introduction: Resource management and job scheduling system.
  • Usage: Submit jobs using the sbatch command, view queue status using squeue.

use.own​

  • Introduction: A special module in the module system that allows users to load their own environment settings.
  • Usage: Add custom module paths using module use /path/to/modules.

Wolfram-Engine​

  • Introduction: The command-line version of Mathematica for symbolic computation.
  • Usage: After starting Wolfram Engine, input expressions directly or use wolframscript to execute scripts.

The above is a basic introduction and simple usage of each software. Actual applications may require referencing official documentation for more detailed information. Some tools may require administrative privileges or other specific configurations to be correctly installed and used.