Software Old

New Software

New software can be installed system-wide at the request of users, provided it meets the following criteria:

• It is either freely available or NU has a site license for it.
• It is compatible with the existing OS environment on Shabyt.
• It can utilize resources available on Shabyt effectively.

For assistance regarding new software packages, please contact Shabyt system administrators at hpcadmin@nu.edu.kz.

Software Priorities

Software applications are installed in accordance with priorities.

• Software which can be installed via EasyBuild application falls under this category. List of supported EasyBuild softwares you can find here: EasyBuild
• Applications that are crucial for User Groups but cannot be installed through EasyBuild fall under this priority.
• Individual user requests. Such requests will be processed only after other priorities have been fulfilled.

Name	Description	Versions
AMD-uProf	AMD uProf is a performance analysis tool for applications running on Windows, Linux & FreeBSD operating systems. It allows developers to better understand the runtime performance of their application and to identify ways to improve its performance.	AMD-uProf/3.5.671
Anaconda3	Anaconda: Python Data Science Platform for Python 3	Anaconda3/2022.05
AOCC	AOCC is a high-performance x86 CPU compiler for C, C++, and Fortran programming languages	AOCC/4.0.0
archspec	Archspec provides a standard set of human-understandable labels for various aspects of a system architecture like CPU, network fabrics, etc. and APIs to detect, query and compare them.	archspec/0.1.3
ATK	ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.	ATK/2.38.0
Automake	Automake – make file builder part of autotools	Automake/1.16.1 Automake/1.16.3 Automake/1.16.4 Automake/1.16.5 (D)
Bison	Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.	Bison/3.5.3 Bison/3.7.1 Bison/3.7.6 Bison/3.8.2 (D)
cairo	Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output.	cairo/1.16.0 cairo/1.17.4 (D)
CGAL	CGAL is an open source software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library.	CGAL/4.14.3
CMake	CMake is the standard for building C++ code	CMake/3.20.1 CMake/3.21.1 CMake/3.22.1 CMake/3.23.1 (D)
CUDA	CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.	CUDA/11.4.1 CUDA/11.7.0 (D)
double-conversion	Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.	double-conversion/3.2.0
Doxygen	Doxygen is a widely-used documentation generator tool in software development. It automates the generation of documentation from source code comments, parsing information about classes, functions, and variables to produce output in formats like HTML and PDF.	Doxygen/1.9.1 Doxygen/1.9.4 (D)
Eigen	Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.	Eigen/3.3.9 Eigen/3.4.0 (D)
ELPA	Eigenvalue SoLvers for Petaflop-Applications.	ELPA/2021.11.001
expat	An XML parser library written in C.	expat/2.2.9
FFTW	FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST)	FFTW/3.3.9 FFTW/3.3.10 (D)
FFmpeg	FFmpeg is the multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play audio stream and video.	FFmpeg/4.3.2 FFmpeg/4.4.2 (D)
FLAC	FLAC is an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.	FLAC/1.3.4
flex	Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.	flex/2.6.4
freetype	FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images).	freetype/2.11.0 freetype/2.12.1 (D)
GCC	The GNU Compiler Collection (GCC) provides C/C++ and Fortran compilers.	GCC/9.3.0 GCC/9.4.0 GCC/10.3.0 GCC/11.2.0 GCC/11.3.0 GCC/12.2.0 (D)
GDAL	GDAL is a translator library for raster and vector geospatial data formats that is released under an MIT style Open Source License by the Open Source Geospatial Foundation. As a library, it presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command line utilities for data translation and processing.	GDAL/3.5.0-foss-2022a
GEOS	GEOS is a C/C++ library for computational geometry with a focus on algorithms used in geographic information systems (GIS) software.	GEOS/3.10.3
GLPK	The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP) problems.	GLPK/5.0
GMP	GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.	GMP/6.2.1
GObject-Introspection	GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate metadata files, in addition to the actual native C library.	GObject-Introspection/1.68.0 GObject-Introspection/1.72.0 (D)
GSL	The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.	GSL/2.7
GTK2	The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.	GTK2/2.24.33
Ghostscript	Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets.	Ghostscript/9.56.1
git	Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.	git/2.32.0 git/2.33.1 git/2.36.0 (D)
HarfBuzz	An OpenType text shaping engine	HarfBuzz/2.8.2 HarfBuzz/4.2.1 (D)
Hypre	Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers.	Hypre/2.21.0-foss-2021a
ICU	ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is widely portable and gives applications the same results on all platforms and between C/C++ and Java software.	ICU/69.1 ICU/71.1 (D)
ImageMagick	ImageMagick® is a free, open-source software suite, used for editing and manipulating digital images.	ImageMagick/7.1.0-37
Jasper	The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard	JasPer/2.0.33
Java	Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.	Java/11.0.16
KaHIP	The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.	KaHIP/3.14
LAMMPS	LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.	LAMMPS/23Jun2022
LLVM	The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.	LLVM/12.0.1 LLVM/14.0.3 (D)
LibTIFF	LibTIFF – Tag Image File Format(TIFF) Library and Utilities	LibTIFF/4.3.0
LittleCMS	OPEN SOURCE small-footprint color management engine	LittleCMS/2.13.1
Lua	Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.	Lua/5.4.4
M4	GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.	M4/1.4.18 M4/1.4.19 (D)
METIS	METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.	METIS/5.1.0
MPFR	The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.	MPFR/4.1.0
MUMPS	A parallel sparse direct solver	MUMPS/5.4.0
Mako	Mako is a template library written in Python. It provides a familiar, non-XML syntax which compiles into Python modules for maximum performance.	Mako/1.1.4 Mako/1.2.0 (D)
Mesa	Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.	Mesa/21.1.7 Mesa/22.0.3 (D)
Meson	Meson is an open source build system meant to be both extremely fast, and, even more importantly, as user friendly as possible.	Meson/0.58.2 Meson/0.62.1 (D)
NASM	NASM: General-purpose x86 assembler	NASM/2.15.05
NCCL	The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective	NCCL/2.10.3
NLopt	NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.	NLopt/2.7.1
NSPR	Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.	NSPR/4.34
NSS
NVHPC/22.7
Ninja
OpenBLAS
OpenFOAM
OpenMPI
OpenSSL
PCRE

Anaconda

Description: "Anaconda" (shortly "conda"), a Python package management, permits the creation of "environments," which are sets of modifiable packages. It accomplishes this by placing them in your residence. This page will take you through conda loading, environment creation, and modification so you may install and utilize any Python packages you require.

Usage: Anaconda could be loaded by: module load Anaconda3/2022.05

Creating the Conda Environment: Every user can create their own environments, and packages that are shared with the system-wide environments will not be reinstalled or copied to your file store; instead, they will be symlinked. This reduces the amount of space required in your /home directory to install numerous Python environments. To build a pristine environment with only Python 3.9 and numpy, execute: conda create -n mynumpy1 python=3.9 numpy To alter an existing environment, such as one of the anaconda installations, you can clone it: conda create --clone mynumpy2 -n mynumpy3

Package Installation Within a Conda Environment: After creating your own environment, you can install more packages or other versions of existing programs. There are two ways to accomplish this: conda and pip. If a package is accessible through conda, it is strongly advised that you use it to install packages. Using conda, you can search for packages: conda search pandas then download the package by following these steps: conda install pandas When attempting to install packages outside of your environment, you will receive a permission denied message. If this occurs, create or activate an environment you own. If a package is not available via conda, you can search for and install it using pip: pip search colormath pip install colormath

Usage of conda Environments: Once the conda module has been loaded, the required conda environments must be loaded or created. See the conda manual for documentation on conda environments. You can load a conda environment with the following: source activate mycondaenv where mycondaenv is the environment's name; unload one with: source deactivate which returns you back to the base environment. You can list all the accessible environments by using: conda env list A set of anaconda environments is provided system-wide; these are installed with the anaconda version number in the environment name and are never updated. Therefore, they will provide a fixed base for alternative environments or for direct use.

Using Conda in conjunction with the SLURM scheduler: Using the Anaconda batch mode To submit jobs to the Slurm job scheduler, you must run your primary application in batch mode from within your Conda environment. There are several stages to take: Create a script for application Create a Slurm script job to execute the application script sbatch is used to submit the job script to the task scheduler. Your application script should provide the necessary sequence of commands for your analysis. A Slurm job script is a Bash shell script of a particular type that the Slurm job scheduler recognizes as a job. Create a batch job submission script like the following and name it myscript.slurm: <clippy show="true">

1. !/bin/bash
2. SBATCH --partition=NVIDIA
3. SBATCH --nodes=1
4. SBATCH --ntasks=1
5. SBATCH --cpu-per-task=8
6. SBATCH --mem=16GB
7. SBATCH --time=1:00:00

module purge eval $(conda shell.bash hook) conda activate myenvironment python script.py </clippy> The following describes each line: Command or Slurm option Description

1. !/bin/bash

Use BASH to execute the script

1. SBATCH

Syntax that allows SLURM to read your requests (ignored by BASH) --partition=NVIDIA Submit job to the NVIDIA partition --nodes=1 Use only one compute node --ntasks=1 Run only one task --cpus-per-task=8 Reserve 8 CPUs for the user --mem=16GB Reserve 16GB of RAM --module purge Purge or clear environment modules --time=1:00:00 Reserve resources for an hour eval $(conda shell.bash hook) Initialize the shell to use Conda conda activate myenvironment Activate your Conda environment, i.e., myenvironment python script.py Use python to run script.py Be sure to alter the requested resources based on your needs, but keep in mind that requesting fewer resources will reduce the waiting time for your work. To fully exploit the resources, particularly the amount of cores, it may be necessary to modify your application script. You can build application scripts and job scripts on your local machine and then move them to the cluster, or you can develop them directly on the cluster using one of the various text editor modules (e.g., nano, micro, vim). Submit the job to the job scheduler using the Slurm's sbatch command: sbatch myscript.slurm To determine the status of your position, enter: myqueue If there is no job status listed, then the job has been finished. The job's findings will be logged and, by default, stored in a plain-text file of the following format: slurm-<jobid>.outin in the identical directory from which the job script was submitted. To access this file's contents, enter: less slurm-<jobid>.out then press q to close the viewer.

CUDA

Description: Nvidia created the parallel computing platform and programming model known as CUDA for use with its GPUs for general computing (graphics processing units). By utilizing the capability of GPUs for the parallelizable portion of the calculation, CUDA enables developers to accelerate computationally heavy applications.

Usage: module load CUDA/11.4.1 To check if CUDA has been loaded, type: nvcc --version

ANSYS

Description: The ANSYS suite of tools can be used to numerically simulate a wide range of structural and fluid dynamics issues encountered in several engineering, physics, medical, aerospace, and automotive sector applications.

Usage: Loading the ANSYS module module load ansys/2022r1 Launching the workbench is accomplished by: runwb2 The workbench provides access to Fluent, CFX, ICEM, Mechanical APDL/model, and many other languages and models. The appropriate GUIs can be launched outside of the workbench using fluent, cfx5pre, icemcfd, and launcher.

GROMACS

Description: GROMACS is a flexible package for performing molecular dynamics, simulating the Newtonian equations of motion for systems containing hundreds of thousands to millions of particles. It is intended for biochemical molecules, such as proteins, lipids, and nucleic acids, with complex bonded interactions. However, GROMACS is fast at calculating nonbonded interactions, so many groups use it for non-biological systems, like polymers.

Usage: To load GROMACS software: module load GROMACS/2021.5-foss-2021b-CUDA-11.4.1 The GROMACS executable is either gmx or gmx mpi if an OpenMPI module is used. When you type gmx help commands, a list of gmx commands and their functions will be displayed.

Batch jobs: Users are encouraged to create their own scripts for batch submissions. Below are examples of batch submission scripts.

Parallel MPI #!/bin/bash #SBATCH --job-name=gromacs #SBATCH --mail-user=<YOUR_NU_ID>@nu.edu.kz #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --output=gmx-%j.out #SBATCH --ntasks=2 #SBATCH --cpus-per-task=4 #SBATCH --ntasks-per-socket=1 #SBATCH --time=24:00:00 #SBATCH --mem-per-cpu=1gb module purge module load OpenMPI/4.1.1-GCC-11.2.0 module load GROMACS/2021.5-foss-2021b-CUDA-11.4.1 export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK srun --mpi=pmix_v3 gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK} -s topol.tpr

Software list

• Environment Module System
• Anaconda
• GCC
• CUDA
• MATLAB
• Apptainer