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| Running jobs on HPC clusters often requires the use of preinstalled software. For instance, executing a Python script requires the appropriate version of Python to be installed. Shabyt facilitates researchers by providing access to necessary software. Users of Shabyt can utilize pre-installed software, install their own, or request the HPC team to install specific software. This section outlines how users can manage software on Shabyt.
| | Shabyt HPC cluster provides a large and diverse set of software, including various compilers, programming languages, libraries, and applications. Users can also install software of their choosing themselves in one of their directories. |
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| === Software Availability (How to Find Software) ===
| | The following guides provide instructions for finding and loading software, building and installing software, as well as using popular applications. |
| To perform tasks on Shabyt, users need to ensure the required software is installed and loaded into the environment. Shabyt offers several software systems that can be loaded using environment modules. If you need software as a dependency, you can search for it using module commands, as detailed in the Module Environments and Commands section.
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| == Software Installation == | | == User Guides == |
| Software installation on the Shabyt system follows specific criteria to ensure compatibility and effective utilization of resources. Users can request the installation of new software if it meets the following conditions:
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| * '''Availability and Licensing:''' The software must be freely available or covered by a site license held by NU. | | * [https://hpc.nu.edu.kz/index.php/Software Environment Module System] |
| * '''Compatibility:''' It should be compatible with the existing operating system environment on Shabyt to ensure seamless integration and functionality.
| | * Anaconda |
| * '''Resource Utilization:''' The software should be able to effectively utilize the resources available on Shabyt, optimizing performance and efficiency.
| | * GCC |
| | | * CUDA |
| For guidance or support regarding the installation of new software packages, users should contact the Shabyt system administrators at hpcadmin@nu.edu.kz.
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| Additionally, software are installed in accordance with priorities.
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| * '''Priority 1:''' Software that can be installed using the EasyBuild application is given first priority. A list of supported EasyBuild software can be found here.
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| * '''Priority 2:''' Applications which can't be installed through EasyBuild, but essential for multiple User Groups are prioritized next. | |
| * '''Priority 3:''' Application which can't be installed through EasyBuild, but essential for individual users. | |
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| It's important to know that this isn't a complete list of all the software in Shabyt system.
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| === Building Software ===
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| If the software you require isn’t available on Shabyt, you have the option to compile it yourself.
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| User also will find detailed information about the most frequently used software on Shabyt, including Ansys, Matlab, CUDA, Gromacs, GCC, LAMMPS, and Apptainer. Additionally, we provide guidance on utilizing Environment Modules to manage your software environment effectively, ensuring that all dependencies are correctly configured, allowing you to focus on your research without the hassle of software conflicts.
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| == Environment Modules[edit | edit source] ==
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| In linux environment variables are values that can change and impact how programs behave on a computer system. They are name-value pairs that all processes can access within a particular user environment or shell session. These variables provide a flexible and convenient method for managing system-wide settings, configuring applications, and customizing system behavior.
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| Shabyt uses Environment modules to dynamically set up environment variables for different software. Module commands set, change, or delete environment variables that are needed for a particular software. The ‘<code>module load</code>‘ command will set ''PATH'', ''LD_LIBRARY_PATH'' and other environment variables such that user may choose a desired version of applications or libraries more easily. More details can be found here.
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| {| class="wikitable"
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| |+Environment module commands
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| !Command
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| !Description
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| |module avail
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| |List of available software
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| |-
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| |module keyword [word]
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| |Search for available modules matching the keyword
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| |-
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| |module spider [word]
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| |Show the details of any modules matching the keyword
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| |-
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| |module whatis [module]
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| |Show the short description about module
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| |-
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| |module load [package1] [package2]
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| |Load the environment for the default version of the modulefile
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| |module load [package]/[version]
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| |Load the environment for the specified version of module
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| |-
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| |module unload [package1] [package2]
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| |Unload previously loaded packages
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| |-
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| |module swap [moduleA] [moduleB]
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| |Unload modulefile A and load modulefile B
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| |-
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| |module list
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| |List any currently loaded module(s)
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| |-
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| |module purge
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| |Unload all currently loaded modules
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| |}
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| == Ansys ==
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| '''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.
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| '''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.
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| == GROMACS ==
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| '''Description:''' GROningen MAchine for Chemical Simulations (GROMACS) is a free, open-source, molecular dynamics package. GROMACS can simulate the Newtonian equations of motion for systems with hundreds to millions of particles. GROMACS is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations), many groups are also using it for research on non-biological systems, e.g. polymers.
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| '''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.
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