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The Library System on Elja

A new library structure has been added to the HPC system. This library structure is called library edda. The main reason for setting up this library system is to minimize redundancy and information overload for users. Where the previous library system contained many libraries with the same programs that users wouldn't even need to use, this library aims to solve this issue.

Library Structure

Core Library | lib-edda​

To start with, we have a core library setup called lib-edda. This core library contains all the software and their dependencies that modulefiles from other libraries use. This file should already be loaded once the user has logged into the HPC cluster. To check if it has been already loaded, the user can simply type into the command line:

# Command:
ml avail

# Result Example:
------------------------------------- /hpcapps/lib-edda/modules/all/Core -------------------------------------
   BLAST/2.11.0-Linux_x86_64    GCC/11.2.0    GCC/13.2.0        GCCcore/11.3.0    Go/1.17.6            Maven/3.6.3               
   EasyBuild/4.9.1              GCC/11.3.0    GCCcore/7.4.0     GCCcore/12.2.0    Java/11.0.20         NVHPC/22.7-CUDA-11.7.0    
   FastQC/0.12.1-Java-11        GCC/12.2.0    GCCcore/8.3.0     GCCcore/12.3.0    Java/17.0.6          binutils/2.40             
   GCC/8.3.0                    GCC/12.3.0    GCCcore/11.2.0    GCCcore/13.2.0    LDC/1.24.0-x86_64    foss/2021b

If, however, the library doesn't appear, then you can load it by typing the following into the command line:

ml use /hpcapps/lib-edda/modules/all/Core

Toolbox Library | lib-tools​

The toolbox library, like other libraries, relies on lib-edda. This library consists of compilers, package managers, and programming languages. To use this library, you can type the following command:

# Loading the library
ml use /hpcapps/lib-tools/modules/all

# View available software in the lib-tools library
ml avail 

---------------------- /hpcapps/lib-tools/modules/all ----------------------
   Anaconda3/2023.09-0                   Python/3.11.3
   Autotools/20220317                    R/4.3.2-gfbf-2023a
   BLIS/0.9.0                            RSTUDIO/v2023.09
   CMake/3.26.3                          SQLite/3.42.0
   FFTW/3.3.10                           UnZip/6.0

Other Libraries​

As mentioned in the previous chapter, all other libraries depend on the core library lib-edda to be used. Those other libraries are listed below in their respective chapters, containing the description of the library, the types of software they contain, and how to load them.

Biology Library | lib-bio​

The Biology library contains packages that are used in the biological field.

Loading the library

# Loading the library
ml use /hpcapps/lib-bio/modules/all

# View available software 
ml avail

# Output example:
-------------------------- /hpcapps/lib-bio/modules/all --------------------------
   BLAST/2.11.0-Linux_x86_64    MUMmer/4.0.0rc1                SAMtools/1.17            
   Bowtie2/2.5.1                Nextflow/23.10.0               SAMtools/1.18       (D)    
   GATK/4.5.0.0-Java-17         PCAngsd/0.940                  SRA-Toolkit/3.0.10         
   IDR/2.0.2                    PLINK/2.00a3.7                 Sambamba/1.0.1             
   Jellyfish/2.3.0              RDP-Classifier/2.13-Java-17    SolexaQA++/v3.1.7.3

You can find more details on available packages in lib-bio here

Chemistry Library | lib-chem​

The Chemistry library contains packages that are used in the chemistry field.

Loading the library

# Loading the library
ml use /hpcapps/lib-chem/modules/all

# View available software 
ml avail

# Output example:
-------------------------------- /hpcapps/lib-chem/modules/all --------------------------------
   ASE/3.22.1    CP2K/2023.1    LAMMPS/23Jun2022-kokkos    OpenMM/8.0.0-OpenMPI-4.1.5    
   Bader/1.05    GPAW/23.9.1    ORCA/5.0.4                 QuantumESPRESSO/7.2

You can find more details on available packages in lib-chem here

Engineering Library | lib-engine​

The Engineering library contains packages that are used in the Engineering field.

Loading the library

# Loading the library
ml use /hpcapps/lib-engine/modules/all

# View available software 
ml avail

# Output example:
-------------------------------- /hpcapps/lib-engine/modules/all --------------------------------
   OpenFOAM/10-OpenMPI-4.1.5

You can find more details on available packages in lib-engine here

Geology Library | lib-geo​

The Geology library contains packages that are used in the Geology field.

Loading the library

# Loading the library
ml use /hpcapps/lib-geo/modules/all

# View available software 
ml avail

# Output example:
-------------------------------- /hpcapps/lib-geo/modules/all --------------------------------
   CloudCompare/2.12.4           HYDROTHERM/3.2.0      ParaView/5.12.0
   GrowClust3D.jl/1.0.0-Julia    ODM/3.3.4             QGIS/3.28.1
   HEC-DSSVue/3.3.26             OrfeoToolbox/9.0.0    fall3d/8.3.0
   HEC-RAS/v61                   PISM/2.1

You can find more details on available packages in lib-geo here

Can't Find Software?​

If a program that you require isn't available in any of these packages, then let us know through irei@hi.is with the title Software to Elja and we will help you out.