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The Library system on Elja

New library structure has been added on the HPC system. This library structure is called library edda. The main reason for setting this library system up is to minimize redundancy and information overload to users. Where in the previous the library system would contain many libraries with the same programs that the user wouldn't even need to use this library however 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 is used to contain all the softwares and their dependencies where 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 in 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 in the following command line:

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

#View availble 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 here below in their respective chapters, containing the description the library, of what type of software they contain and how to load it.

Biology library | lib-bio​

The Biology library contains the 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 availble packages in lib-bio here

Chemistry library | lib-chem​

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

Loading the library

# loading the library
ml use /hpcapps/lib-bio/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 availble packages in lib-chem here

engineering library | lib-engine​

The Engineering library contains the 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 availble packages in lib-engine here

geology library | lib-geo​

The geology library contains the packages that are used in the Engineering 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 availble packages in lib-engine here

Can't find Software?​

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