University of Cape Town
UCT High Performance Computing Facility

Thu Nov 21 08:30:02 SAST 2024
- Packages installed
- Basic architecture
- Scheduler configuration
- Interconnect
- Worker node architecture


Packages installed
Package Version Description Install
Abaqus 2024 Finite Element Analysis for Mechanical Engineering and Civil Engineering software/abaqus-2024
Ansys 2024R1 v241 Engineering simulation module load software/ansys-2024R1-v241
Ansys 2023R1 v231 Engineering simulation module load software/ansys-2023R1-v231
bamtools 2.5.2 Toolkit for handling BAM files module load software/bamtools-2.5.2
bbmap 39.08 Splice-aware global aligner for DNA and RNA sequencing reads module load software/bbmap-39.08
bcftools 1.20 Flexible generic format for storing nucleotide sequence alignment module load software/bcftools-1.20
bedtools 2.31.0 Genome arithmetic module load software/bedtools-2.31.0
bowtie2 2.5.4 Tool for aligning sequencing reads to long reference sequences module load software/bowtie2-2.5.4
bwa 0.7.18 Mapping DNA sequences against a large reference genome module load software/bwa-0.7.18
Cell Ranger 8.0.0 Pipeline for analysing single cell 3' RNA-seq data module load software/cellranger-8.0.0
DIA-NN 1.9.2 Proteomics data processing /opt/exp_soft/singularity-containers/diann
diamond 2.1.9 Sequence aligner for protein and translated DNA searches module load software/diamond-2.1.9
dorado 0.7.2 Basecaller for Oxford Nanopore reads module load software/dorad0-0.7.2
FastQC 0.12.1 Quality control application for high throughput sequence data module load software/FastQC-0.12.1
FreeBayes 1.3.6 Bayesian haplotype-based genetic polymorphism discovery and genotyping module load software/freebayes-1.3.6
FreeSurfer 7.4.1 Structural and Functional Neuroimaging data module load software/freesurfer-7.4.1
FreeSurfer 5.3.0 Structural and Functional Neuroimaging data module load software/freesurfer-5.3.0
FSL 6.0.7.12 Analysis tools for FMRI MRI and diffusion brain imaging data module load software/fsl-6.0.7.12
gcc 12.3.0 C C++ Fortran GNU compiler suite module load compilers/gcc-12.3.0
gcc 11.4.1 C C++ Fortran GNU compiler suite default
gcc 11.2.0 C C++ Fortran GNU compiler suite module load compilers/gcc-11.2.0
gffread 0.12.8 Format conversions filtering FASTA sequence extraction and more module load software/gffread-0.12.8
gmstar 6.2 InSAR processing system module load software/gmstar-6.2
gnuParallel 20240922 Shell tool for executing jobs in parallel - CONTACT HPC ADMINS BEFORE USING!!! module load software/gnu-parallel-20240922
gromacs 2024.2 Molecular dynamics module load software/gromacs-2024.2
hisat2 2.2.1 Graph-based alignment of next generation sequencing reads module load software/hisat2-2.2.1
iqtree2 2.3.4 Phylogenomic inference module load software/iqtree2-2.3.4
Java 21 Java language development kit module load java/jdk-21
Java 17 Java language development kit module load java/jdk-17
Java 11 Java language development kit default
jellyfish 2.3.1 Tool for fast memory-efficient counting of k-mers in DNA module load software/jellyfish-2.3.1
Julia 1.10.3 Julia compiler module load compilers/julia-1.10.3
kallisto 0.46.1 Quantifying abundances of transcripts from RNA-Seq data module load software/kallisto-0.46.1
Mathematica 14.0 Technical computing module load software/mathematica-14.0
MATLAB R2024b MATLAB base package and all toolboxes module load software/matlab-R2024b
MATLAB R2023a MATLAB base package and all toolboxes module load software/matlab-R2023a
MATLAB R2022b MATLAB base package and all toolboxes module load software/matlab-R2022b
MaxQuant 2.6.2.0 Quantitative proteomics software package module load software/MaxQuant-2.6.2.0 (and read instructions!)
miniconda-3 Python 3.12 Miniconda version of python module load python/miniconda3-py3.12
miniconda-3 Python 3.12 + user libraries Miniconda version of python module load python/miniconda3-py3.12-usr
mothur 1.48.1 Software to analyze community sequence data module load software/mothur-1.48.1
MUMmer 3.23 Rapid alignment of entire genomes module load mummer-3.2.3
ncbi-blast 2.15.0 Basic Local Alignment Search Tool all worker nodes
Nextflow 23.04.3 Data-driven computational pipeline module load software/nextflow-23.04.3
Octave 7.3.0 High-level language for numerical computations all worker nodes
OpenFoam 2306 CFD software /opt/exp_soft/singularity-containers/openfoam
OpenFoam 2106 CFD software /opt/exp_soft/singularity-containers/openfoam
openmpi 5.0.3 Open source Message Passing Interface implementation mpi/openmpi-5.0.3
picard 2.20.1 Java-based command-line utilities that manipulate SAM files java -jar /opt/exp_soft/picard-2.20.1/picard.jar
plink 2.0.0a Whole genome association analysis toolset module load software/plink-2.00a
qiime2 amplicon 2024.5 Microbiome analysis package module load python/qiime2-amplicon
qiime2 metagenome 2024.5 Microbiome analysis package module load python/qiime2-metagenome
qiime2 tiny 2024.5 Microbiome analysis package module load python/qiime2-tiny
quast 5.2.0 Genome assembly quality assessment tool module load software/quast-5.2.0
Python various See miniconda above
R 4.4.1 Statistical computing default
R 4.3.3 Statistical computing module load R/R-4.3.3
R 4.3.3 + user libraries Statistical computing module load R/R-4.3.3-usr
ROOT 6.30.06 Open source data analysis framework for high energy physics all worker nodes
RSEM 1.3.3 Accurate quantification of gene and isoform expression from RNA-Seq data module load software/RSEM-1.3.3
salmon 1.10.0 Transcript quantification from RNA-seq data module load software/salmon-1.10.0
samtools 1.20 Flexible generic format for storing nucleotide sequence alignment module load software/samtools-1.20
SKESA 2.4.0 Short read assembler module load software/skesa-2.4.0
snap 9.0 Earth Observation processing module load software/snap-9.0
snap 8.0 Earth Observation processing module load software/snap-8.0
SPAdes 4.0.0 St. Petersburg genome assembler module load software/SPAdes-4.0.0
sratoolkit 3.1.1 SRA data tools module load sratoolkit-3.1.1
STAR 2.7.11b Spliced Transcripts Alignment to a Reference module load software/STAR-2.7.11b
subread 2.0.6 Next-gen sequencing read data processing module load software/subread-2.0.6
trimal 1.5 Removal of spurious sequences or poorly aligned regions from a multiple sequence alignment module load software/trimal-1.5
TrimGalore 0.6.10 Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files module load software/TrimGalore-0.6.10
Trimmomatic 0.40-rc1 A flexible read trimming tool for Illumina NGS data module load software/Trimmomatic-0.40-rc1
Trinity 2.15.2 RNA-Seq de novo transcriptome assembly module load software/trinity-2.15.2
Trinotate 4.0.2 Transcriptome and protein data search module load software/Trinotate-4.0.2
vasp 6.4.3 Atomic scale materials modelling module load software/vasp.6.4.3
vasp 6.3.0-VTST Atomic scale materials modelling with VTST tools module load software/vasp.6.3.0-vtst
vcftools 0.16.1 Maps short reads to a reference genome module load software/vcftools-0.1.16



Architecture: x86_64
Operating System: Rocky Linux release 9.4 (Blue Onyx)
Kernel: Linux srvrochpc001 5.14.0-427.24.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Mon Jul 8 17:47:19 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux
Cluster scheduler: SLURM 23.11.5
Parallel libraries: OpenMPI, MPICH, PMI2, PMIx5



Scheduler: Multifactor Partition Priority

The scheduler does not preempt jobs. Job queueing priority is weighted heavily towards partition priority with a slight bias towards wait time:

PreemptType=preempt/none
PriorityType=priority/multifactor
PriorityDecayHalfLife=14-0
PriorityFavorSmall=NO
PriorityMaxAge=14-0
PriorityWeightAge=5000
PriorityWeightFairshare=1000
PriorityWeightJobSize=1000
PriorityWeightPartition=10000
PriorityWeightQOS=10
AccountingStorageEnforce=limits
SelectType=select/cons_res
SelectTypeParameters=CR_Core_Memory
MpiDefault=pmix (v5)



Network topology 
SwitchName=switch-0 Switches=switch-1,switch-2
SwitchName=switch-1 Nodes=srvrochpc[100-115,207,218-224],srvrocgpu[012-015] LinkSpeed=100
SwitchName=switch-2 Nodes=srvrocpod001 LinkSpeed=100



Worker Nodes
Server Partition Type CORES CPUs Cores per CPU CPU type Speed Cache FSB RAM Chips GRES
srvrochpc100.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc101.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc102.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc103.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc104.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc105.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc106.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc107.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc108.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc109.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc110.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc111.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc112.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc113.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc114.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc115.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 384GB 4800MHz
srvrochpc207.uct.ac.za ada Dell C6620 40 2 24 Xeon 6138 2000 MHz 20 MB 10 GT/s 384GB 2666MHz
srvrochpc218.uct.ac.za ada Dell C6620 40 2 24 Xeon 6138 2000 MHz 20 MB 10 GT/s 384GB 2666MHz
srvrochpc219.uct.ac.za ada Dell C6620 40 2 24 Xeon 6138 2000 MHz 20 MB 10 GT/s 384GB 2666MHz
srvrochpc220.uct.ac.za ada Dell C6620 40 2 24 Xeon 6138 2000 MHz 20 MB 10 GT/s 384GB 2666MHz
srvrochpc221.uct.ac.za ada Dell C6620 40 2 24 Xeon 6138 2000 MHz 20 MB 10 GT/s 384GB 2666MHz
srvrochpc222.uct.ac.za ada Dell C6620 40 2 24 Xeon 6138 2000 MHz 20 MB 10 GT/s 384GB 2666MHz
srvrochpc223.uct.ac.za ada Dell C6620 40 2 24 Xeon 6138 2000 MHz 20 MB 10 GT/s 384GB 2666MHz
srvrochpc224.uct.ac.za ada Dell C6620 40 2 24 Xeon 6138 2000 MHz 20 MB 10 GT/s 384GB 2666MHz
srvrocgpu012.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 512GB 4800MHz
srvrocgpu013.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 512GB 4800MHz
srvrocgpu014.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 512GB 4800MHz
srvrocgpu015.uct.ac.za ada Dell C6620 48 2 24 Xeon 6442 2600 MHz 60 MB 16 GT/s 512GB 4800MHz