| Packages installed | |||
| Package | Version | Description | Install |
| Ansys | 2024R1 v241 | Engineering simulation | module load software/ansys-2024R1-v241 |
| 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 | 1.9.1 | Proteomics data processing | module load software/diann-1.9.1 |
| 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 |
| 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 |
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],srvrocgpu[012-014] 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 | ||||||
| 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 | ||||||