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HPC @ QMUL

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HPC @ QMUL

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Introduction
Introduction
HPC compute nodes
HPC compute nodes
- Overview
- DDG nodes
- DDY nodes
- EHC nodes
- RDG nodes
- SBG nodes
- SDX nodes
- SMF nodes
- SRM nodes
- VHM nodes
- XDG nodes
- XHG nodes
- XLG nodes
- Andrena cluster
Using the cluster
Using the cluster
- Citing Apocrita in publications
- Moving from Grid Engine to Slurm
- Slurm Quick Reference
- Submitting jobs
  Submitting jobs
- Using arrays
- Monitoring jobs
- Debugging jobs
- Using modules
- Using GPUs
- Compiling C, C++ and Fortran Code
- Choosing a Python distribution
- Tuning job requests
- Job statistics
- Man pages
Storage
Storage
- Storage systems
- Quotas
- Scratch
- Archive
- Using $TMPDIR
- Moving data
- Deleting files
- Backups and snapshots
- Public datasets
- Globus
  Globus
Application documentation
Application documentation
- Overview
- Application list
- Apptainer containers
  Apptainer containers
- Languages
  Languages
  - Miniforge
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- General applications
  General applications
  - Dua
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  - Metis
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  - Pigz
  - SQLite
  - Zstd
- Bioinformatics applications
  Bioinformatics applications
  - ABySS
  - ANGSD
  - ANNOVAR
  - BamTools
  - BamUtil
  - BCFtools
  - Bcl2fastq
  - BEDOPS
  - Bedtools
  - BGEN
  - Bismark
  - BLAST+
  - Bowtie
  - Bowtie2
  - BUCKy
  - BUSCO
  - BWA
  - Canu
  - Cell Ranger
  - Cufflinks
  - DIAMOND
  - Ensembl-VEP
  - Entrez
  - FastME
  - Fastqc
  - FreeBayes
  - GATK
  - Genometools
  - Jellyfish
  - Kraken2
  - MAFFT
  - MAKER
  - MaSuRCA
  - MCL
  - Minimap2
  - MIRA
  - Muscle
  - Nextflow
  - PGAP
  - Plink
  - PRANK
  - Qctool
  - Qualimap
  - QUAST
  - RAxML
  - RAxML Next Generation
  - RELION
  - RepeatMasker
  - RepeatModeler
  - RSEM
  - Salmon
  - SAMtools
  - Seqtk
  - SHAPEIT5
  - Space Ranger
  - SPAdes
  - SRA Tools
  - Stacks
  - STAR
  - Subread
  - TransDecoder
  - Trim Galore
  - Trimmomatic
  - VCFtools
  - Wtdbg2
- Chemistry applications
  Chemistry applications
  - VASP
- Engineering applications
  Engineering applications
  - Abaqus
  - Ansys
  - COMSOL
  - CST Studio
  - OpenFOAM
  - STAR-CCM+
  - CST Studio
- Machine learning
  Machine learning
  - PyTorch
  - TensorFlow
- Mathematical applications
  Mathematical applications
  - Matlab
OnDemand
OnDemand
- Overview
- COLMAP
- CST Studio
- IGV
- Jupyter
- MeshLab
- ParaView
- RStudio
- STAR-CCM+
- Stata
- TensorBoard
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Tier 2 HPC
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Cheatsheets
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