Applications by availability

Applications available on

• Mahti — CSC supercomputer for massively parallel jobs
• Puhti — CSC supercomputer for small and medium jobs
• LUMI — EuroHPC supercomputer for CPU and especially GPU jobs

Interactive web applications available on

• Mahti web interface
• Puhti web interface
• LUMI web interface

Mahti

• Alphafold — Protein 3D structure prediction
• Amber — Molecular dynamics suite
• AMS — Modelling suite providing the ADF engine
• AMS-GUI — AMS integrated GUI
• ANSYS — ANSYS Academic engineering simulation software suite
• compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
• CP2K — DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
• cProfile — Built-in profiler for Python programs
• CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
• cuda-gdb — Nvidia extension of the GNU debugger GDB
• DDT — Parallel debugger
• Elmer — Open source multi-physics FEM package
• Gaussian — Versatile computational chemistry package
• GDAL — for geospatial data formats
• gdb — GNU debugger for compiled programs
• Geoconda — Python libraries for spatial analysis
• GPAW — Versatile DFT package
• GROMACS — Fast and versatile classical molecular dynamics
• HyperQueue — Scheduler for sub-node tasks
• IDL — Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
• JAX — Autograd and XLA, brought together for high-performance machine learning
• Julia Language — High-level, high-performance dynamic programming language for numerical computing
• LAMMPS — Fast molecular dynamics engine with large force field selection
• Maestro — Versatile drug discovery and materials modeling suite
• Molden — Processing program for molecular and electronic structure calculations
• MOLPRO — Package for accurate ab initio quantum chemistry calculations
• NAMD — Highly scalable classical molecular dynamics
• ncu — Nvidia CUDA kernel profiler
• Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
• nsys — Nvidia GPU and CPU profiler
• nvprof — Nvidia profiling tool that collects and views profiling data
• NWChem — A computational chemistry software package designed to perform well on parallel HPC systems
• Open Babel — Program to interconvert file formats currently used in molecular modeling
• OpenFOAM — Open source C++ tool box for continuum mechanics problems
• ORCA — General purpose quantum chemistry package
• PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
• ParaView — Free open-source visualization application
• PDAL — for point cloud translations and processing
• pdb — Built-in Python debugger
• perf — Command line tool for performance analysis
• PLUMED — Library and tools for enhanced sampling methods
• Python — The programming language and its modules at CSC
• PyTorch — Machine learning framework for Python
• Qiskit — open-source toolkit for useful quantum computing
• Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
• r-env — R and RStudio Server
• RAPIDS — Suite of libraries for data analytics and machine learning on GPUs
• Scalasca — Performance profiler for parallel programs
• Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
• TensorFlow — Deep learning library for Python
• TURBOMOLE — Efficient program package for electronic structure calculations
• VASP — Ab initio DFT electronic structures
• VisIt — Free open-source visualization application
• VMD — Molecular visualization program

Puhti

• ABAQUS — Dassault Systemes' SIMULIA academic research suite
• Alphafold — Protein 3D structure prediction
• Amber — Molecular dynamics suite
• AMS — Modelling suite providing the ADF engine
• AMS-GUI — AMS integrated GUI
• ANSYS — ANSYS Academic engineering simulation software suite
• ArcGIS Python API — Spatial analysis and data science
• BamTools — Tools for working with BAM formatted files
• BayeScan — Tool for identifying candidate loci under natural selection based on allele frequencies in populations
• BioPerl — Perl environment with bioperl extension
• Biopython — Python environment with biopython and other bioinformatics related Python libraries
• BLAST — Sequence similarity search tool for nucleotides and proteins
• Blender — 3D modeling, visualization and rendering software
• Bowtie2 — Short read aligner
• BRAKER — Automatic genome annotator for eucaryots
• BWA — Short read aligner
• CD-HIT — Sequence clustering and redundancy removal tool
• Chipster_genomes — Tool to download aligner indexes used by Chipster to Puhti
• CloudCompare — for visualizing, editing and processing point clouds
• compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
• COMSOL Multiphysics — General-purpose simulation software
• COSMO-RS — Toolbox for predictive property calculation of liquids
• CP2K — DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
• cProfile — Built-in profiler for Python programs
• CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
• CSD — Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools
• cuda-gdb — Nvidia extension of the GNU debugger GDB
• Cutadapt — Trimming high-throughput sequencing reads
• DDT — Parallel debugger
• Diamond — Sequence similarity search tool for proteins and nucleotides
• Elmer — Open source multi-physics FEM package
• EMBOSS — Toolkit for classical sequence analysis
• Entrez Direct — Entrez direct - command line tool to search and retrieve data from NCBI
• Exonerate — A generic tool for pairwise sequence comparison
• FastQC — Quality control tool for high throughput sequence data
• FORCE — for mass-processing of medium-resolution satellite images
• Freebayes — Genetic variant detector
• Gaussian — Versatile computational chemistry package
• GDAL — for geospatial data formats
• gdb — GNU debugger for compiled programs
• Geoconda — Python libraries for spatial analysis
• GOLD — Protein Ligand Docking Software
• GPAW — Versatile DFT package
• Grace — Plotting tool for xvg-files in particular
• GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• GROMACS — Fast and versatile classical molecular dynamics
• HMMER — Toolkit to create and use sequence profile hidden Markov models
• HUMAnN — Profiling microbial pathways with metagenomic data
• HyperQueue — Scheduler for sub-node tasks
• IDL — Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
• Illumina BaseSpace — Command line client for retrieving data from the Illumina BaseSpace environment
• Intel Trace Analyzer and Collector (ITAC) — MPI profiling and tracing tool
• Intel VTune Profiler — Performance analysis tool for single core and threading performance
• InterProScan — Protein signature/motif search tool
• iPyrad — toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS)
• JAX — Autograd and XLA, brought together for high-performance machine learning
• Julia Language — High-level, high-performance dynamic programming language for numerical computing
• Kraken — Taxonomic sequence classification system
• Krona visualization tool — Visualization tool for taxonomic classification and other hierarchical data
• LAMMPS — Fast molecular dynamics engine with large force field selection
• LAStools — for LiDAR datasets
• Lazypipe — A stand-alone pipeline for identifying viruses in host-associated or environmental samples
• MACS2/3 — ChIP-Seq analysis tool
• Maestro — Versatile drug discovery and materials modeling suite
• MATLAB — High-level technical computing language
• Megahit — Metagenomics assembly
• MetaPhlAn — Profiling the composition of microbial communities with metagenomic data
• Minimap2 — Short read aligner
• MIRA — Whole genome shotgun and EST sequence Assembler
• Molden — Processing program for molecular and electronic structure calculations
• MOLPRO — Package for accurate ab initio quantum chemistry calculations
• Mothur — Package for microbial community analysis of amplicon sequencing data
• MrBayes — Program for inferring phylogenies using Bayesian methods
• NAMD — Highly scalable classical molecular dynamics
• NASA Ames Stereo Pipeline (ASP) — for processing stereo images
• ncu — Nvidia CUDA kernel profiler
• Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
• nsys — Nvidia GPU and CPU profiler
• nvprof — Nvidia profiling tool that collects and views profiling data
• NWChem — A computational chemistry software package designed to perform well on parallel HPC systems
• Octave — High-level interpreted language for numerical computations
• Open Babel — Program to interconvert file formats currently used in molecular modeling
• OpenDroneMap (ODM) — for processing aerial drone imagery
• OpenFOAM — Open source C++ tool box for continuum mechanics problems
• ORCA — General purpose quantum chemistry package
• Orfeo ToolBox (Open Source processing of remote sensing images) — for remote sensing applications
• PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
• PANNZER2/SANSPANZ — Automatic protein annotation tool
• ParaView — Free open-source visualization application
• PCL — for 2D/3D image and point cloud processing
• PDAL — for point cloud translations and processing
• pdb — Built-in Python debugger
• perf — Command line tool for performance analysis
• Picard Tools — Tools for working with SAM,BAM,CRAM and VCF files
• PLUMED — Library and tools for enhanced sampling methods
• Prokka — Rapid prokaryotic genome annotation
• Python — The programming language and its modules at CSC
• Python Data — Collection of Python libraries for data analytics and machine learning
• PyTorch — Machine learning framework for Python
• QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• QIIME — Package for microbial community analysis of amplicon sequencing data
• Qiskit — open-source toolkit for useful quantum computing
• Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
• R for GIS — R spatial analysis libraries
• r-env — R and RStudio Server
• RAPIDS — Suite of libraries for data analytics and machine learning on GPUs
• RAxML — Program for inferring phylogenies with likelihood
• Roary — Pan genome pipeline
• RStudio IDE — Integrated development environment for R
• SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• SageMath — Free open-source mathematics software system
• SALMON — Program to produce transcript-level quantification estimates from RNA-seq data
• SAMtools — Utilities for managing SAM/BAM formatted alignment files
• Scalasca — Performance profiler for parallel programs
• Seismic Unix — for processing of 2D seismic or GPR data sets.
• Sen2Cor — for atmospheric-, terrain and cirrus correction of the Sentinel-2 products
• Sen2mosaic — for download, preprocessing and mosaicing of Sentinel-2 products
• Seqtk — Tool for processing sequences in the FASTA or FASTQ format
• Snakemake — Snakemake is a scientific workflow management system for creating scalable, portable, and reproducible workflows
• SNAP — for remote sensing applications
• SOFI3D — for 3D finite-difference seismic wave simulation
• SPAdes — Genome assembly
• Stacks — Pipeline for building loci from short-read sequences (e.g. RAD-seq data)
• STAR — Short read aligner
• Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
• Structure — Inference of population structure in genetics
• TensorFlow — Deep learning library for Python
• TmoleX — GUI for setting up and analyzing TURBOMOLE jobs
• TopHat — Splice junction mapper for RNA-Seq reads
• Trimmomatic — Trim Illumina paired-end and single-read data
• Trinity — Transcriptome assembly tool
• TURBOMOLE — Efficient program package for electronic structure calculations
• VASP — Ab initio DFT electronic structures
• Velvet — Genome assembler
• VirusDetect — Virus identification with sRNA data
• VisIt — Free open-source visualization application
• VMD — Molecular visualization program
• Whisper — General-purpose speech recognition model
• WhiteboxTools — an advanced geospatial data analysis platform
• wtdbg2 — Fast assembler for long-read data
• XHMM (eXome-Hidden Markov Model) — Copy number variation calling from targeted sequencing data
• Zonation — Spatial conservation prioritization framework

LUMI

• Accelerated visualization — A selection of GPU accelerated visualization applications
• Amber — Molecular dynamics suite
• ANSYS — ANSYS Academic engineering simulation software suite
• Blender — 3D modeling, visualization and rendering software
• Cirq-on-iqm — open-source cirq adapter for quantum computing
• CP2K — DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
• Desktop — Remote desktop environment
• Elmer — Open source multi-physics FEM package
• GDAL — for geospatial data formats
• Geoconda — Python libraries for spatial analysis
• GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• GROMACS — Fast and versatile classical molecular dynamics
• HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
• HyperQueue — Scheduler for sub-node tasks
• JAX — Autograd and XLA, brought together for high-performance machine learning
• Julia Language — High-level, high-performance dynamic programming language for numerical computing
• Julia-Jupyter — Interactive computational environment for Julia
• Jupyter — Interactive computational environment for Python
• LAMMPS — Fast molecular dynamics engine with large force field selection
• MATLAB — High-level technical computing language
• NAMD — Highly scalable classical molecular dynamics
• Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
• NMRLipids — NMRLipids databank containing MD simulations
• OpenFOAM — Open source C++ tool box for continuum mechanics problems
• PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows
• ParaView — Free open-source visualization application
• PDAL — for point cloud translations and processing
• Pennylane — Free open-source software framework for quantum machine learning and quantum computing
• perf — Command line tool for performance analysis
• PLUMED — Library and tools for enhanced sampling methods
• PyTorch — Machine learning framework for Python
• QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• Qiskit — open-source toolkit for useful quantum computing
• Qiskit-on-iqm — open-source qiskit adapter for quantum computing
• Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
• SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software
• TensorBoard — The visualization toolkit for TensorFlow
• TensorFlow — Deep learning library for Python
• VisIt — Free open-source visualization application
• Visual Studio Code — Source code editor

Mahti web interface

• CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
• Desktop — Remote desktop environment
• Julia-Jupyter — Interactive computational environment for Julia
• Jupyter — Interactive computational environment for Python
• Jupyter for courses — A version of the Jupyter app for course environments
• Maestro — Versatile drug discovery and materials modeling suite
• TensorBoard — The visualization toolkit for TensorFlow
• Visual Studio Code — Source code editor
• VMD — Molecular visualization program

Puhti web interface

• Accelerated visualization — A selection of GPU accelerated visualization applications
• Blender — 3D modeling, visualization and rendering software
• CloudCompare — for visualizing, editing and processing point clouds
• COMSOL Multiphysics — General-purpose simulation software
• CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
• Desktop — Remote desktop environment
• Grace — Plotting tool for xvg-files in particular
• GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• Julia-Jupyter — Interactive computational environment for Julia
• Jupyter — Interactive computational environment for Python
• Jupyter for courses — A version of the Jupyter app for course environments
• Maestro — Versatile drug discovery and materials modeling suite
• MATLAB — High-level technical computing language
• ParaView — Free open-source visualization application
• QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• RStudio IDE — Integrated development environment for R
• SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• SNAP — for remote sensing applications
• TensorBoard — The visualization toolkit for TensorFlow
• VisIt — Free open-source visualization application
• Visual Studio Code — Source code editor
• VMD — Molecular visualization program
• Zonation — Spatial conservation prioritization framework

LUMI web interface

• Accelerated visualization — A selection of GPU accelerated visualization applications
• Blender — 3D modeling, visualization and rendering software
• Desktop — Remote desktop environment
• GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• Julia-Jupyter — Interactive computational environment for Julia
• Jupyter — Interactive computational environment for Python
• MATLAB — High-level technical computing language
• ParaView — Free open-source visualization application
• QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
• TensorBoard — The visualization toolkit for TensorFlow
• VisIt — Free open-source visualization application
• Visual Studio Code — Source code editor

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