========== Software ========== Most software on the Hoffman2 Cluster is available via :ref:`environmental modules `. A list of applications available via modules can be generated entering at the :ref:`terminal prompt ` via the command: .. code-block:: bash $ all_apps_via_modules or the module for a particular application can be searched via: .. code-block:: bash $ modules_lookup -m Some applications are available via :ref:`python ` or :ref:`mamba ` and will not be visible until a python or mamba modules are loaded. To request or suggest software installation or updates, please submit via our `helpdesk `__. Only software/applications that is :ref:`required by multiple groups ` may be centrally installed or you and your group will receive given guidance on how to perform software installation in your :ref:`$HOME ` or, if applicable, in your :ref:`group project directory `. Available software on the Hoffman2 Cluster organized by category is discussed below, for faster navigation use the menu (which, depending on your device, might be located in the sidebar or accessible via the collapsed menu icon: ≡): .. _software-by-category: .. list-table:: Software/Applications categories :widths: 5 5 5 :header-rows: 1 :class: tight-table * - Productivity - Development - Discipline * - :ref:`Hoffman2 Cluster tools` - :ref:`Compilers` - :ref:`Bioinformatics and biostatistics` * - :ref:`Environmental modules` - :ref:`Debuggers ` - :ref:`Chemistry and chemical engineering` * - :ref:`Containers` - :ref:`Build tools ` - :ref:`Engineering and mathematics` * - :ref:`Editors` - :ref:`Programming languages` - :ref:`Physics` * - :ref:`Programming libraries` - :ref:`Statistics` - :ref:`Visualization and rendering` * - :ref:`Miscellaneous` - :ref:`Jupyter Notebooks/Lab ` - .. toctree:: :maxdepth: 2 Hoffman2 Cluster tools ====================== A collection of commands designed to show the status of specific user attributes on the cluster. The commands are designed to be issued from a :ref:`terminal ` connected to the Hoffman2 Cluster. .. _H2-inhouse: .. list-table:: :widths: 15 15 15 15 * - :ref:`check_usage` - :ref:`myresources` - :ref:`myjobs` - :ref:`myquota` * - :ref:`passwd` - :ref:`set_qrsh_env` - :ref:`shownews` - :ref:`webshare` .. include:: H2/H2-check_usage.inc .. include:: H2/H2-myresources.inc .. include:: H2/H2-myjobs.inc .. include:: H2/H2-myquota.inc .. include:: H2/H2-passwd.inc .. include:: H2/H2-set_qrsh_env.inc .. include:: H2/H2-shownews.inc .. include:: H2/H2-webshare.inc Environmental modules ===================== .. include:: Environmental/Environmental-modules.inc Containers ========== .. include:: Containers/Containers-apptainer.inc Editors ======= .. _edit: .. list-table:: :widths: 15 15 15 15 * - :ref:`Emacs` - :ref:`Gedit` - :ref:`Nano` - :ref:`Vi/Vim/Evim` .. include:: Editors/Editors-emacs.inc .. include:: Editors/Editors-gedit.inc .. include:: Editors/Editors-nano.inc .. include:: Editors/Editors-vi-vim-evim.inc Compilers ========= .. _comp: .. List-table:: :widths: 15 15 15 15 :class: tight-table * - :ref:`GNU Compiler Collection (gcc)` - :ref:`Intel C/C++ & Fortran compilers` - :ref:`NVIDIA HPC SDK (PGI C/C++ compiler)` - :ref:`Nvidia CUDA` .. include:: Compilers/Compilers-GNU-compiler-collection.inc .. include:: Compilers/Compilers-Intel-compilers.inc .. include:: Compilers/Compilers-PGI-compiler.inc .. include:: Compilers/Compilers-CUDA.inc Debuggers and profilers ======================= .. _debug: .. List-table:: :widths: 15 15 15 15 15 :class: tight-table * - :ref:`GNU Debugger` - :ref:`DDD` - :ref:`Intel Advisor` - :ref:`Intel VTune Profiler` - :ref:`Valgrind Tools` .. include:: Debuggers/Debuggers-GNU-debugger.inc .. include:: Debuggers/Debuggers-DDD.inc .. include:: Debuggers/Debuggers-Intel-Advisor.inc .. include:: Debuggers/Debuggers-Intel-VTune-Profiler.inc .. include:: Debuggers/Debuggers-Valgrind.inc Build automation tools ====================== .. _build: .. List-table:: :widths: 15 15 :class: tight-table * - :ref:`GNU Make` - :ref:`CMake` .. include:: Build/Build-GNU-make.inc .. include:: Build/Build-Cmake.inc Programming languages ===================== For C/C++ or FORTRAN see :ref:`Compilers`. .. _lang: .. List-table:: :widths: 15 15 15 15 15 :class: tight-table * - :ref:`D/GDC` - :ref:`Java` - :ref:`Julia` - :ref:`mono` - :ref:`perl` * - :ref:`POP-C++` - :ref:`Python` - :ref:`R` - :ref:`Ruby` - :ref:`tcl` .. include:: Language/Language-gdc.inc .. include:: Language/Language-java.inc .. include:: Language/Language-julia.inc .. include:: Language/Language-mono.inc .. include:: Language/Language-perl.inc .. include:: Language/Language-activeperl.inc .. include:: Language/Language-popc++.inc .. include:: Language/Language-python.inc .. include:: Language/Language-mamba.inc .. include:: Language/Language-ruby.inc .. include:: Language/Language-tcl.inc Programming libraries ===================== .. _libs: .. List-table:: :widths: 15 15 15 15 15 15 :class: tight-table * - :ref:`ARPACK` - :ref:`ATLAS` - :ref:`BLAS` - :ref:`BOOST C++` - :ref:`CUDNN` - :ref:`FFTW` * - :ref:`GNU GSL` - :ref:`HDF` - :ref:`LAPACK` - :ref:`Intel MKL` - :ref:`NetCDF` - :ref:`PETSc` * - :ref:`ScaLAPACK` - :ref:`Trilinos` - :ref:`zlib` - - - .. include:: Libraries/Libraries-arpack.inc .. include:: Libraries/Libraries-atlas.inc .. include:: Libraries/Libraries-blas.inc .. include:: Libraries/Libraries-boostc++.inc .. include:: Libraries/Libraries-cudnn.inc .. include:: Libraries/Libraries-fftw.inc .. include:: Libraries/Libraries-gnugsl.inc .. include:: Libraries/Libraries-hdf.inc .. include:: Libraries/Libraries-lapack.inc .. include:: Libraries/Libraries-intelmkl.inc .. include:: Libraries/Libraries-netcdf.inc .. include:: Libraries/Libraries-petsc.inc .. include:: Libraries/Libraries-scalapack.inc .. include:: Libraries/Libraries-trilinos.inc .. include:: Libraries/Libraries-zlib.inc Bioinformatics and biostatistics ================================ .. _biostat: .. list-table:: :widths: 15 15 15 15 15 15 :class: tight-table * - :ref:`Affymetrix-APT ` - :ref:`Annovar` - :ref:`BAMTools` - :ref:`BEDtools` - :ref:`Bowtie` - :ref:`BWA` * - :ref: `Cellranger` - :ref:`Cufflinks` - :ref:`Galaxy` - :ref:`GATK` - :ref:`IMPUTE2` - :ref:`InsPecT` * - :ref:`MAQ` - :ref:`Picard tools` - :ref:`PLINK` - :ref:`SAMtools` - :ref:`SOLAR` - :ref:`TopHat` * - :ref:`Treemix` - :ref:`VEGAS` - - - - .. include:: Bioinformatics/Bioinformatics-affymetrics.inc .. include:: Bioinformatics/Bioinformatics-annovar.inc .. include:: Bioinformatics/Bioinformatics-bamtools.inc .. include:: Bioinformatics/Bioinformatics-bedtools.inc .. include:: Bioinformatics/Bioinformatics-bowtie.inc .. include:: Bioinformatics/Bioinformatics-bwa.inc .. include:: Bioinformatics/Bioinformatics-cellranger.inc .. include:: Bioinformatics/Bioinformatics-cufflinks.inc .. include:: Bioinformatics/Bioinformatics-galaxy.inc .. include:: Bioinformatics/Bioinformatics-gatk.inc .. include:: Bioinformatics/Bioinformatics-impute2.inc .. include:: Bioinformatics/Bioinformatics-inspect.inc .. include:: Bioinformatics/Bioinformatics-maq.inc .. include:: Bioinformatics/Bioinformatics-picardtools.inc .. include:: Bioinformatics/Bioinformatics-plink.inc .. include:: Bioinformatics/Bioinformatics-samtools.inc .. include:: Bioinformatics/Bioinformatics-solar.inc .. include:: Bioinformatics/Bioinformatics-tophat.inc .. include:: Bioinformatics/Bioinformatics-treemix.inc .. include:: Bioinformatics/Bioinformatics-vegas.inc Chemistry and chemical engineering ================================== .. _chem: .. list-table:: :widths: 15 15 15 15 :class: tight-table * - :ref:`Amber` - :ref:`CP2K` - :ref:`CPMD` - :ref:`Gaussian` * - :ref:`GaussView` - :ref:`GROMACS` - :ref:`Jmol` - :ref:`LAMMPS` * - :ref:`Molden` - :ref:`MOPAC` - :ref:`NAMD` - :ref:`NWChem` * - :ref:`Open Babel` - :ref:`Q-Chem` - :ref:`Quantum ESPRESSO` - :ref:`RosettaMatch` * - :ref:`VMD` - - - .. include:: Chemistry/Chemistry-amber.inc .. include:: Chemistry/Chemistry-cp2k.inc .. include:: Chemistry/Chemistry-cpmd.inc .. include:: Chemistry/Chemistry-gaussian.inc .. include:: Chemistry/Chemistry-gaussview.inc .. include:: Chemistry/Chemistry-gromacs.inc .. include:: Chemistry/Chemistry-jmol.inc .. include:: Chemistry/Chemistry-lammps.inc .. include:: Chemistry/Chemistry-molden.inc .. include:: Chemistry/Chemistry-mopac.inc .. include:: Chemistry/Chemistry-namd.inc .. include:: Chemistry/Chemistry-nwchem.inc .. include:: Chemistry/Chemistry-openbabel.inc .. include:: Chemistry/Chemistry-qchem.inc .. include:: Chemistry/Chemistry-quantum-expresso.inc .. include:: Chemistry/Chemistry-rosetta-match.inc .. include:: Chemistry/Chemistry-vmd.inc Engineering and mathematics =========================== .. _engin: .. List-table:: :widths: 15 15 15 15 15 15 15 :class: tight-table * - :ref:`ABAQUS` - :ref:`Ansys` - :ref:`COMSOL` - :ref:`Maple` - :ref:`MATLAB` - :ref:`Mathematica` - :ref:`NCO` * - :ref:`Octave` - :ref:`Opensees` - - - - - .. include:: Engineering/Engineering-abaqus.inc .. include:: Engineering/Engineering-ansys.inc .. include:: Engineering/Engineering-comsol.inc .. include:: Engineering/Engineering-maple.inc .. include:: Engineering/Engineering-mathematica.inc .. include:: Engineering/Engineering-matlab.inc .. include:: Engineering/Engineering-nco.inc .. include:: Engineering/Engineering-octave.inc .. include:: Engineering/Engineering-opensees.inc Physics ======= .. _phys: .. List-table:: :widths: 15 15 :class: tight-table * - :ref:`CERN ROOT` - :ref:`Geant4` .. include:: Physics/Physics-cernroot.inc .. include:: Physics/Physics-geant4.inc Statistics ========== .. _stat: .. List-table:: :widths: 15 15 15 :class: tight-table * - :ref:`R` - :ref:`Rstudio` - :ref:`Stata` .. include:: Statistics/Statistics-r.inc .. include:: Statistics/Statistics-rstudio.inc .. include:: Statistics/Statistics-stata.inc Visualization and rendering =========================== .. _vis: .. List-table:: :widths: 15 15 15 15 15 15 :class: tight-table * - :ref:`GnuPlot` - :ref:`GRACE` - :ref:`Graphviz` - :ref:`IDL` - :ref:`ImageMagick` - :ref:`Maya` * - :ref:`NCAR` - :ref:`OpenDx` - :ref:`ParaView` - :ref:`POV-Ray` - :ref:`VTK` - .. include:: Visualization/Visualization-gnuplot.inc .. include:: Visualization/Visualization-grace.inc .. include:: Visualization/Visualization-graphviz.inc .. include:: Visualization/Visualization-idl.inc .. include:: Visualization/Visualization-imagemagick.inc .. include:: Visualization/Visualization-maya.inc .. include:: Visualization/Visualization-ncar.inc .. include:: Visualization/Visualization-opendx.inc .. include:: Visualization/Visualization-paraview.inc .. include:: Visualization/Visualization-povray.inc .. include:: Visualization/Visualization-vtk.inc Miscellaneous ============= .. List-table:: :widths: 15 15 15 :class: tight-table * - :ref:`cURL` - :ref:`Lynx` - :ref:`MIGRATE-N` * - :ref:`SVN subversion` - :ref:`TeXLive` - :ref:`tmux` .. include:: Miscellaneous/Miscellaneous-curl.inc .. include:: Miscellaneous/Miscellaneous-lynx.inc .. include:: Miscellaneous/Miscellaneous-migraten.inc .. include:: Miscellaneous/Miscellaneous-svnsubversion.inc .. include:: Miscellaneous/Miscellaneous-texlive.inc .. include:: Miscellaneous/Miscellaneous-tmux.inc