========== Software ========== Most software on Hoffman2 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 Some applications are available via python or Anaconda and will not be visible until a python or anaconda 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 `. .. _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:`Statistics` * - :ref:`Integrated development environments` - :ref:`Programming libraries` - :ref:`Visualization and rendering` * - :ref:`Miscellaneous` - - .. 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 15 :class: tight-table * - :ref:`GNU Compiler Collection (gcc)` - :ref:`Intel C/C++ & Fortran compilers` - :ref:`NAG Fortran compiler` - :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-NAG-compiler.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 ===================== .. _lang: .. List-table:: :widths: 15 15 15 15 15 15 :class: tight-table * - :ref:`C/C++` - :ref:`D/GDC` - :ref:`Fortran` - :ref:`Java` - :ref:`Julia` - :ref:`mono` * - :ref:`perl` - :ref:`POP-C++` - :ref:`Python` - :ref:`R` - :ref:`Ruby` - :ref:`tcl` .. include:: Language/Language-c.inc .. include:: Language/Language-gdc.inc .. include:: Language/Language-fortran.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-anaconda.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 Integrated development environments =================================== .. _ide: .. List-table:: :widths: 15 15 15 15 :class: tight-table * - :ref:`Eclipse` - :ref:`NetBeans` - :ref:`Rstudio` - :ref:`Spyder` .. include:: IDE/IDE-eclipse.inc .. include:: IDE/IDE-netbeans.inc .. include:: IDE/IDE-spyder.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 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:`GrADS` - :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-grads.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 15 15 :class: tight-table * - :ref:`CERN ROOT` - :ref:`cURL` - :ref:`Geant` - :ref:`Lynx` - :ref:`MIGRATE-N` * - :ref:`SVN subversion` - :ref:`TeXLive` - :ref:`tmux` - - .. include:: Miscellaneous/Miscellaneous-cernroot.inc .. include:: Miscellaneous/Miscellaneous-curl.inc .. include:: Miscellaneous/Miscellaneous-geant.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