Multiple softwares and tools analysis which can complete your work environment are available on HPCaVe platform. A standard Linux distribution is installed on scratchalpha and scratchbeta, along with standard tools used for development which are available by default.
The other available packages (compilers, parallel libraries…), described on tables below need to be loaded before using them.
However here are some useful commands you need to know before :
- List all available modules
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module avail |
- Load a module
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module load modules_names |
Example:
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module load intel/intel-mpi/4.1.0.024 intel/intel-compilers-18.0/18.0 |
- List loaded modules
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module list |
Example:
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module list |
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1 2 3 4 |
Currently Loaded Module files: 1) mpt/2.16 4) intel/intel-fc-18.0/18.0 2) intel/intel-mpi/4.1.0.024 5) intel/intel-compilers-18.0/18.0 3) intel/intel-cc-18.0/18.0 |
- Unload a module from your environment
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module unload module_name |
- Unload all modules from your environment
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module purge |
- Print the content of a module
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module display module_name |
Example:
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module display module_name |
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1 2 3 |
------------------------------- /opt/dev/Modules/Compilers -------------------------------- cmake/3.9 intel/intel-compilers-17.2/17.2 intel/intel-cc-13/13.0.1.117 intel/intel-compilers-18.0/18.0 |
Softwares Tables
| COMPILERS | |||
| NAME | VERSION | DISTRIBUTION | USAGE |
| Intel FC Compiler 2017 | 2017 Release 2 | Module | Fortran Compiler |
| Intel CC Compiler 2017 | 2017 Release 2 | Module | C C++Compiler |
| Intel MPI Compiler 2017 | 2017 Release 2 | Module | mpi Compiler |
| Intel CC Compiler 2018 | 2018 Base release | Module | Fortran Compiler |
| Intel FC Compiler 2018 | 2018 Base release | Module | C C++Compiler |
| Intel MPI Compiler 2018 | 2018 Base release | Module | mpi Compiler |
| Intel FC Compiler 2013 | 2013 Update 5 | Module | Fortran Compiler |
| Intel CC Compiler 2013 | 2013 Update 5 | Module | C C++Compiler |
| Intel MPI Compiler 2013 | 2013 Update 5 | Module | mpi Compiler |
| SGI MPT Performance Suite | 2.16 (Lastest. Default) | Module | mpi Compiler |
| Open MPI Compiler | 1.10.3 | OS | mpi Compiler |
| Open MPI Compiler | 3.0.0 | Module | mpi Compiler |
| LLVM | 3.8.0 | OS | clang llvm compiler |
| JavaC | 1.8.0 | OS | Java Compiler |
| GCC | 4.8.5 | OS | GNU Compiler |
| GCC 6 | 6.2 | OS | GNU Compiler 6.2 Toolchain |
| Cmake | 3.5.2 | OS | GNU compiler Make Cmake |
| CMake | 3.9 | Module | GNU compilateur Make Cmake |
| Bison | 2.7.6 | OS | yacc Compiler |
| GHC | 4.8.2 | OS | Glasgow Haskell Compiler |
| scons | 2.3.0 | OS | Alternative to make |
| LIBRAIRIES | |||
| NAME | VERSION | DITRIBUTION | USAGE |
| Boost | 1.61 | OS | optimization library |
| Boost | 1.65 | Module | optimization library |
| Blas | 3.5 | OS | scientist library |
| Blas | 3.5.3 | Module | scientist library |
| Cairo | 1.15.2 | OS | vectorial images library |
| Cblas | 20110120-7.8 | OS | scientist library |
| cfitsio | 3.41 | OS | flexible tranport image system library |
| cgal | 4.7 | OS | geometric computation library |
| dune | 2.4 | OS | hardware library CPU features |
| elpa | 2016.05 | OS | scientist library |
| eigen | 3.2.2 | OS | eigen solver library |
| fftw2 | 2.1 | OS | scientist library |
| fftw3 | 3.3.5 | OS / Module with petsc | scientist library |
| geos | 3.6.1 | OS | Open Source geometry engine library |
| gsl | 2.4 | OS and Module | scientist library |
| hdf | 4.2.11 | OS | scientist library |
| hdf5 | 1.1 | OS and Module with petsc | scientist library |
| hdf5 | Conda env | scientist library | |
| lapack | 3.5.0 | OS | scientist library |
| lapacke | 3.5 | OS | scientist library |
| HYPRE | 2.8.0b | OS | scientist library |
| exiv2 | 0.23 | OS | photo metadata editor |
| libjpeg | 62.1.0 | OS | graphic jpeg library |
| liblzma | 5.0.5 | OS | lzma library |
| libpng | 1.6.8 | OS | graphic png library |
| libtiff | 4.0.8 | OS | graphic tIFF library |
| libxslt | 1.1.28 | OS | xml library |
| libxml2 | 2.9.4 | OS | xml library |
| metis | 5.1.0 | OS and Module via petsc | scientist library |
| mpc | 1.03 | OS | arithmetic complex number |
| mpfr | 3.1.2 | OS | multiple precision computing library |
| mumps | 4.9.2 | OS | scientist library |
| mumps | 5.1.1 | Module via petsc | scientist library |
| mvapich2 | 2.2.12 | OS | Network based computing library |
| netcdf4 | 4.4.1 | OS and module via petsc | scientist library |
| openMPI | 1.1 | OS Default | message passing interface |
| OpenMPI | 3.0.0 | Module | message passing interface |
| openblas | 0.2.20 | OS | scientist library |
| pARMS | 3.2 | OS and Module via petsc | scientist library |
| plumed | 4.2 | Module | free energy calculation library |
| pnetcdf | 1.7.0 | OS | scientist library |
| pastix | 5.2.2 | OS and Module via petsc | scientist library |
| pcre | 8.39 | OS | perl compatible regular expression lib |
| pcre2 | 10.30.26 | OS | perl compatible regular expression lib |
| petsc | 3.4.3 | OS | scientist library |
| petsc | 3.8 | Module | scientist library |
| scalapack | 2.0.2 | OS and Module via petsc | scientist library |
| scotch | 6.0.4 | OS | scientist library |
| slepc | 3.4.3 | OS | scientist library |
| slepc | 3.8.2 | Module | scientist library |
| superlu | 5.2 | OS and Module via petsc | scientist library |
| tetgen | 1.5 | OS and Module via petsc | scientist library |
| triangle | 1.6.1 | OS and Module via petsc | scientist library |
| trlan | 201009 | OS | scientist library |
| udunits | 2.2.25 | OS | arithmetic complex number manipulation |
| udunits2 | 2.2.25 | OS | arithmetic complex number manipulation |
| FRAMEWORKS | |||
| NAME | VERSION | DITRIBUTION | USAGE |
| CP2K | 5.1.2 | Module | quantum chemistry and solid state physics software |
| FDS | 6 | Module | Fire dynamics simulator |
| GMP | 6.1.2 | OS | Linux multiplrécision Tools |
| GMP ECM | 7.0.4 | OS | Elliptic Curve Method for Integer Factorization |
| Global Array | 6.4.3 | Module | Partitioned Global Address Space (PGAS) programming model |
| Gromacs | 2016..3-2.1 | OS | GROningen MAchine for Chemical Simulations |
| Gromacs | 5.1.4 with Cuda support | Module | GROningen MAchine for Chemical Simulations |
| Gtk2 | 2.24.31 | OS | Graphical User Interface developpement |
| Gtk3 | 3.20.10 | OS | Graphical User Interface developpement |
| Harfbuzz | 1.4.5 | OS | Rendu polices vectorielles |
| harfbuzz | Conda | Rendu polices vectorielles | |
| Jags | 4.4 | OS | Gibbs Sampler |
| Jags | 4.3 | Module | Gibbs Sampler |
| Java OpenJDK | 1.8 | OS | Java Toolkit |
| Java OpenJDK | 1.7 | OS | Java Toolkit |
| LAMPPS | 20130412 | OS | Molecular Dynamic Simulation |
| LAMPPS | 2017 | Module | Molecular Dynamic Simulation |
| NAMD | 2012 & 2017 | Module | parallel molecular dynamics code |
| NCBI Blast | 6.1 | OS | The Basic Local Alignment Search Too |
| OpenFOAM | 4.1 | Module | Solver and Physical Models |
| OpenBugs | 2.3 | Module | Bayesian Inference Gibbs Sampler |
| Orca | 3.20.3 | OS | modern electronic structure program package |
| Paraview | 5.2 | Conda environnement | Visualisation de modèles |
| Quantum espresso | 5.1.2 | OS | Open-Source computer codes for electronic-structure calculation |
| Quantum espresso | 6.2 | Module | Open-Source computer codes for electronic-structure calculation |
| ufraw | 0.19 | OS | photo rendering manipulation |
| ufraw | 0.22 | Module with intel mpi | photo rendering manipulation |
| Cuda | 9 | Module | Cuda developpement Toolkit GPU Nodes |
| IMPORTANT PYTHON PACKAGES | |||
| NAME | VERSION | DISTRIBUTION | USAGE |
| Alabaster | module load python-X | ||
| Bioconductor | source activate myenv | ||
| blast | |||
| boost | |||
| Bowtie | |||
| Harffbuzz | |||
| Hdf5 | |||
| Ipython | |||
| Jedi | |||
| Lua | |||
| MKL | |||
| Netcdf | |||
| Numpy | |||
| petsc | |||
| R | |||
| rna-seq | |||
| Scikit | Present in respective conda | ||
| ScipY | |||
| scotch | |||
| slepsc | |||
| Spyder | |||
| Sympy | environnement | ||
| Torch | iscd.upmc.fr/mesu | ||
| Werkzeug | |||
| Ypda | |||
| DEBUG - VERSIONNING | |||
| NAME | VERSION | DISTRIBUTION | USAGE |
| CVS | 1.12.12 | OS | Versionning and download tool |
| Git | 2.12 | OS | Versionning and download tool |
| Intel Itac 2013 | 2013 Update 5 | Module | Debug bench |
| Intel Itac 2017 | 2017 Update 2 | Module | Debug bench |
| Intel Itac 2018 | 2018 Release | Module | Debug bench |
| Intel TBB | 2018 et 2013 | Module | Debug |
| Intel Vtune | 2018 et 2013 | Module | |
| Mercurial | 2.8.2 | OS | Versionning and download tool |
| Subversion | 1.8.19 | OS | Versionning and download tool |
| IDE - TEXT EDITORS | |||
| NAME | VERSION | DISTRIBUTION | USAGE |
| eclipse | 4.4 | OS | IDE java |
| emacs | 24.3 | OS | Editeur texte |
| expat | 2.1.0 | OS | XML Parser |
| gedit | 3.2 | OS | Editeur texte |
| gvim | 7.4 | OS | Editeur texte |
| nano | 2.7 | OS | Editeur texte |
| texlive | 2013 | OS | LaTEX |
| tk | 8.6 | OS | Interpreteur Tcl |
| vim | 7.4 | OS | Editeur texte |
| vte | 0.44 | OS | Terminal emulator |
| vte2 | 0.28 | OS | Terminal emulator |
| xalan C C++ | 1.11 | OS | XML Parser |
| xalan Java | 2.7 | OS | XML Parser Java |
| xerces C C++ | 3.1.4 | OS | XML Parser |
| xerces Java | 2.8.1 | OS | XML Parser Java |
| X ORG - LIBS MESA | |||
| NAME | VERSION | DISTRIBUTION | USAGE |
| freeglut | 2.8.1 | OS | Libraries graphiques |
| gegl | 0.2.0 | OS | Libraries graphiques |
| glew | 1.10 | OS | Libraries graphiques |
| glu | 9.0.0 | OS | Libraries graphiques |
| glucat | 0.8 | OS | Libraries graphiques |
| Gtk2 | 2.0.0 | OS | Libraries graphiques |
| Gtk3 | 3.20.10 | OS | Libraries graphiques |
| libQT5 | 5.6.1 | OS | Libraries graphiques |
| MeSA | 11.2.1 | OS | Libraries graphiques |
| mmg3d5 | 2017 | Module | simplicial remeshing |
| TOOLS | |||
| NAME | VERSION | DISTRIBUTION | USAGE |
| bzip | 1.06 | OS | compression |
| blktrace | 1.0.5 | OS | IO tracing mechanism |
| curl | 7.37 | OS | downoads |
| Docbook | 4.5 | OS | Documentation maker |
| doxygen | 1.8.6 | OS | Documentation maker |
| ffmpeg | 3.3.4 | OS | Traitement flux audio video |
| flex | 2.5 | OS | Fast lexical analyzer |
| gmsh | 2.1 | OS | mesh visualiseur |
| gnuplot | 4.6.5 | OS | grapheur |
| graphviz | 2.28 | OS | grapheur |
| gzip | 1.6.7 | OS | compression |
| Imagemagic | 6.8.8 | OS | image manipulateur |
| lcms | 1.19 | OS | Color management library |
| lcms2 | 2.2.7 | OS | Color management library |
| lensfun | 0.2.8 | OS | Photo Lens adjustement tool |
| mathomatic | 16.0.4 | OS | Computer algebra system |
| medit | 2017 | Module | mesh visualiseur |
| mpiplace | 2 | OS and Modules | Optimisation MPI |
| NCO | 4.7 | Module | NetCDF Toolkit |
| ncurses | 5.9 | OS | Developpement API |
| Ncview | 2.1.7 | Module | NetCDF visualiseur |
| openjpeg2 | 2.1.2 | OS | Outils JPEG |
| perfboost | 1.16 | OS Module | Optimisation MPI |
| perfcatcher | 26 | Module | Benchmark |
| screen | 4.0.4 | OS | Sessions SSH détachables |
| wget | 1314 | OS | download |
| xjobs | 2017 | Module | Parallel multiple commands |
| xz | 5.0.5 | OS | compression |
| zlib | 1.2.8 | OS | compression |
| LANGUAGE | |||
| NAME | VERSION | DISTRIBUTION | USAGE |
| Freefem++ | 3.6 | Module | resolution of partial differential equation |
| lua | 5.2 | OS | |
| lua | Conda environnement | ||
| Octave | 4.2 | OS | |
| Perl | 5.18 | OS | |
| Perl | 5.2 | Conda environnement | |
| Python | 2.7.13 | OS | |
| Python | 2.7.13 | Conda environnement | |
| Python3 | 3.4.6 | OS | |
| Python3 | 3.6 | Conda environnement | |
| Ryby | 2.1 | OS | |
| tcl | 8.6 | OS | |
| tcsh | 6.18 | OS | |
| vtk6 | 6.3 | OS | |
| zsh | 5.0.5 | OS |