Removed SW indexes

docs.it4i/anselm-cluster-documentation/software/index.md

-# Anselm Cluster Software
-
-## [Modules](../../modules-anselm)
-
--   List of available modules
-    ## [COMSOL](comsol-multiphysics)
--   A finite element analysis, solver and Simulation software
-    ## [ParaView](paraview)
--   An open-source, multi-platform data analysis and visualization application
-    ## [Compilers](compilers)
--   Available compilers, including GNU, INTEL and UPC compilers
-    ## [NVIDIA CUDA](nvidia-cuda)
--   A guide to NVIDIA CUDA programming and GPU usage
-    ## [GPI-2](gpi2)
--   A library that implements the GASPI specification
-    ## [OpenFOAM](openfoam)
--   A free, open source CFD software package
-    ## [ISV Licenses](isv_licenses)
--   A guide to managing Independent Software Vendor licenses
-    ## [Intel Xeon Phi](intel-xeon-phi)
--   A guide to Intel Xeon Phi usage
-    ## [Virtualization](kvirtualization)
-    ## [Java](java)
--   Java on ANSELM
-    ## [Operating System](operating-system)
--   The operating system, deployed on ANSELM
-    ## Intel Suite
--   The Intel Parallel Studio XE
-    ### [Introduction](intel-suite/introduction)
-    ### [Intel MKL](intel-suite/intel-mkl)
-    ### [Intel Compilers](intel-suite/intel-compilers)
-    ### [Intel IPP](intel-suite/intel-integrated-performance-primitives)
-    ### [Intel TBB](intel-suite/intel-tbb)
-    ### [Intel Debugger](intel-suite/intel-debugger)
-    ## MPI
--   Message Passing Interface libraries
-    ### [Introduction](mpi/mpi)
-    ### [MPI4Py (MPI for Python)](mpi/mpi4py-mpi-for-python)
-    ### [Running OpenMPI](mpi/Running_OpenMPI)
-    ### [Running MPICH2](mpi/running-mpich2)
-    ## Numerical Libraries
--   Libraries for numerical computations
-    ### [Intel numerical libraries](numerical-libraries/intel-numerical-libraries)
-    ### [PETSc](numerical-libraries/petsc)
-    ### [Trilinos](numerical-libraries/trilinos)
-    ### [FFTW](numerical-libraries/fftw)
-    ### [GSL](numerical-libraries/gsl)
-    ### [MAGMA for Intel Xeon Phi](numerical-libraries/magma-for-intel-xeon-phi)
-    ### [HDF5](numerical-libraries/hdf5)
-    ## Omics Master
-    ### [Diagnostic component (TEAM)](omics-master/diagnostic-component-team)
-    ### [Prioritization component (BiERapp)](omics-master/priorization-component-bierapp)
-    ### [Overview](omics-master/overview)
-    ## Debuggers
--   A collection of development tools
-    ### [Valgrind](debuggers/valgrind)
-    ### [PAPI](debuggers/papi)
-    ### [Allinea Forge (DDT,MAP)](debuggers/allinea-ddt)
-    ### [Total View](debuggers/total-view)
-    ### [CUBE](debuggers/cube)
-    ### [Intel VTune Amplifier](debuggers/intel-vtune-amplifier)
-    ### [VNC](debuggers/debuggers)
-    ### [Scalasca](debuggers/scalasca)
-    ### [Score-P](debuggers/score-p)
-    ### [Intel Performance Counter Monitor](debuggers/intel-performance-counter-monitor)
-    ### [Allinea Performance Reports](debuggers/allinea-performance-reports)
-    ### [Vampir](debuggers/vampir)
-    ## Numerical Languages
--   Interpreted languages for numerical computations
-    ### [Introduction](numerical-languages/introduction)
-    ### [R](numerical-languages/r)
-    ### [MATLAB 2013-2014](numerical-languages/matlab_1314)
-    ### [MATLAB](numerical-languages/matlab)
-    ### [Octave](numerical-languages/octave)
-    ## Chemistry
--   Tools for computational chemistry
-    ### [Molpro](chemistry/molpro)
-    ### [NWChem](chemistry/nwchem)
-    ## ANSYS
--   An engineering simulation software
-    ### [Introduction](ansys/ansys)
-    ### [ANSYS CFX](ansys/ansys-cfx)
-    ### [ANSYS LS-DYNA](ansys/ansys-ls-dyna)
-    ### [ANSYS MAPDL](ansys/ansys-mechanical-apdl)
-    ### [LS-DYNA](ansys/ls-dyna)
-    ### [ANSYS Fluent](ansys/ansys-fluent)

docs.it4i/salomon/software/index.md

-# Salomon Cluster Software
-
-## [Modules](../../modules-salomon)
-
--   List of Available Modules
-    ## [Compilers](compilers)
--   Available compilers, including GNU, INTEL and UPC compilers
-    ## [Intel Xeon Phi](intel-xeon-phi)
--   A guide to Intel Xeon Phi usage
-    ## [Java](java)
--   Java on the cluster
-    ## [Operating System](operating-system)
--   The operating system, deployed on Salomon cluster
-    ## Intel Suite
--   The Intel Parallel Studio XE
-    ### [Introduction](intel-suite/intel-parallel-studio-introduction)
-    ### [Intel MKL](intel-suite/intel-mkl)
-    ### [Intel Compilers](intel-suite/intel-compilers)
-    ### [Intel IPP](intel-suite/intel-integrated-performance-primitives)
-    ### [Intel TBB](intel-suite/intel-tbb)
-    ### [Intel Debugger](intel-suite/intel-debugger)
-    ### [Intel Inspector](intel-suite/intel-inspector)
-    ### [Intel Trace Analyzer and Collector](intel-suite/intel-trace-analyzer-and-collector)
-    ### [Intel Advisor](intel-suite/intel-advisor)
-    ## MPI
--   Message Passing Interface libraries
-    ### [Introduction](mpi/mpi)
-    ### [MPI4Py (MPI for Python)](mpi/mpi4py-mpi-for-python)
-    ### [Running Open MPI](mpi/Running_OpenMPI)
-    ## Debuggers
--   A collection of development tools
-    ### [Introduction](debuggers/Introduction)
-    ### [Valgrind](debuggers/valgrind)
-    ### [Allinea Forge (DDT,MAP)](debuggers/allinea-ddt)
-    ### [Total View](debuggers/total-view)
-    ### [Intel VTune Amplifier XE](debuggers/intel-vtune-amplifier)
-    ### [Aislinn](debuggers/aislinn)
-    ### [Allinea Performance Reports](debuggers/allinea-performance-reports)
-    ### [Vampir](debuggers/vampir)
-    ## Numerical Languages
--   Interpreted languages for numerical computations
-    ### [Introduction](numerical-languages/introduction)
-    ### [R](numerical-languages/r)
-    ### [MATLAB](numerical-languages/matlab)
-    ### [Octave](numerical-languages/octave)
-    ## Chemistry
--   Tools for computational chemistry
-    ### [Molpro](chemistry/molpro)
-    ### [Phono3py](chemistry/phono3py)
-    ### [NWChem](chemistry/nwchem)
-    ## COMSOL
--   A finite element analysis, solver and Simulation software
-    ### [COMSOL](comsol/comsol-multiphysics)
-    ### [Licensing and Available Versions](comsol/licensing-and-available-versions)
-    ## ANSYS
--   An engineering simulation software
-    ### [Introduction](ansys/ansys)
-    ### [Workbench](ansys/workbench)
-    ### [ANSYS CFX](ansys/ansys-cfx)
-    ### [ANSYS LS-DYNA](ansys/ansys-ls-dyna)
-    ### [ANSYS MAPDL](ansys/ansys-mechanical-apdl)
-    ### [ANSYS Fluent](ansys/ansys-fluent)
-    ### [Setting license preferences](ansys/licensing)
-    ### [Licensing and Available Versions](ansys/setting-license-preferences)