Merge branch 'soft_consolidation' into 'master'

Soft consolidation See merge request !25

Merge branch 'soft_consolidation' into 'master'
083dc8a2 · Lukáš Krupčík · bd4f62ad · 9538bfea · 083dc8a2 · 083dc8a2
Commit 083dc8a2 authored 8 years ago by Lukáš Krupčík
--- a/docs.it4i/anselm-cluster-documentation/software/index.md
+++ b/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 licences
+## [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)
+### [Priorization 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)
--- a/docs.it4i/salomon/software/index.md
+++ b/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 OpenMPI](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)
--- a/it4i_theme/nav.html
+++ b/it4i_theme/nav.html
@@ -29,4 +29,4 @@
      {% endif %}
    {% endif %}
  </li>
-{% endif %}
\ No newline at end of file
+{% endif %}
--- a/material/nav.html
+++ b/material/nav.html
+{% if not nav_item.title.startswith("&nbsp;") %}
 {% if nav_item.children %}
  <li>
    <span class="section">{{ nav_item.title }}</span>
@@ -29,4 +30,5 @@
      {% endif %}
    {% endif %}
  </li>
-{% endif %}
\ No newline at end of file
+{% endif %}
+{% endif %}
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -37,7 +37,8 @@ pages:
    - Job Submission and Execution: anselm-cluster-documentation/job-submission-and-execution.md
    - Capacity computing: anselm-cluster-documentation/capacity-computing.md
    - Storage: anselm-cluster-documentation/storage.md
-  - Anselm Cluster Software:
+  - Anselm Cluster Software: anselm-cluster-documentation/software/index.md
+  - '&nbsp;Anselm Cluster Software':
    - Modules: modules-anselm.md
    - COMSOL: anselm-cluster-documentation/software/comsol-multiphysics.md
    - ParaView: anselm-cluster-documentation/software/paraview.md
@@ -50,19 +51,19 @@ pages:
    - Virtualization: anselm-cluster-documentation/software/kvirtualization.md
    - Java: anselm-cluster-documentation/software/java.md
    - Operating System: anselm-cluster-documentation/software/operating-system.md
-  - Anselm Cluster Intel Suite:
+  - '&nbsp;Anselm Cluster Intel Suite':
    - Introduction: anselm-cluster-documentation/software/intel-suite/introduction.md
    - Intel MKL: anselm-cluster-documentation/software/intel-suite/intel-mkl.md
    - Intel Compilers: anselm-cluster-documentation/software/intel-suite/intel-compilers.md
    - Intel IPP: anselm-cluster-documentation/software/intel-suite/intel-integrated-performance-primitives.md
    - Intel TBB: anselm-cluster-documentation/software/intel-suite/intel-tbb.md
    - Intel Debugger: anselm-cluster-documentation/software/intel-suite/intel-debugger.md
-  - Anselm Cluster MPI:
+  - '&nbsp;Anselm Cluster MPI':
    - Introduction: anselm-cluster-documentation/software/mpi/mpi.md
    - MPI4Py (MPI for Python): anselm-cluster-documentation/software/mpi/mpi4py-mpi-for-python.md
    - Running OpenMPI: anselm-cluster-documentation/software/mpi/Running_OpenMPI.md
    - Running MPICH2: anselm-cluster-documentation/software/mpi/running-mpich2.md
-  - Anselm Cluster Numerical Libraries:
+  - '&nbsp;Anselm Cluster Numerical Libraries':
    - Intel numerical libraries: anselm-cluster-documentation/software/numerical-libraries/intel-numerical-libraries.md
    - PETSc: anselm-cluster-documentation/software/numerical-libraries/petsc.md
    - Trilinos: anselm-cluster-documentation/software/numerical-libraries/trilinos.md
@@ -70,11 +71,11 @@ pages:
    - GSL: anselm-cluster-documentation/software/numerical-libraries/gsl.md
    - MAGMA for Intel Xeon Phi: anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md
    - HDF5: anselm-cluster-documentation/software/numerical-libraries/hdf5.md
-  - Anselm Cluster Omics Master:
+  - '&nbsp;Anselm Cluster Omics Master':
    - Diagnostic component (TEAM): anselm-cluster-documentation/software/omics-master/diagnostic-component-team.md
    - Priorization component (BiERApp): anselm-cluster-documentation/software/omics-master/priorization-component-bierapp.md
    - Overview: anselm-cluster-documentation/software/omics-master/overview.md
-  - Anselm Cluster Debuggers:
+  - '&nbsp;Anselm Cluster Debuggers':
    - Valgrind: anselm-cluster-documentation/software/debuggers/valgrind.md
    - PAPI: anselm-cluster-documentation/software/debuggers/papi.md
    - Allinea Forge (DDT,MAP): anselm-cluster-documentation/software/debuggers/allinea-ddt.md
@@ -87,16 +88,16 @@ pages:
    - Intel Performance Counter Monitor: anselm-cluster-documentation/software/debuggers/intel-performance-counter-monitor.md
    - Allinea Performance Reports: anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
    - Vampir: anselm-cluster-documentation/software/debuggers/vampir.md
-  - Anselm Cluster Numerical Languages:
+  - '&nbsp;Anselm Cluster Numerical Languages':
    - Introduction: anselm-cluster-documentation/software/numerical-languages/introduction.md
    - R: anselm-cluster-documentation/software/numerical-languages/r.md
    - Matlab 2013-2014: anselm-cluster-documentation/software/numerical-languages/matlab_1314.md
    - Matlab: anselm-cluster-documentation/software/numerical-languages/matlab.md
    - Octave: anselm-cluster-documentation/software/numerical-languages/octave.md
-  - Anselm Cluster Chemistry:
+  - '&nbsp;Anselm Cluster Chemistry':
    - Molpro: anselm-cluster-documentation/software/chemistry/molpro.md
    - NWChem: anselm-cluster-documentation/software/chemistry/nwchem.md
-  - Anselm Cluster Ansys:
+  - '&nbsp;Anselm Cluster Ansys':
    - Introduction: anselm-cluster-documentation/software/ansys/ansys.md
    - ANSYS CFX: anselm-cluster-documentation/software/ansys/ansys-cfx.md
    - ANSYS LS-DYNA: anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md
@@ -121,14 +122,15 @@ pages:
    - Job submission and execution: salomon/job-submission-and-execution.md
    - Capacity computing: salomon/capacity-computing.md
    - Storage: salomon/storage.md
-  - Salomon Cluster Software:
+  - Salomon Cluster Software: salomon/software/index.md
+  - '&nbsp;Salomon Cluster Software':
    - Modules: modules-salomon.md
    - UV Modules: modules-salomon-uv.md
    - Compilers: salomon/software/compilers.md
    - Intel Xeon Phi: salomon/software/intel-xeon-phi.md
    - Java: salomon/software/java.md
    - Operating System: salomon/software/operating-system.md
-  - Salomon Cluster Intel Suite:
+  - '&nbsp;Salomon Cluster Intel Suite':
    - Introduction: salomon/software/intel-suite/intel-parallel-studio-introduction.md
    - Intel MKL: salomon/software/intel-suite/intel-mkl.md
    - Intel Compilers: salomon/software/intel-suite/intel-compilers.md
@@ -138,11 +140,11 @@ pages:
    - Intel Inspector: salomon/software/intel-suite/intel-inspector.md
    - Intel Trace Analyzer and Collector: salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
    - Intel Advisor: salomon/software/intel-suite/intel-advisor.md
-  - Salomon Cluster MPI:
+  - '&nbsp;Salomon Cluster MPI':
    - Introduction: salomon/software/mpi/mpi.md
    - MPI4Py (MPI for Python): salomon/software/mpi/mpi4py-mpi-for-python.md
    - Running OpenMPI: salomon/software/mpi/Running_OpenMPI.md
-  - Salomon Cluster Debuggers:
+  - '&nbsp;Salomon Cluster Debuggers':
    - Introduction: salomon/software/debuggers/Introduction.md
    - Valgrind: salomon/software/debuggers/valgrind.md
    - Allinea Forge (DDT,MAP): salomon/software/debuggers/allinea-ddt.md
@@ -151,19 +153,19 @@ pages:
    - Aislinn: salomon/software/debuggers/aislinn.md
    - Allinea Performance Reports: salomon/software/debuggers/allinea-performance-reports.md
    - Vampir: salomon/software/debuggers/vampir.md
-  - Salomon Cluster Numerical Languages:
+  - '&nbsp;Salomon Cluster Numerical Languages':
    - Introduction: salomon/software/numerical-languages/introduction.md
    - R: salomon/software/numerical-languages/r.md
    - Matlab: salomon/software/numerical-languages/matlab.md
    - Octave: salomon/software/numerical-languages/octave.md
-  - Salomon Cluster Chemistry:
+  - '&nbsp;Salomon Cluster Chemistry':
    - Molpro: salomon/software/chemistry/molpro.md
    - Phono3py: salomon/software/chemistry/phono3py.md
    - NWChem: salomon/software/chemistry/nwchem.md
-  - Salomon Cluster Comsol:
+  - '&nbsp;Salomon Cluster Comsol':
    - COMSOL: salomon/software/comsol/comsol-multiphysics.md
    - Licensing and Available Versions: salomon/software/comsol/licensing-and-available-versions.md
-  - Salomon Cluster Ansys:
+  - '&nbsp;Salomon Cluster Ansys':
    - Introduction: salomon/software/ansys/ansys.md
    - Workbench: salomon/software/ansys/workbench.md
    - ANSYS CFX: salomon/software/ansys/ansys-cfx.md