Update mkdocs.yml

mkdocs.yml

@@ -57,135 +57,48 @@ pages:
     - Storage: anselm/storage.md
     - Network: anselm/network.md
     - PRACE User Support: anselm/prace.md
-  - 'Software':
-    - Lmod Environment: software/lmod.md
-    - Modules Matrix: modules-matrix.md
-    - Job Features: job-features.md
-    - Singularity Container: software/singularity.md  
-    - EasyBuild: software/easybuild.md
-    - Spack: software/spack.md
-    - Salomon Software:
-      - Available Modules: modules-salomon.md
-      - Available Modules on UV: modules-salomon-uv.md
-      - 'Machine learning':
-        - Introduction: salomon/software/machine-learning/introduction.md
-        - TensorFlow: salomon/software/machine-learning/tensorflow.md
-      - 'ANSYS':
-        - Introduction: salomon/software/ansys/ansys.md
-        - ANSYS CFX: salomon/software/ansys/ansys-cfx.md
-        - ANSYS Fluent: salomon/software/ansys/ansys-fluent.md
-        - ANSYS LS-DYNA: salomon/software/ansys/ansys-ls-dyna.md
-        - ANSYS MAPDL: salomon/software/ansys/ansys-mechanical-apdl.md
-        - Workbench: salomon/software/ansys/workbench.md
-        - Setting License Preferences: salomon/software/ansys/licensing.md
-        - Licensing and Available Versions: salomon/software/ansys/setting-license-preferences.md
-      - 'Bioinformatics':
-        - Bioinformatics Applications: software/bioinformatics.md
-      - 'Chemistry':
-        - Molpro: salomon/software/chemistry/molpro.md
-        - NWChem: salomon/software/chemistry/nwchem.md
-        - Phono3py: salomon/software/chemistry/phono3py.md
-        - ORCA: software/orca.md
-      - Compilers: salomon/software/compilers.md
-      - 'COMSOL':
-        - COMSOL: salomon/software/comsol/comsol-multiphysics.md
-        - Licensing and Available Versions: salomon/software/comsol/licensing-and-available-versions.md
-      - 'Debuggers':
-        - Introduction: salomon/software/debuggers/Introduction.md
-        - Aislinn: salomon/software/debuggers/aislinn.md
-        - Allinea Forge (DDT,MAP): salomon/software/debuggers/allinea-ddt.md
-        - Allinea Performance Reports: salomon/software/debuggers/allinea-performance-reports.md
-        - Intel VTune Amplifier XE: salomon/software/debuggers/intel-vtune-amplifier.md
-        - Total View: salomon/software/debuggers/total-view.md
-        - Valgrind: salomon/software/debuggers/valgrind.md
-        - Vampir: salomon/software/debuggers/vampir.md
-      - 'Intel Suite':
-        - Introduction: salomon/software/intel-suite/intel-parallel-studio-introduction.md
-        - Intel Advisor: salomon/software/intel-suite/intel-advisor.md
-        - Intel Compilers: salomon/software/intel-suite/intel-compilers.md
-        - Intel Debugger: salomon/software/intel-suite/intel-debugger.md
-        - Intel IPP: salomon/software/intel-suite/intel-integrated-performance-primitives.md
-        - Intel Inspector: salomon/software/intel-suite/intel-inspector.md
-        - Intel MKL: salomon/software/intel-suite/intel-mkl.md
-        - Intel TBB: salomon/software/intel-suite/intel-tbb.md
-        - Intel Trace Analyzer and Collector: salomon/software/intel-suite/intel-trace-analyzer-and-collector.md
-      - Intel Xeon Phi: salomon/software/intel-xeon-phi.md
-      - Java: salomon/software/java.md
-      - 'MPI':
-        - Introduction: salomon/software/mpi/mpi.md
-        - MPI4Py (MPI for Python): salomon/software/mpi/mpi4py-mpi-for-python.md
-        - Running Open MPI: salomon/software/mpi/Running_OpenMPI.md
-      - 'Numerical Languages':
-        - Introduction: salomon/software/numerical-languages/introduction.md
-        - Matlab: salomon/software/numerical-languages/matlab.md
-        - Octave: salomon/software/numerical-languages/octave.md
-        - R: salomon/software/numerical-languages/r.md    
-        - OpenCoarrays: salomon/software/numerical-languages/opencoarrays.md
-      - Operating System: salomon/software/operating-system.md
-      - ParaView: salomon/software/paraview.md
-    - Anselm Software:
-      - Available Modules: modules-anselm.md
-      - 'Machine learning':
-        - Introduction: anselm/software/machine-learning/introduction.md
-        - TensorFlow: anselm/software/machine-learning/tensorflow.md
-      - 'ANSYS':
-        - Introduction: anselm/software/ansys/ansys.md
-        - ANSYS CFX: anselm/software/ansys/ansys-cfx.md
-        - ANSYS Fluent: anselm/software/ansys/ansys-fluent.md
-        - ANSYS LS-DYNA: anselm/software/ansys/ansys-ls-dyna.md
-        - ANSYS MAPDL: anselm/software/ansys/ansys-mechanical-apdl.md
-        - LS-DYNA: anselm/software/ansys/ls-dyna.md
-      - 'Bioinformatics':
-        - Bioinformatics Applications: software/bioinformatics.md
-      - 'Debuggers':
-        - Allinea Forge (DDT,MAP): anselm/software/debuggers/allinea-ddt.md
-        - Allinea Performance Reports: anselm/software/debuggers/allinea-performance-reports.md
-        - CUBE: anselm/software/debuggers/cube.md
-        - Intel Performance Counter Monitor: anselm/software/debuggers/intel-performance-counter-monitor.md
-        - Intel VTune Amplifier: anselm/software/debuggers/intel-vtune-amplifier.md
-        - PAPI: anselm/software/debuggers/papi.md
-        - Scalasca: anselm/software/debuggers/scalasca.md
-        - Score-P: anselm/software/debuggers/score-p.md
-        - Total View: anselm/software/debuggers/total-view.md
-        - VNC: anselm/software/debuggers/debuggers.md
-        - Valgrind: anselm/software/debuggers/valgrind.md
-        - Vampir: anselm/software/debuggers/vampir.md
-      - 'Chemistry':
-        - Molpro: anselm/software/chemistry/molpro.md
-        - NWChem: anselm/software/chemistry/nwchem.md
-        - ORCA: software/orca.md
-      - COMSOL: anselm/software/comsol-multiphysics.md
-      - Compilers: anselm/software/compilers.md
-      - GPI-2: anselm/software/gpi2.md
-      - 'Intel Suite':
-        - Introduction: anselm/software/intel-suite/introduction.md
-        - Intel Compilers: anselm/software/intel-suite/intel-compilers.md
-        - Intel Debugger: anselm/software/intel-suite/intel-debugger.md
-        - Intel IPP: anselm/software/intel-suite/intel-integrated-performance-primitives.md
-        - Intel MKL: anselm/software/intel-suite/intel-mkl.md
-        - Intel TBB: anselm/software/intel-suite/intel-tbb.md
-      - Intel Xeon Phi: anselm/software/intel-xeon-phi.md
-      - ISV Licenses: anselm/software/isv_licenses.md
-      - Java: anselm/software/java.md
-      - 'MPI':
-        - Introduction: anselm/software/mpi/mpi.md
-        - MPI4Py (MPI for Python): anselm/software/mpi/mpi4py-mpi-for-python.md
-        - Running Open MPI: anselm/software/mpi/Running_OpenMPI.md
-        - Running MPICH2: anselm/software/mpi/running-mpich2.md
-      - 'Numerical Languages':
-        - Introduction: anselm/software/numerical-languages/introduction.md
-        - Matlab 2013-2014: anselm/software/numerical-languages/matlab_1314.md
-        - Matlab: anselm/software/numerical-languages/matlab.md
-        - Octave: anselm/software/numerical-languages/octave.md
-        - R: anselm/software/numerical-languages/r.md
-      - 'Numerical Libraries':
-        - FFTW: anselm/software/numerical-libraries/fftw.md
-        - GSL: anselm/software/numerical-libraries/gsl.md
-        - HDF5: anselm/software/numerical-libraries/hdf5.md
-        - Intel Numerical Libraries: anselm/software/numerical-libraries/intel-numerical-libraries.md
-        - MAGMA for Intel Xeon Phi: anselm/software/numerical-libraries/magma-for-intel-xeon-phi.md
-        - PETSc: anselm/software/numerical-libraries/petsc.md
-        - Trilinos: anselm/software/numerical-libraries/trilinos.md
+  - Software:
+    - Modules:
+      - Lmod Environment: software/modules/lmod.md
+      - Intel Xeon Phi Environment: software/mic/mic_environment.md
+      - Modules Matrix: modules-matrix.md
+      - Job Features: job-features.md
+      - Available Salomon Modules: modules-salomon.md
+      - Available Salomon Modules on UV: modules-salomon-uv.md
+      - Available Salomon Modules on PHI Cards: modules-salomon-phi.md
+      - Available Anselm Modules: modules-anselm.md
+    - ISV Licenses: software/isv_licenses.md
+    - Bioinformatics:
+      - Bioinformatics Applications: software/bio/bioinformatics.md
+      - Omics Master:
+        - Overview: software/bio/omics-master/overview.md
+        - Diagnostic Component (TEAM): software/bio/omics-master/diagnostic-component-team.md
+        - Priorization Component (BiERApp): software/bio/omics-master/priorization-component-bierapp.md
+    - CAE:
+      - COMSOL:
+        - COMSOL: software/cae/comsol/comsol-multiphysics.md
+        - Licensing and Available Versions: software/cae/comsol/licensing-and-available-versions.md
+    - Chemistry:
+      - Molpro: software/chemistry/molpro.md
+      - Orca: software/chemistry/orca.md
+      - NWChem: software/chemistry/nwchem.md
+      - Phono3py: software/chemistry/phono3py.md
+    - Compilers: software/compilers.md
+    - Debuggers:
+      - Introduction: software/debuggers/Introduction.md
+      - Aislinn: software/debuggers/aislinn.md
+      - Allinea Forge (DDT,MAP): software/debuggers/allinea-ddt.md
+      - Allinea Performance Reports: software/debuggers/allinea-performance-reports.md
+      - CUBE: software/debuggers/cube.md
+      - Intel Performance Counter Monitor: software/debuggers/intel-performance-counter-monitor.md
+      - Intel VTune Amplifier XE: software/debuggers/intel-vtune-amplifier.md
+      - PAPI: software/debuggers/papi.md
+      - Scalasca: software/debuggers/scalasca.md
+      - Score-P: software/debuggers/score-p.md
+      - Total View: software/debuggers/total-view.md
+      - Valgrind: software/debuggers/valgrind.md
+      - Vampir: software/debuggers/vampir.md
+    - GPU:
       - NVIDIA CUDA: anselm/software/nvidia-cuda.md
     - Intel:
       - Intel Suite:
@@ -285,4 +198,4 @@ markdown_extensions:
 
 google_analytics:
   - 'UA-90498826-1'
-  - 'auto'
+  - 'auto'
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