pages added to software from soft/sal and soft/ans

docs.it4i/software/java.md

+# Java
+
+Java is available on the cluster. Activate java by loading the Java module
+
+```console
+$ ml Java
+```
+
+Note that the Java module must be loaded on the compute nodes as well, in order to run java on compute nodes.
+
+Check for java version and path
+
+```console
+$ java -version
+$ which java
+```
+
+With the module loaded, not only the runtime environment (JRE), but also the development environment (JDK) with the compiler is available.
+
+```console
+$ javac -version
+$ which javac
+```
+
+Java applications may use MPI for inter-process communication, in conjunction with Open MPI. Read more on <http://www.open-mpi.org/faq/?category=java>. This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact [cluster support](https://support.it4i.cz/rt/).

docs.it4i/software/operating-system.md

+# Anselm
+
+The operating system on Anselm is Linux - [**Red Hat Enterprise Linux release 6.x**](https://en.wikipedia.org/wiki/Red_Hat_Enterprise_Linux).
+
+# Salomon
+
+The operating system on Salomon is Linux - [**CentOS 6.x**](https://en.wikipedia.org/wiki/CentOS)
+
+The CentOS Linux distribution is a stable, predictable, manageable and reproducible platform derived from the sources of Red Hat Enterprise Linux (RHEL).

mkdocs.yml

@@ -3,7 +3,7 @@ theme_dir: 'material'
 docs_dir: docs.it4i
 site_favicon: img/favicon.ico
 
-extra_css: 
+extra_css:
    - src/css.css
 
 # Repository
@@ -58,11 +58,14 @@ pages:
     - Remote Visualization: anselm/remote-visualization.md
     - PRACE User Support: anselm/prace.md
   - 'Software':
+    - Operating System: software/operating-system.md
     - Lmod Environment: software/lmod.md
     - Modules Matrix: modules-matrix.md
-    - Singularity Container: software/singularity.md  
+    - Singularity Container: software/singularity.md
     - EasyBuild: software/easybuild.md
     - Spack: software/spack.md
+    - Bioinformatics: software/bioinformatics.md
+    - Java: software/java.md
     - Salomon Software:
       - Available Modules: modules-salomon.md
       - Available Modules on UV: modules-salomon-uv.md
@@ -78,8 +81,6 @@ pages:
         - 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
@@ -109,7 +110,6 @@ pages:
         - 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
@@ -118,9 +118,8 @@ pages:
         - 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    
+        - 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
@@ -134,8 +133,6 @@ pages:
         - 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
@@ -165,7 +162,6 @@ pages:
         - 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
@@ -191,7 +187,6 @@ pages:
         - Priorization Component (BiERApp): anselm/software/omics-master/priorization-component-bierapp.md
         - Overview: anselm/software/omics-master/overview.md
       - OpenFOAM: anselm/software/openfoam.md
-      - Operating System: anselm/software/operating-system.md
       - ParaView: anselm/software/paraview.md
       - Virtualization: anselm/software/virtualization.md
   - PBS Pro Documentation: pbspro.md