diff --git a/docs.it4i/software/java.md b/docs.it4i/software/java.md new file mode 100644 index 0000000000000000000000000000000000000000..83c3738c0802e612ba84c25868771c44fa51a1ab --- /dev/null +++ b/docs.it4i/software/java.md @@ -0,0 +1,25 @@ +# 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/). diff --git a/docs.it4i/software/operating-system.md b/docs.it4i/software/operating-system.md new file mode 100644 index 0000000000000000000000000000000000000000..5f022fdff9bc624befd9f0082ae38f675c52e5ff --- /dev/null +++ b/docs.it4i/software/operating-system.md @@ -0,0 +1,9 @@ +# 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). diff --git a/mkdocs.yml b/mkdocs.yml index 05169fdaca7e74df38930d50a9a9f8d4cd9248e2..ef4b539168f9913be25a4479ef7b3b01b5b78f6c 100644 --- a/mkdocs.yml +++ b/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