====== How To Guides ======

===== Video tutorials for newcomers =====
If you are a new user to the CHPC, please watch these videos:
  * [[https://youtu.be/fCM8ZaFn4rs|Setting up a cluster password and logging in for the first time]]
  * [[https://youtu.be/CIEVMlrKXF4|The CHPC's service nodes and using the module system]]
  * [[https://youtu.be/mQjh8J_aMYU|Test running in an interactive PBS session]]
  * [[https://youtu.be/MEwi4uxM5hc|Running an application in batch mode under PBS]]

===== Tips and Tricks =====
[[howto:TipsAndTricks|Tips & tricks for common tasks.]] :!: ** Please read this.  The information is based on hard won experience. ** :!:


===== If you need more memory =====
As of May 2025, 41 compute nodes have had more memory added, cannibalizing memory modules from nodes that have failed permanently.  These 24-core nodes now have 256 GB of RAM each.  You can access these nodes by including the directive ''mem=250gb'' in your resource request line.  These nodes work with the usual queues such as smp, normal or large.

<code>
#PBS -l select=1:ncpus=24:mpiprocs=24:mem=250gb 
</code>

Only use these nodes if you need more than 128 GB of RAM, but less than the 1TB available on the "fat nodes".


===== Using the Intel compilers =====
As of December 2025, there is no license for the Intel Parallel-studio compilers.  However, all is not lost.  The "classic" compilers and MPI are installed in the directory:
<code>
/home/apps/chpc/compmech/compilers/intel_2021.3/oneapi
</code>

The most recent Lengau-compatible version of the OneAPI suite is installed in:
<code>
/home/apps/chpc/compmech/compilers/intel/oneapi
</code>

=== Classic Intel compiler and MPI ===
To use the "classic" suite, use the following settings:
<code>
. /home/apps/chpc/compmech/compilers/intel_2021.3/oneapi/compiler/2021.3.0/env/vars.sh
. /home/apps/chpc/compmech/compilers/intel_2021.3/oneapi/mkl/2021.3.0/env/vars.sh
. /home/apps/chpc/compmech/compilers/intel_2021.3/oneapi/mpi/2021.3.0/env/vars.sh
export CC=icc
export CXX=icpc
export FC=ifort
export F90=ifort
export F77=ifort
export MPICC=mpiicc
export MPICXX=mpiicpc
export MPIFORT=mpiifort
export MPIF77=mpiifort
export MPIF90=mpiifort
</code>

It is not necessary to use a machinefile for multi-node MPI runs.

=== OneAPI compilers and MPI ===
Post-2024 OneAPI compilers are not compatible with Lengau's operating system.  To use the most recent compatible version, use the following settings:
<code>
. /home/apps/chpc/compmech/compilers/intel/oneapi/setvars.sh
export CC=icx
export CXX=icpx
export FC=ifx
export F90=ifx
export F77=ifx
export MPICC=mpiicx
export MPICXX=mpiicpx
export MPIFORT=mpiifx
export MPIF77=mpiifx
export MPIF90=mpiifx
export I_MPI_HYDRA_BOOTSTRAP=ssh
</code>

It is not necessary to use a machinefile for multi-node MPI runs.  However, the default bootstrap method using pbsdsh does not work, hence the need to set ''I_MPI_HYDRA_BOOTSTRAP''.  This is a typical command mpi run command:
<code>
mpirun -np 96 myMPIprogram.exe
</code>







===== Transferring data to DIRISA =====
Long-term data storage through [[howto:Dirisa|DIRISA.]] 




===== Transferring data with Globus =====
[[howto:Globus|Here are instructions for using Globus to transfer data]]



===== Compilers and Interpreters =====

A number of computer languages are available on the cluster. The
preferred way to set up your environment to use a specific toolset
is to load the appropriate modules to activate the needed libraries
and set up the paths for the correct binaries. 


  * [[howto:Compilers]]



===== Dealing with software licensing =====
Commercial software involves dealing with [[howto:licensing|licensing.]]


===== Ssh-tunneling with MobaXterm =====
Here is a [[https://youtu.be/lil4eagB8oY|tutorial video]] on ssh-tunneling with MobaXterm.


===== Gaussian at CHPC =====

  * [[howto:gaussian|Running Gaussian on the CHPC cluster]]

===== Computational Mechanics =====
  *[[OpenFOAM|How to use OpenFOAM and build your own code on the CHPC systems]]
  *[[ansys|Using Ansys/Fluent at the CHPC]]
  *[[ansysmechanical|Using Ansys/Mechanical at the CHPC]]
  *[[cfx|Using Ansys/CFX at the CHPC]]
  *[[forte|Using Ansys Forte at the CHPC]]
  *[[starccm|Using STAR-CCM+ at the CHPC]]
  *[[CFD-Ace|Using ESI CFD-Ace at the CHPC]]
  *[[abaqus|Running Abaqus on the CHPC]]
  *[[mfix|Using MFIX at the CHPC]]
  *[[liggghts|Using LIGGGHTS and lammps at the CHPC]]
  *[[SU2|Using SU2 at the CHPC]]
  *[[FDS|Using the Fire Dynamics Simulator FDS at the CHPC]]
  *[[Rocky DEM|Using the discrete element code Rocky DEM at the CHPC]]
  *[[howto:ultrafluidx|Using Altair's UltraFluidX LBM code at the CHPC]]
  *[[Palabos|Using the lattice-Boltzman code Palabos at the CHPC]]
  *[[AMR-Wind|Using the wind-energy code AMR-Wind at the CHPC]]

===== Computational Electromagnetics =====
  *[[feko|How to use Feko at the CHPC]]


===== Bioinformatics =====

  *[[bioinformatics|How to use pre-installed bioinformatics tools]]

===== Cosmology and Astrophysics =====
  *[[COSMOMC]]
  *[[cosmopmc]]
  *[[Gadget-2]]
  *[[Casacore]]
  *[[AOFlagger]]
===== GPU Computing =====
  *[[guide:gpu|GPU Cluster overview and generic instructions]]
  *[[gpu_namd|How to run NAMD]]
  *[[gpu_gromacs|How to run Gromacs]]

===== Gromacs =====
  *[[gromacs|How to run Gromacs]]

===== DLPoly =====

  *[[dlpoly]] Material Sciences application

===== Python at the CHPC =====

  * [[howto:python:start]]
  * [[research:ml|Running Tensorflow]]
  * [[tipsntricks:ipython_notebook]]

===== R for Statistical Computing =====

  * [[howto:R|Using R on the CHPC cluster]]

===== MPI Java =====

  * [[howto:Java|Using Java on the CHPC cluster]]

===== Co-Array Fortran =====

  * [[howto:coarrayFortran|Using Co-array Fortran on the CHPC cluster]]

===== Omni Compiler =====

  * [[howto:omniCompiler|Using Omni Compiler on the CHPC cluster]]

===== Tuning and Analysis Tools =====

  * [[howto:tune]]

===== Building Essential Tools =====

  *[[compiling_gcc|Installing GCC 4.7.1 from source]]
  *[[compiling_Python_2_7_3|Installing Python 2.7.3 from source]]
  *[[compiling_octave|Installing Octave 3.6.3 from source]]
  *[[compiling_R|Installing R 2.15.1 from source]]
  
===== Remote Visualization =====

  *[[remote_viz|Remote OpenGL visualization with TurboVNC and VirtualGL]] 
  *[[paraview|Using Paraview]]
  *[[gnuplot|Using Gnuplot]]
  *[[ncview|Using ncview]]
  *[[visit|Using VisIt]]
  *[[grace|Using grace]]
  *[[p4vasp|Using p4vasp]]
  *[[vesta|Using Vesta]]

===== Matlab at CHPC =====
  *[[matlab|Using Matlab on the cluster]]


===== Earth Sciences =====

  *[[wrf|Running the WRF model]] 
  *[[CDO|Using Climate Data Operator (CDO)]]

===== Windows applications =====
  *[[windows|Running Windows applications]]