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--- howto:start [2023/07/14 13:24]
ccrosby [Transferring data to DIRISA]
+++ howto:start [2026/02/24 10:42] (current)
ccrosby [Using the Intel compilers]
@@ Line 12: / Line 12: @@
-===== Transferring data to DIRISA =====
+===== If you need more memory =====
-High-performance computing is closely related to "big data".  Many HPC users both use and generate very large data sets.  The CHPC's default recommendation to users is:
+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.
-  * Feel free to use the CHPC's lustre storage as "work space".  It is large, fast and designed for parallel computing.
-  * Lustre is **not** a safe space for storing important data sets.
-  * Expedite post-processing and remove raw data.
-  * Store post-processed data somewhere safe.
-However, the CHPC recognizes that this workflow is not universal.  Many research groups own or produce very large data sets that need to be stored safely for sharing or future re-use.  This is where the [[https://www.dirisa.ac.za/|Data Intensive Research Initiative of South Africa]] comes into play.  Like the CHPC, DIRISA is also part of South Africa's [[https://www.nicis.ac.za/|National Integrated Cyber Infrastructure System]].  DIRISA operates storage systems that **are** designed for long-term safe storage of research data.
+<code>
+#PBS -l select=1:ncpus=24:mpiprocs=24:mem=250gb
+</code>
-=== DIRISA Object Stores ===
+Only use these nodes if you need more than 128 GB of RAM, but less than the 1TB available on the "fat nodes".
-DIRISA operates two object stores:
-  * [[http://irods.org|iRODS]] is an acronym for  Integrated Rule-Oriented Data System
-  * The Long Term Archive (LTA) is a tape-based system
-These storage systems can be accessed by way of DIRISA's web-based [[https://www.dirisa.ac.za/deposit-data/|Data Deposit Tool]].
+===== 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.]]
@@ Line 51: / Line 106: @@
 ===== 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.
@@ Line 62: / Line 121: @@
   *[[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]]
@@ Line 72: / Line 132: @@
   *[[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 =====
@@ Line 142: / Line 203: @@
   *[[p4vasp|Using p4vasp]]
   *[[vesta|Using Vesta]]
+===== Matlab at CHPC =====
+  *[[matlab|Using Matlab on the cluster]]
 ===== Earth Sciences =====
@@ Line 148: / Line 213: @@
   *[[CDO|Using Climate Data Operator (CDO)]]
+===== Windows applications =====
+  *[[windows|Running Windows applications]]

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