Command Line Interface
Users interact with an HPC system through a command line interface (CLI), there are... y this is especially true for Unix-like operating systems like Linux, because for the typically Linux based cluster systems graphical user interfaces (GUIs) are rarely avai... The secure shell is a prerequisite for using HPC systems, because it is needed to log in, and to copy fil
Queuing-System (SLURM) and Jobfiles
Target audience: Beginners in Environmental Modules and the Queuing-System SLURM
Important info:
Big parts of this script wa... to how to use Environment Modules, a widely used system for handling different software environments (bas... b submission and cancellation
Monitoring job and system information
Retrieving accounting information
J
e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
NAMD ... igh-performance simulations of large biomolecular systems using force fields.
LAMMPS - A parallel, clas... als, soft matter and coarse-grained or mesoscopic systems.
LIGGGHTS - An Open Source Discrete Element M... age.
GOMC - A software for simulating molecular systems using the Metropolis Monte Carlo algorithm.
To
ten, sind einige wenige Grundkenntnisse mit Linux-System erforderlich.
Zur Arbeit auf dem Cluster stellen ... ystem
Auf dem Phoenix ist das Environment Modules System (kurz Modules) installiert.
Module verändern/erwe... ###############
cat << EOF > ${env_file}
mp_file_system = (DETECT,DETECT)
EOF
node_list=$(scontrol show ... ster you will need a little experience with Linux systems.
At first you need to connect via SSH to userna
ween the user's home computer and the server file system. This can be done by navigating through a graphic... ample dragging and dropping files into their file-system on the server.
WinSCP therefore provides an easy... files to the server
You should now see the file system of your local machine on the left and the content... d ExampleJob.job and upload it to our remote file system. The jobfile, which does nothing at all, looks as