OBM Clusters
Contents
Getting started
Get an account
Connect to our workstations
On nodes and files
Run a program
Guidelines for use of computer equipment at the METU Physics department
Definitions
Purpose
Application
Good Faith
Data Safety
Respect for Other Users Privacy
Proper Use
Awareness of the Purposes for Use of Resources
Rights
Liability
Surveillance
Sanctions
Complaints
Resources
Workstations
Overview
Individual Workstation information
Single Board Computers
Overview
Account
Getting an account
Getting started on the machine (account, quota, password)
How to get an account and a CPU quota
Logging in for the first time
First-time setup
Log in with SSH
Obtain a new password
Quotas
Jobs
Dos and don’ts
Batch system
Creating a job script
How to pass command-line parameters to the job script
Walltime
Job script examples
Basic examples
OpenMP and MPI
SLURM Workload Manager
SLURM Parameter
Differences between CPUs and tasks
Settings for OpenMP and MPI jobs
Job related environment variables
Partitions (queues) and services
General job limitations
Interactive jobs
Starting an interacitve job
Keeping interactive jobs alive
Managing jobs
Job status descriptions in squeue
Monitoring your jobs
SLURM commands
CPU load and memory consumption of your job
Running MPI jobs
Intel MPI
OpenMPI
Software
Which software is installed on our cluster
Changes in application software
Missing or new software
Conda
Software Module Scheme
Which modules are currently loaded?
Which modules are available?
How to load a module
How to unload a module
Which version of a module is the default?
How do I switch to a different version of a module?
Python, R, Matlab and Perl
Python
MATLAB
Linux command line
New on Linux systems?
General comments about licenses
Application guides
Quantum Espresso
VASP (Vienna Ab initio Simulation Package)
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS)
Storage
Storage and backup
Available file system
Home area
NAS area
Work/scratch areas
Closing of user account
Privacy of user data
Management of many small files (> 10000)
Compression of data
Binary data and endianness
Transferring files to/from our group cluster
Carbon (Head node and home directories)
Mistake Not… (NAS server)
Code development
Compilers
Usage of the Intel ifort compiler
Usage of the Intel C/C++ compilers
Usage of the NVIDIA (PGI) compilers
Environment modules
Index