If you have never used a Cluster, or are not familiar with this cluster, YOU WILL WANT to read and follow the examples in the document to become familiar with how to run jobs on HPC. It is a common practice for new users to ignore this manual and simply try to run jobs without understanding what they are doing. Such carelessness can and WILL easily impact hundreds/thousands of critical jobs and users currently running on the cluster.
If your actions compromise the health of the HPC cluster, your account will be LOCKED so please make sure you run through the examples below before you embark on running jobs. Some important remarks to avoid this:
Using a High Performance Computing Cluster such as the HPC Cluster requires at a minimum some basic understanding of the Linux Operating System. It is outside the scope of this manual to explain Linux commands and/or how parallel programs such as MPI work. This manual (replace this with this page) simply explains how to run jobs on the HPC cluster.
When you login to HPC you are connected to what is called a login node. The HPC Cluster has several major components:
● Login nodes: The login nodes are meant for simple tasks such as submitting jobs, checking on job status, editing (emacs, vi), and performing simple tasks.
● A Head node: The head node runs all of the cluster critical services.
● Compute nodes: The compute nodes are the workhorse of the cluster. For
computational work both Serial or Parallel, in Batch mode or Interactive
mode, you will be using the compute nodes.
(Add how to use them in these different modes.)
Use a secure shell client, e.g. MobaXterm
1) Here is the direct link to download the mobaxterm program
2) Once you have mobaxterm installed follow this guide
Note if you have cygwin installed, you can open a cygwin-terminal and then use ssh the same as for Linux and
If you aren’t sure what cygwin is, you can safely ignore the above line.
Use ssh on the command line
Note: Username is your HPC username
Use MobaXterm. This is a GUI-based scp client for MS Windows-based computers that has a drag-and-drop
facility and an inbuilt file editor. If you have cygwin installed, you can open a cygwin-terminal and then use ssh the
same as Linux and Mac below.
● Download MobaXterm
Use the scp on the command line
scp file-to-name USERNAME@login.kuacc.ku.edu.tr:/HOME_DIR/SUB_FOLDER/new-filename
This will copy the file to a SUB_FOLDER and renaming it to new-filename
The script is submitted to the job management system (queueing system) and if the requested resources
(processors, memory, etc) are available on the system, the job will by run.
If not, it will be placed in a queue until such time as the resources do become available. In order to provide a fair share of the resources among users, the priority of jobs in the queue may be varied based on how much resources someone has used, so it is possible that jobs may not run in the order in which they have been submitted to the queue.
Jobs are submitted to the system with the command below:
See the page about SLURM Queueing System Commands for more information on creating job submission scripts.
The job flags are used with SBATCH command. The syntax for the SLURM directive in a script is “#SBATCH<flag>”. Some of the flags are used with the srun and salloc commands, as well for interactive jobs.
If your problem is in any topic listed above, then It is very important that you read the document and watch the video.
Alternatively you can sent an email to IT@ku.edu.tr this will create a support ticket automatically.
When reporting problems, please give as much information as you can to help us in diagnosis, for example:
● Your username
● Queue/partition name
● Job ID(s)
● A copy of any error messages
● Command used to submit the job(s)
● Path(s) to scripts called by the submission command
● Path(s) to output files from your jobs
● When the problem occurred
● What commands or programs you were trying to execute at the time
● A pointer to the program you were trying to run or compile