Difference between revisions of "JUSTUS2/Getting Started"
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+ | <!-- |
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+ | Here is a short list of things you may need to do first when you get onto the cluster |
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+ | == Basics == |
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+ | * log in to the cluster: [[JUSTUS2/Login]] |
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+ | * get accustomed with the linux commandline: |
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+ | ** [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC/The_Command_Line introduction on the (external) hpc wiki] or |
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+ | ** linux course at [https://training.bwhpc.de/ training.bwhpc.de] |
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+ | == Running an Example with Preinstalled Software == |
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+ | * scientific software: read on how to load [[Software Modules]] |
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+ | * continue reading until you found that there are example job scripts: [[Environment_Modules#Software_job_examples]] |
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+ | * submit a sample job from a software as mentioned in the job example. Also see: [[JUSTUS2/Slurm]] |
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+ | * monitor your job: [[JUSTUS2/Slurm#Monitoring_Your_Jobs]] |
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+ | == Running Your Own Calculations == |
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+ | * transfer your own data to the cluster: [[Data Transfer]] |
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+ | * adapt the sample job script to run your own job |
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+ | Note that your jobs should not write/read much on the lustre filesystem while the job runs, but either use the ram disk in /tmp or request /scratch if the space of the ram disk isn't sufficient. The [[BwForCluster_JUSTUS_2_Slurm_HOWTO#How_to_clean-up_or_save_files_before_a_job_times_out.3F| Slurm Howto]] shows how to copy and clean up your data from /tmp or /scratch at the end of the job |
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+ | --> |
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+ | == General Workflow of Running a Calculation == |
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+ | On a compute cluster, you do not simply run log in and your software, but you write a "job script" that contains all commands to run and process your job and send this into a waiting queue to be run on one of several hundred computers. |
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− | * [[JUSTUS2/Login|log in]] to the cluster |
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+ | |||
− | * read on how to load [[Software Modules]] |
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+ | How this is done is described in a little more detail here: [[Running Calculations]] |
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− | * continue until you reached [[Environment_Modules#Software_job_examples]] |
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+ | |||
− | * submit a sample job from a software as mentioned there |
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+ | == Get access to the cluster == |
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+ | |||
+ | Follow the registration process for the bwForCluster. → [[Registration/bwForCluster|How to Register for a bwForCluster]] |
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+ | |||
+ | == Login to the Cluster == |
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+ | |||
+ | Setup service password and 2FA token and login to the cluster. → [[JUSTUS2/Login|Login JUSTUS2]] |
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+ | |||
+ | == Get Accustomed with the Linux Commandline == |
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+ | |||
+ | HPC Wiki (external site) → [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC/The_Command_Line Introduction to Linux Commandline] |
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+ | |||
+ | Training course → [https://training.bwhpc.de/ Linux course on training.bwhpc.de] |
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+ | |||
+ | == Transfer your data to the cluster == |
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+ | |||
+ | Get familiar with available file systems on the cluster. → [[Hardware_and_Architecture_(bwForCluster_JUSTUS_2)#Storage_Architecture|File Systems]] |
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+ | |||
+ | Transfer your data to the cluster using appropriate tools. → [[Data Transfer|Data Transfer]] |
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+ | |||
+ | == Find information about installed software and examples == |
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+ | |||
+ | Compiler, Libraries and application software are provided as software modules. Learn how to work with |
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+ | [[Environment_Modules|software modules]]. → [[JUSTUS2/Software|Software]] |
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+ | <!-- Overview of available software modules → [https://www.bwhpc.de/software.php https://www.bwhpc.de/software.php], select <code>Cluster → bwForCluster JUSTUS 2</code> --> |
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+ | |||
+ | Run sample script from a pre-installed software (Software job examples in the page above) |
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+ | |||
+ | == Submit your application as a batch job == |
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+ | |||
+ | Get familiar with available nodes types on the cluster. → [[Hardware_and_Architecture_(bwForCluster_JUSTUS_2)|Hardware and Architecture]] |
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+ | |||
+ | Submit and monitor your jobs with Slurm commands. |
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+ | * → [[JUSTUS2/Running Your Calculations|Running Your Calculations]] - a very brief introduction. |
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+ | * → [[BwForCluster_JUSTUS_2_Slurm_HOWTO| extensive Slurm HOWTO on specific tasks]] |
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+ | |||
+ | == Acknowledge the cluster == |
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+ | |||
+ | Remember to mention the cluster in your publications. → [[bwForCluster JUSTUS 2 Acknowledgement|Acknowledgement]] |
Latest revision as of 21:10, 6 May 2024
Contents
1 General Workflow of Running a Calculation
On a compute cluster, you do not simply run log in and your software, but you write a "job script" that contains all commands to run and process your job and send this into a waiting queue to be run on one of several hundred computers.
How this is done is described in a little more detail here: Running Calculations
2 Get access to the cluster
Follow the registration process for the bwForCluster. → How to Register for a bwForCluster
3 Login to the Cluster
Setup service password and 2FA token and login to the cluster. → Login JUSTUS2
4 Get Accustomed with the Linux Commandline
HPC Wiki (external site) → Introduction to Linux Commandline
Training course → Linux course on training.bwhpc.de
5 Transfer your data to the cluster
Get familiar with available file systems on the cluster. → File Systems
Transfer your data to the cluster using appropriate tools. → Data Transfer
6 Find information about installed software and examples
Compiler, Libraries and application software are provided as software modules. Learn how to work with software modules. → Software
Run sample script from a pre-installed software (Software job examples in the page above)
7 Submit your application as a batch job
Get familiar with available nodes types on the cluster. → Hardware and Architecture
Submit and monitor your jobs with Slurm commands.
- → Running Your Calculations - a very brief introduction.
- → extensive Slurm HOWTO on specific tasks
8 Acknowledge the cluster
Remember to mention the cluster in your publications. → Acknowledgement