Difference between revisions of "JUSTUS2/Getting Started"
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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 |
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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| + | == 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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| + | |||
| + | How this is done is described in a little more detail here: [[Running Calculations]] |
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== Get access to the cluster == |
== Get access to the cluster == |
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Follow the registration process for the bwForCluster. → [[Registration/bwForCluster|How to Register for a bwForCluster]] |
Follow the registration process for the bwForCluster. → [[Registration/bwForCluster|How to Register for a bwForCluster]] |
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| − | == Login to the |
+ | == Login to the Cluster == |
Setup service password and 2FA token and login to the cluster. → [[JUSTUS2/Login|Login JUSTUS2]] |
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 == |
== Transfer your data to the cluster == |
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== Find information about installed software and examples == |
== 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 |
+ | Compiler, Libraries and application software are provided as software modules. Learn how to work with |
| + | [[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> --> |
<!-- 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 == |
== 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]] |
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. |
+ | Submit and monitor your jobs with Slurm commands. |
| + | * → [[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 == |
== Acknowledge the cluster == |
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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
