JUSTUS2/Getting Started: Difference between revisions
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Here is a short list of things you may need to do first when you get onto the cluster |
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]] |
* log in to the cluster: [[JUSTUS2/Login]] |
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* get accustomed with the linux commandline: |
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* get accustomed with the linux commandline: [https://www.uni-ulm.de/?id=linux-ex1 exercises1] [https://www.uni-ulm.de/?id=linux-ex2 exercises2] [https://www.uni-ulm.de/?id=linux-ex1 exercises3] or linux course at [https://training.bwhpc.de/ training.bwhpc.de] |
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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]] |
* 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]] |
* 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]] |
* 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]] |
* 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]] |
* transfer your own data to the cluster: [[Data Transfer]] |
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* adapt the sample job script to run your own job |
* 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 |
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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== 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. → [[JUSTUS2/Slurm|Batch System Slurm]] |
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== Acknowledge the cluster == |
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Remember to mention the cluster in your publications. → [[bwForCluster JUSTUS 2 Acknowledgement|Acknowledgement]] |
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Revision as of 09:58, 22 May 2023
Get access to the cluster
Follow the registration process for the bwForCluster. → How to Register for a bwForCluster
Login to the Cluster
Setup service password and 2FA token and login to the cluster. → Login JUSTUS2
Get Accustomed with the Linux Commandline
HPC Wiki (external site) → Introduction to Linux Commandline
Training course → Linux course on training.bwhpc.de
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
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)
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. → Batch System Slurm
Acknowledge the cluster
Remember to mention the cluster in your publications. → Acknowledgement