Data Movement

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(Job Scripts: Adding instructions for interactive session.)
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==Job Scripts==
 
==Job Scripts==
  
If the data that you are moving is large, then you should always use an interactive session or a job script for your data movement. This ensures that the process for your data movement isn't occupying login nodes for a long time, and instead is performing these operations on a compute node.
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If the data that you are moving is large, then you should always use an interactive session or a job script for your data movement. This ensures that the process for your data movement isn't using and slowing login nodes for a long time, and instead is performing these operations on a compute node.
  
 
===Interactive session===
 
===Interactive session===
 +
 +
* Start an interactive session using srun
 +
<pre>
 +
srun --ntasks=4 --mem-per-cpu=4096 --time=08:00:00 --partition=medium --job-name=JOB_NAME --pty /bin/bash
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</pre>
 +
 +
* Start an rsync process to start the transfer, once you have moved from login001 to c00XX node:
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<pre>
 +
[build@c0051 Salmon]$ rsync -aP SOURCE_PATH DESTINATION_PATH
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</pre>
  
 
===Job Script===
 
===Job Script===
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</pre>
 
</pre>
  
'''NOTE:''' Please change the time required and the corresponding [https://docs.uabgrid.uab.edu/wiki/SLURM#Slurm_Partitions partition] according to your need.
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'''NOTE:'''  
 +
* Please change the time required and the corresponding [https://docs.uabgrid.uab.edu/wiki/SLURM#Slurm_Partitions partition] according to your need.
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* After modifications to the given job script, submit it using : '''sbatch JOB_SCRIPT'''

Revision as of 13:10, 14 December 2016

There are various tools which you can utilize to help you move data within the HPC cluster, such as mv, cp, scp etc. One of the most powerful tools for data movement on Linux is rsync, which we'll be using in our example scripts below.

Contents

Procedure

rr

Job Scripts

If the data that you are moving is large, then you should always use an interactive session or a job script for your data movement. This ensures that the process for your data movement isn't using and slowing login nodes for a long time, and instead is performing these operations on a compute node.

Interactive session

  • Start an interactive session using srun
srun --ntasks=4 --mem-per-cpu=4096 --time=08:00:00 --partition=medium --job-name=JOB_NAME --pty /bin/bash
  • Start an rsync process to start the transfer, once you have moved from login001 to c00XX node:
[build@c0051 Salmon]$ rsync -aP SOURCE_PATH DESTINATION_PATH

Job Script

#!/bin/bash
#
#SBATCH --job-name=test
#SBATCH --output=res.txt
#SBATCH --ntasks=1
#SBATCH --partition=express
#
# Time format = HH:MM:SS, DD-HH:MM:SS
#
#SBATCH --time=10:00
#
# Mimimum memory required per allocated  CPU  in  MegaBytes. 
#
#SBATCH --mem-per-cpu=2048
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=YOUR_EMAIL_ADDRESS

rsync -aP SOURCE_PATH DESTINATION_PATH

NOTE:

  • Please change the time required and the corresponding partition according to your need.
  • After modifications to the given job script, submit it using : sbatch JOB_SCRIPT
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