Difference between revisions of "Kennedy manual"

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====slurm commands====
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*[[quick start]]
  
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#[[creating ssh keys and logging on]]
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#[[logging on to Kennedy]]
  
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Temporary quick start info can be found here. This is a work in progress until something official is made up.
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*[[pull and push to to and from MARVIN]]
  
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https://github.com/peterthorpe5/How_to_use_Kennedy_HPC
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*[[filezilla data transfer]]
  
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*[[slurm commands]]
  
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The following are command line commands, or tags you can put in your shell script to achieve certain functionality.
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*[[submit a job and monitor queues]]
  
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request_48_thread_1.3TBRAM
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*[[samba like connection]]
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#!/bin/bash -l  '''# not the -l is essential now'''
 
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#SBATCH -J fly_pilon  #jobname
 
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#SBATCH -N 1    #node
 
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#SBATCH --ntasks-per-node=48
 
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#SBATCH --threads-per-core=2
 
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#SBATCH -p bigmem
 
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#SBATCH --nodelist=kennedy150  # this is the specific node. This one has 1.5TB RAM
 
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#SBATCH --mem=1350GB
 
  
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*[[Conda]]
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CONDA: http://stab.st-andrews.ac.uk/wiki/index.php/Conda#conda
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Training: github.com/peterthorpe5/Sys_admin/tree/master/cluster_course
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Note: on Kennedy, you may need to make programs executable to run. This is a know bug. Locate where the install have just gone, move to that directory and run
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chmod u+x prog(s)_of_interest. often in th elib folder
  
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test_conda_activate
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The error that indicates this kind of error is:
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#!/bin/bash -l
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  libptf77blas.so.3: '''cannot open shared object file
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#SBATCH -J conda_test  #jobname
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'''
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#SBATCH -N 1    #node
 
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#SBATCH --tasks-per-node=1
 
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#SBATCH -p bigmem    # big mem if for the BIOINF community
 
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#SBATCH --mail-type=END    # email at the end of the job
 
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  #SBATCH --mail-user=$USER@st-andrews.ac.uk      # your email address
 
  
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cd /gpfs1/home/$USER/
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==syntax highlighting in Nano==
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do the following
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pyv="$(python -V 2>&1)"
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  cp /gpfs1/apps/kennedy_sys_admin/misc/.nanorc ./
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echo "$pyv"
 
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# conda to activate the software
 
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echo $PATH
 
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conda activate spades
 
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pyv="$(python -V 2>&1)"
 
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echo "$pyv"
 
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conda deactivate
 
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conda activate python27
 
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pyv="$(python2 -V 2>&1)"
 
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echo "$pyv"
 
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  12threads_bigMeme_30G_RAM
 
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!/bin/bash -l  # essential
 
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#SBATCH -J trimmo  #jobname
 
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#SBATCH -N 1    #node
 
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#SBATCH --ntasks-per-node=12
 
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#SBATCH --threads-per-core=2
 
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#SBATCH -p bigmem
 
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#SBATCH --mem=30GB
 

Latest revision as of 11:48, 7 May 2020

  1. creating ssh keys and logging on
  2. logging on to Kennedy
CONDA: http://stab.st-andrews.ac.uk/wiki/index.php/Conda#conda
Training: github.com/peterthorpe5/Sys_admin/tree/master/cluster_course

Note: on Kennedy, you may need to make programs executable to run. This is a know bug. Locate where the install have just gone, move to that directory and run 

chmod u+x prog(s)_of_interest. often in th elib folder

The error that indicates this kind of error is: 

libptf77blas.so.3: cannot open shared object file

syntax highlighting in Nano

do the following 

cp /gpfs1/apps/kennedy_sys_admin/misc/.nanorc ./
Retrieved from "http://stab.st-andrews.ac.uk/wiki/index.php?title=Kennedy_manual&oldid=3495"