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Logging into the secure cluster

  1. VPN Connection :

  • LINUX:

    vpn connect anyconnect.missouri.edu

    -- Comment : select "vsecure4" VPN

    ssh [email protected]

1.1 Data Location:

ls -alrt /group/socialteam/shared/phi_data

Useful Server Commands

Go do the data directory:

cd /group/socialteam/shared/phi_data

List all the files:

ls /group/socialteam/shared/phi_data

List all the files in order of how recent they are, and with additional info like size and date:

ls -lart /group/socialteam/shared/phi_data

Show the top row of the file

head -1 /group/socialteam/shared/phi_data/[file-name]

SHow the top 10 rows of the file:

head /group/socialteam/shared/phi_data/[file-name]

copy a file so you can add columns, etc.

cp /group/socialteam/shared/phi_data/[file-name] /group/socialteam/shared/phi_data/[NEWFILE]

make a new directory

mkdir /group/socialteam/shared/phi_data/[new-directory-name]

Loading

  1. module avail - lists modules available
  2. module load "R/R-3.3.1"
  • This just loads your path [socialteam.gogginss@src-login ~]$ module load R/R-3.3.1 [socialteam.gogginss@src-login ~]$ echo $PATH /home/cluster/rcss-spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/R-3.3.1-y7hviwqorqpyeetllgchzoin4fzhprvb/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/socialteam.gogginss/.local/bin:/home/socialteam.gogginss/bin
  • r/r-3.4.3 is an R version available, $ module load r/r-3.4.3 should work.
  1. sinfo : provides cluster status (partition, nodes, state and name of nodes)
  2. srun -N3 -n3 -t 0-00:04:00 hostname (this is the worlds fastest ssh)
  • if the nodes are available, please grab them
  • "-N" number of nodes
  • "-n" number of tasks across the notes
  • "-t" time : 0 days, 4 minutes in this example
  • hostname reports back the true hostname of the nodes running the tasks

  1. Interacting with R : To do so interactively

    srun -N 1 --pty R -t 0-00:10:00 --no-save

  • number of nodes,
  • "--pty" : puts the result back to my terminal
  • "R" is "R"
  • "--no-save" : is an R option
  • "-t" : Keep in mind that we are putting our feet on people in the cluster.

  1. Running the job

    sbatch rscript.sh

    Submitted batch job 158

  2. Next Steps

  • sacct

  1. Master data is here:

    /group/socialteam/shared/masterdata_file

SLURM DOCS: http://docs.rnet.missouri.edu/SLURM/slurm