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Jun 19th, 2019
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  1. res <- foreach(i = seq_len(nrow(combs)) %dopar% {
  2. G1 <- split[[combs[i,1]]]
  3. G2 <- split[[combs[i,2]]]
  4. dat.i <- cbind(data[,G1], data[,G2])
  5. rho.i <- cor_rho(dat.i)
  6. }
  7.  
  8. > combs
  9. [,1] [,2]
  10. [1,] 1 2
  11. [2,] 1 3
  12. [3,] 1 4
  13. [4,] 1 5
  14. [5,] 2 3
  15. [6,] 2 4
  16. [7,] 2 5
  17. [8,] 3 4
  18. [9,] 3 5
  19. [10,] 4 5
  20.  
  21. #!/bin/bash
  22. #SBATCH -o job-%A_task.out
  23. #SBATCH --job-name=paral_cor
  24. #SBATCH --partition=normal
  25. #SBATCH --time=1-00:00:00
  26. #SBATCH --mem=126G
  27. #SBATCH --cpus-per-task=32
  28.  
  29. #Set up whatever package we need to run with
  30.  
  31. module load gcc/8.1.0 openblas/0.3.3 R
  32.  
  33. # SET UP DIRECTORIES
  34.  
  35. OUTPUT="$HOME"/$(date +"%Y%m%d")_parallel_nodes_test
  36. mkdir -p "$OUTPUT"
  37.  
  38. export FILENAME=~/RHO_COR.R
  39.  
  40. #Run the program
  41.  
  42. Rscript $FILENAME > "$OUTPUT"
  43.  
  44. for i in my_argument
  45. do Rscript $FILENAME -i > "$OUTPUT"
  46. done
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