clustering/Makefile

   1 #srun_cdsc='srun -p comdata-int -A comdata --time=300:00:00 --time-min=00:15:00 --mem=100G --ntasks=1 --cpus-per-task=28'
   2 srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh
   3 similarity_data=/gscratch/comdata/output/reddit_similarity
   4 clustering_data=/gscratch/comdata/output/reddit_clustering
   5 kmeans_selection_grid=--max_iters=[3000] --n_inits=[10] --n_clusters=[100,500,1000,1250,1500,1750,2000]
   6 hdbscan_selection_grid=--min_cluster_sizes=[2,3,4,5] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf]
   7 affinity_selection_grid=--dampings=[0.5,0.6,0.7,0.8,0.95,0.97,0.99] --preference_quantiles=[0.1,0.3,0.5,0.7,0.9] --convergence_iters=[15]
   8
   9 authors_10k_input=$(similarity_data)/subreddit_comment_authors_10k.feather
  10 authors_10k_input_lsi=$(similarity_data)/subreddit_comment_authors_10k_LSI
  11 authors_10k_output=$(clustering_data)/subreddit_comment_authors_10k
  12 authors_10k_output_lsi=$(clustering_data)/subreddit_comment_authors_10k_LSI
  13
  14 authors_tf_10k_input=$(similarity_data)/subreddit_comment_authors-tf_10k.feather
  15 authors_tf_10k_input_lsi=$(similarity_data)/subreddit_comment_authors-tf_10k_LSI
  16 authors_tf_10k_output=$(clustering_data)/subreddit_comment_authors-tf_10k
  17 authors_tf_10k_output_lsi=$(clustering_data)/subreddit_comment_authors-tf_10k_LSI
  18
  19 terms_10k_input=$(similarity_data)/subreddit_comment_terms_10k.feather
  20 terms_10k_input_lsi=$(similarity_data)/subreddit_comment_terms_10k_LSI
  21 terms_10k_output=$(clustering_data)/subreddit_comment_terms_10k
  22 terms_10k_output_lsi=$(clustering_data)/subreddit_comment_terms_10k_LSI
  23
  24 all:terms_10k authors_10k authors_tf_10k terms_10k_lsi authors_10k_lsi authors_tf_10k_lsi
  25
  26 terms_10k:${terms_10k_output}/kmeans/selection_data.csv ${terms_10k_output}/affinity/selection_data.csv ${terms_10k_output}/hdbscan/selection_data.csv
  27
  28 authors_10k:${authors_10k_output}/kmeans/selection_data.csv ${authors_10k_output}/hdbscan/selection_data.csv ${authors_10k_output}/affinity/selection_data.csv
  29
  30 authors_tf_10k:${authors_tf_10k_output}/kmeans/selection_data.csv ${authors_tf_10k_output}/hdbscan/selection_data.csv ${authors_tf_10k_output}/affinity/selection_data.csv
  31
  32 terms_10k_lsi:${terms_10k_output_lsi}/kmeans/selection_data.csv ${terms_10k_output_lsi}/affinity/selection_data.csv ${terms_10k_output_lsi}/hdbscan/selection_data.csv
  33
  34 authors_10k_lsi:${authors_10k_output_lsi}/kmeans/selection_data.csv ${authors_10k_output_lsi}/hdbscan/selection_data.csv ${authors_10k_output_lsi}/affinity/selection_data.csv
  35
  36 authors_tf_10k_lsi:${authors_tf_10k_output_lsi}/kmeans/selection_data.csv ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv ${authors_tf_10k_output_lsi}/affinity/selection_data.csv
  37
  38 ${authors_10k_output}/kmeans/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py kmeans_clustering.py
  39         $(srun_singularity) python3 kmeans_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/kmeans --savefile=${authors_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid)
  40
  41 ${terms_10k_output}/kmeans/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py kmeans_clustering.py
  42         $(srun_singularity) python3 kmeans_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/kmeans  --savefile=${terms_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid)
  43
  44 ${authors_tf_10k_output}/kmeans/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py kmeans_clustering.py
  45         $(srun_singularity) python3 kmeans_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/kmeans --savefile=${authors_tf_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid)
  46
  47 ${authors_10k_output}/affinity/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py affinity_clustering.py
  48         $(srun_singularity) python3 affinity_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/affinity --savefile=${authors_10k_output}/affinity/selection_data.csv $(affinity_selection_grid)
  49
  50 ${terms_10k_output}/affinity/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py affinity_clustering.py
  51         $(srun_singularity) python3 affinity_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/affinity  --savefile=${terms_10k_output}/affinity/selection_data.csv $(affinity_selection_grid)
  52
  53 ${authors_tf_10k_output}/affinity/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py affinity_clustering.py
  54         $(srun_singularity) python3 affinity_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/affinity --savefile=${authors_tf_10k_output}/affinity/selection_data.csv $(affinity_selection_grid)
  55
  56 ${authors_10k_output}/hdbscan/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py hdbscan_clustering.py
  57         $(srun_singularity) python3 hdbscan_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/hdbscan --savefile=${authors_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
  58
  59 ${terms_10k_output}/hdbscan/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py hdbscan_clustering.py
  60         $(srun_singularity) python3 hdbscan_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/hdbscan  --savefile=${terms_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
  61
  62 ${authors_tf_10k_output}/hdbscan/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py hdbscan_clustering.py
  63         $(srun_singularity) python3 hdbscan_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/hdbscan --savefile=${authors_tf_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
  64
  65
  66 ## LSI Models
  67 ${authors_10k_output_lsi}/kmeans/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py kmeans_clustering.py
  68         $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/kmeans --savefile=${authors_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid)
  69
  70 ${terms_10k_output_lsi}/kmeans/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py kmeans_clustering.py
  71         $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/kmeans  --savefile=${terms_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid)
  72
  73 ${authors_tf_10k_output_lsi}/kmeans/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py kmeans_clustering.py
  74         $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/kmeans --savefile=${authors_tf_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid)
  75
  76 ${authors_10k_output_lsi}/affinity/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py affinity_clustering.py
  77         $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/affinity --savefile=${authors_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid)
  78
  79 ${terms_10k_output_lsi}/affinity/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py affinity_clustering.py
  80         $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/affinity  --savefile=${terms_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid)
  81
  82 ${authors_tf_10k_output_lsi}/affinity/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py affinity_clustering.py
  83         $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/affinity --savefile=${authors_tf_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid)
  84
  85 ${authors_10k_output_lsi}/hdbscan/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py hdbscan_clustering.py
  86         $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/hdbscan --savefile=${authors_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
  87
  88 ${terms_10k_output_lsi}/hdbscan/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py hdbscan_clustering.py
  89         $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/hdbscan  --savefile=${terms_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
  90
  91 ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py hdbscan_clustering.py
  92         $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/hdbscan --savefile=${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid)
  93
  94 ${terms_10k_output_lsi}/best_hdbscan.feather:${terms_10k_output_lsi}/hdbscan/selection_data.csv pick_best_clustering.py
  95         $(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2
  96
  97 ${authors_tf_10k_output_lsi}/best_hdbscan.feather:${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv pick_best_clustering.py
  98         $(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2
  99
 100 clean_affinity:
 101         rm -f ${authors_10k_output}/affinity/selection_data.csv
 102         rm -f ${authors_tf_10k_output}/affinity/selection_data.csv
 103         rm -f ${terms_10k_output}/affinity/selection_data.csv
 104
 105 clean_kmeans:
 106         rm -f ${authors_10k_output}/kmeans/selection_data.csv
 107         rm -f ${authors_tf_10k_output}/kmeans/selection_data.csv
 108         rm -f ${terms_10k_output}/kmeans/selection_data.csv
 109
 110 clean_hdbscan:
 111         rm -f ${authors_10k_output}/hdbscan/selection_data.csv
 112         rm -f ${authors_tf_10k_output}/hdbscan/selection_data.csv
 113         rm -f ${terms_10k_output}/hdbscan/selection_data.csv
 114
 115 clean_authors:
 116         rm -f ${authors_10k_output}/affinity/selection_data.csv
 117         rm -f ${authors_10k_output}/kmeans/selection_data.csv
 118         rm -f ${authors_10k_output}/hdbscan/selection_data.csv
 119
 120 clean_authors_tf:
 121         rm -f ${authors_tf_10k_output}/affinity/selection_data.csv
 122         rm -f ${authors_tf_10k_output}/kmeans/selection_data.csv
 123         rm -f ${authors_tf_10k_output}/hdbscan/selection_data.csv
 124
 125 clean_terms:
 126         rm -f ${terms_10k_output}/affinity/selection_data.csv
 127         rm -f ${terms_10k_output}/kmeans/selection_data.csv
 128         rm -f ${terms_10k_output}/hdbscan/selection_data.csv
 129
 130 clean_lsi_affinity:
 131         rm -f ${authors_10k_output_lsi}/affinity/selection_data.csv
 132         rm -f ${authors_tf_10k_output_lsi}/affinity/selection_data.csv
 133         rm -f ${terms_10k_output_lsi}/affinity/selection_data.csv
 134
 135 clean_lsi_kmeans:
 136         rm -f ${authors_10k_output_lsi}/kmeans/selection_data.csv
 137         rm -f ${authors_tf_10k_output_lsi}/kmeans/selection_data.csv
 138         rm -f ${terms_10k_output_lsi}/kmeans/selection_data.csv
 139
 140 clean_lsi_hdbscan:
 141         rm -f ${authors_10k_output_lsi}/hdbscan/selection_data.csv
 142         rm -f ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv
 143         rm -f ${terms_10k_output_lsi}/hdbscan/selection_data.csv
 144
 145 clean_lsi_authors:
 146         rm -f ${authors_10k_output_lsi}/affinity/selection_data.csv
 147         rm -f ${authors_10k_output_lsi}/kmeans/selection_data.csv
 148         rm -f ${authors_10k_output_lsi}/hdbscan/selection_data.csv
 149
 150 clean_lsi_authors_tf:
 151         rm -f ${authors_tf_10k_output_lsi}/affinity/selection_data.csv
 152         rm -f ${authors_tf_10k_output_lsi}/kmeans/selection_data.csv
 153         rm -f ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv
 154
 155 clean_lsi_terms:
 156         rm -f ${terms_10k_output_lsi}/affinity/selection_data.csv
 157         rm -f ${terms_10k_output_lsi}/kmeans/selection_data.csv
 158         rm -f ${terms_10k_output_lsi}/hdbscan/selection_data.csv
 159
 160 clean: clean_affinity clean_kmeans clean_hdbscan
 161
 162 PHONY: clean clean_affinity clean_kmeans clean_hdbscan clean_authors clean_authors_tf clean_terms terms_10k authors_10k authors_tf_10k
 163
 164 # $(clustering_data)/subreddit_comment_authors_30k.feather/SUCCESS:selection.py $(similarity_data)/subreddit_comment_authors_30k.feather clustering.py
 165 #       $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors_30k.feather $(clustering_data)/subreddit_comment_authors_30k $(selection_grid) -J 10 && touch $(clustering_data)/subreddit_comment_authors_30k.feather/SUCCESS
 166
 167 # $(clustering_data)/subreddit_comment_terms_30k.feather/SUCCESS:selection.py $(similarity_data)/subreddit_comment_terms_30k.feather clustering.py
 168 #       $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_terms_30k.feather $(clustering_data)/subreddit_comment_terms_30k $(selection_grid) -J 10 && touch $(clustering_data)/subreddit_comment_terms_30k.feather/SUCCESS
 169
 170 # $(clustering_data)/subreddit_authors-tf_similarities_30k.feather/SUCCESS:clustering.py $(similarity_data)/subreddit_comment_authors-tf_30k.feather
 171 #       $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors-tf_30k.feather $(clustering_data)/subreddit_comment_authors-tf_30k $(selection_grid) -J 8 && touch $(clustering_data)/subreddit_authors-tf_similarities_30k.feather/SUCCESS
 172
 173
 174 # $(clustering_data)/subreddit_comment_authors_100k.feather:clustering.py $(similarity_data)/subreddit_comment_authors_100k.feather
 175 #        $(srun_singularity) python3 clustering.py $(similarity_data)/subreddit_comment_authors_100k.feather $(clustering_data)/subreddit_comment_authors_100k.feather ---max_iter=400 --convergence_iter=15 --preference_quantile=0.85 --damping=0.85
 176
 177 # $(clustering_data)/comment_terms_100k.feather:clustering.py $(similarity_data)/subreddit_comment_terms_100k.feather
 178 #       $(srun_singularity) python3 clustering.py $(similarity_data)/comment_terms_10000.feather $(clustering_data)/comment_terms_10000.feather ---max_iter=1000 --convergence_iter=15 --preference_quantile=0.9 --damping=0.5
 179
 180 # $(clustering_data)/subreddit_comment_author-tf_100k.feather:clustering.py $(similarity_data)/subreddit_comment_author-tf_100k.feather
 181 #       $(srun_singularity) python3 clustering.py $(similarity_data)/subreddit_comment_author-tf_100k.parquet $(clustering_data)/subreddit_comment_author-tf_100k.feather ---max_iter=400 --convergence_iter=15 --preference_quantile=0.5 --damping=0.85
 182
 183
 184 # it's pretty difficult to get a result that isn't one huge megacluster. A sign that it's bullcrap
 185 # /gscratch/comdata/output/reddit_clustering/wang_similarity_10000.feather:clustering.py /gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather
 186 #       ./clustering.py /gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather /gscratch/comdata/output/reddit_clustering/wang_similarity_10000.feather ---max_iter=400 --convergence_iter=15 --preference_quantile=0.9 --damping=0.85
 187
 188 # /gscratch/comdata/output/reddit_tsne/subreddit_author_tf_similarities_10000.feather:fit_tsne.py /gscratch/comdata/output/reddit_similarity/subreddit_author_tf_similarities_10000.parquet
 189
 190 #       start_spark_and_run.sh 1 fit_tsne.py --similarities=/gscratch/comdata/output/reddit_similarity/subreddit_author_tf_similarities_10000.parquet --output=/gscratch/comdata/output/reddit_tsne/subreddit_author_tf_similarities_10000.feather
 191
 192
 193 # /gscratch/comdata/output/reddit_tsne/wang_similarity_10000.feather:fit_tsne.py /gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather
 194
 195 #       python3 fit_tsne.py --similarities=/gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather --output=/gscratch/comdata/output/reddit_tsne/wang_similarity_10000.feather
 196
 197 # /gscratch/comdata/output/reddit_tsne/comment_authors_10000.feather:clustering.py /gscratch/comdata/output/reddit_similarity/comment_authors_10000.feather
 198 # #     $srun_cdsc python3
 199 #       start_spark_and_run.sh 1 fit_tsne.py --similarities=/gscratch/comdata/output/reddit_similarity/comment_authors_10000.feather --output=/gscratch/comdata/output/reddit_tsne/comment_authors_10000.feather