X-Git-Url: https://code.communitydata.science/cdsc_reddit.git/blobdiff_plain/14ab979f5910637809dec24617276eb7bd0d9554..9345f9de9437d5965ad4ee5874bc24199e077d48:/clustering/Makefile diff --git a/clustering/Makefile b/clustering/Makefile index 338f0a6..7ecefcd 100644 --- a/clustering/Makefile +++ b/clustering/Makefile @@ -1,55 +1,36 @@ -#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' -srun_singularity=source /gscratch/comdata/users/nathante/cdsc_reddit/bin/activate && srun_singularity.sh -similarity_data=/gscratch/comdata/output/reddit_similarity -clustering_data=/gscratch/comdata/output/reddit_clustering -selection_grid="--max_iter=3000 --convergence_iter=15,30,100 --damping=0.5,0.6,0.7,0.8,0.85,0.9,0.95,0.97,0.99, --preference_quantile=0.1,0.3,0.5,0.7,0.9" -#selection_grid="--max_iter=3000 --convergence_iter=[15] --preference_quantile=[0.5] --damping=[0.99]" -all:$(clustering_data)/subreddit_comment_authors_10k/selection_data.csv $(clustering_data)/subreddit_comment_authors-tf_10k/selection_data.csv $(clustering_data)/subreddit_comment_terms_10k/selection_data.csv -# $(clustering_data)/subreddit_comment_authors_30k.feather/SUCCESS $(clustering_data)/subreddit_authors-tf_similarities_30k.feather/SUCCESS -# $(clustering_data)/subreddit_comment_terms_30k.feather/SUCCESS +srun_singularity=srun -p compute-bigmem -A comdata --time=48:00:00 --mem=362G -c 40 /bin/bash -c +similarity_data=../../data/reddit_similarity +clustering_data=../../data/reddit_clustering +kmeans_selection_grid=--max_iters=[3000] --n_inits=[10] --n_clusters=[100,500,1000,1250,1500,1750,2000] +hdbscan_selection_grid=--min_cluster_sizes=[2,3,4,5] --min_samples=[2,3,4,5] --cluster_selection_epsilons=[0,0.01,0.05,0.1,0.15,0.2] --cluster_selection_methods=[eom,leaf] +affinity_selection_grid=--dampings=[0.5,0.6,0.7,0.8,0.95,0.97,0.99] --preference_quantiles=[0.1,0.3,0.5,0.7,0.9] --convergence_iters=[15] -$(clustering_data)/subreddit_comment_authors_10k/selection_data.csv:selection.py $(similarity_data)/subreddit_comment_authors_10k.feather clustering.py - $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors_10k.feather $(clustering_data)/subreddit_comment_authors_10k $(clustering_data)/subreddit_comment_authors_10k/selection_data.csv $(selection_grid) -J 20 +authors_tf_10k_input_lsi=$(similarity_data)/subreddit_comment_authors-tf_10k_LSI +authors_tf_10k_output_lsi=$(clustering_data)/subreddit_comment_authors-tf_10k_LSI -$(clustering_data)/subreddit_comment_terms_10k/selection_data.csv:selection.py $(similarity_data)/subreddit_comment_terms_10k.feather clustering.py - $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_terms_10k.feather $(clustering_data)/subreddit_comment_terms_10k $(clustering_data)/subreddit_comment_terms_10k/selection_data.csv $(selection_grid) -J 20 +all:authors_tf_10k_lsi -$(clustering_data)/subreddit_comment_authors-tf_10k/selection_data.csv:clustering.py $(similarity_data)/subreddit_comment_authors-tf_10k.feather - $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors-tf_10k.feather $(clustering_data)/subreddit_comment_authors-tf_10k $(clustering_data)/subreddit_comment_authors-tf_10k/selection_data.csv $(selection_grid) -J 20 +authors_tf_10k_lsi:${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 -# $(clustering_data)/subreddit_comment_authors_30k.feather/SUCCESS:selection.py $(similarity_data)/subreddit_comment_authors_30k.feather clustering.py -# $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_authors_30k.feather $(clustering_data)/subreddit_comment_authors_30k $(selection_grid) -J 10 && touch $(clustering_data)/subreddit_comment_authors_30k.feather/SUCCESS +## LSI Models +${authors_tf_10k_output_lsi}/kmeans/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py kmeans_clustering.py + $(srun_singularity) -c "source ~/.bashrc; python3 kmeans_clustering_lsi.py --inpath=${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)" -# $(clustering_data)/subreddit_comment_terms_30k.feather/SUCCESS:selection.py $(similarity_data)/subreddit_comment_terms_30k.feather clustering.py -# $(srun_singularity) python3 selection.py $(similarity_data)/subreddit_comment_terms_30k.feather $(clustering_data)/subreddit_comment_terms_30k $(selection_grid) -J 10 && touch $(clustering_data)/subreddit_comment_terms_30k.feather/SUCCESS +${authors_tf_10k_output_lsi}/affinity/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py affinity_clustering.py + $(srun_singularity) -c "source ~/.bashrc; python3 affinity_clustering_lsi.py --inpath=${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)" -# $(clustering_data)/subreddit_authors-tf_similarities_30k.feather/SUCCESS:clustering.py $(similarity_data)/subreddit_comment_authors-tf_30k.feather -# $(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 $(clustering_data)/subreddit_authors-tf_similarities_30k.feather/SUCCESS +${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py hdbscan_clustering.py + $(srun_singularity) -c "source ~/.bashrc; python3 hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/hdbscan --savefile=${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid)" +${authors_tf_10k_output_lsi}/best_hdbscan.feather:${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv pick_best_clustering.py + $(srun_singularity) -c "source ~/.bashrc; python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2" -# $(clustering_data)/subreddit_comment_authors_100k.feather:clustering.py $(similarity_data)/subreddit_comment_authors_100k.feather -# $(srun_singularity) python3 clustering.py $(similarity_data)/subreddit_comment_authors_100k.feather $(clustering_data)/subreddit_comment_authors_100k.feather ---max_iter=400 --convergence_iter=15 --preference_quantile=0.85 --damping=0.85 +${authors_tf_10k_input_lsi}: + $(MAKE) -C ../similarities -# $(clustering_data)/comment_terms_100k.feather:clustering.py $(similarity_data)/subreddit_comment_terms_100k.feather -# $(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 +clean: + rm -f ${authors_tf_10k_output_lsi}/affinity/selection_data.csv + rm -f ${authors_tf_10k_output_lsi}/kmeans/selection_data.csv + rm -f ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv -# $(clustering_data)/subreddit_comment_author-tf_100k.feather:clustering.py $(similarity_data)/subreddit_comment_author-tf_100k.feather -# $(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 - - -# it's pretty difficult to get a result that isn't one huge megacluster. A sign that it's bullcrap -# /gscratch/comdata/output/reddit_clustering/wang_similarity_10000.feather:clustering.py /gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather -# ./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 - -# /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 - -# 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 - - -# /gscratch/comdata/output/reddit_tsne/wang_similarity_10000.feather:fit_tsne.py /gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather - -# python3 fit_tsne.py --similarities=/gscratch/comdata/output/reddit_similarity/wang_similarity_10000.feather --output=/gscratch/comdata/output/reddit_tsne/wang_similarity_10000.feather - -# /gscratch/comdata/output/reddit_tsne/comment_authors_10000.feather:clustering.py /gscratch/comdata/output/reddit_similarity/comment_authors_10000.feather -# # $srun_cdsc python3 -# 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 +PHONY: clean