X-Git-Url: https://code.communitydata.science/cdsc_reddit.git/blobdiff_plain/c19079136428953fbfea7f35ad9ffdfc4c574deb..9345f9de9437d5965ad4ee5874bc24199e077d48:/clustering/Makefile?ds=sidebyside diff --git a/clustering/Makefile b/clustering/Makefile index 559a85c..7ecefcd 100644 --- a/clustering/Makefile +++ b/clustering/Makefile @@ -1,218 +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=srun -p compute-bigmem -A comdata --time=48:00:00 --mem=362G -c 40 -similarity_data=/gscratch/comdata/output/reddit_similarity -clustering_data=/gscratch/comdata/output/reddit_clustering +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] - -umap_hdbscan_selection_grid=--min_cluster_sizes=[2] --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] --n_neighbors=[5,15,25,50,75,100] --learning_rate=[1] --min_dist=[0,0.1,0.25,0.5,0.75,0.9,0.99] --local_connectivity=[1] --densmap=[True,False] --n_components=[2,5,10] - 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] -authors_10k_input=$(similarity_data)/subreddit_comment_authors_10k.feather -authors_10k_input_lsi=$(similarity_data)/subreddit_comment_authors_10k_LSI -authors_10k_output=$(clustering_data)/subreddit_comment_authors_10k -authors_10k_output_lsi=$(clustering_data)/subreddit_comment_authors_10k_LSI - -authors_tf_10k_input=$(similarity_data)/subreddit_comment_authors-tf_10k.feather authors_tf_10k_input_lsi=$(similarity_data)/subreddit_comment_authors-tf_10k_LSI -authors_tf_10k_output=$(clustering_data)/subreddit_comment_authors-tf_10k authors_tf_10k_output_lsi=$(clustering_data)/subreddit_comment_authors-tf_10k_LSI -terms_10k_input=$(similarity_data)/subreddit_comment_terms_10k.feather -terms_10k_input_lsi=$(similarity_data)/subreddit_comment_terms_10k_LSI -terms_10k_output=$(clustering_data)/subreddit_comment_terms_10k -terms_10k_output_lsi=$(clustering_data)/subreddit_comment_terms_10k_LSI - -all:terms_10k authors_10k authors_tf_10k terms_10k_lsi authors_10k_lsi authors_tf_10k_lsi - -terms_10k:${terms_10k_output}/kmeans/selection_data.csv ${terms_10k_output}/affinity/selection_data.csv ${terms_10k_output}/hdbscan/selection_data.csv - -authors_10k:${authors_10k_output}/kmeans/selection_data.csv ${authors_10k_output}/hdbscan/selection_data.csv ${authors_10k_output}/affinity/selection_data.csv - -authors_tf_10k:${authors_tf_10k_output}/kmeans/selection_data.csv ${authors_tf_10k_output}/hdbscan/selection_data.csv ${authors_tf_10k_output}/affinity/selection_data.csv - -terms_10k_lsi:${terms_10k_output_lsi}/kmeans/selection_data.csv ${terms_10k_output_lsi}/affinity/selection_data.csv ${terms_10k_output_lsi}/hdbscan/selection_data.csv - -authors_10k_lsi:${authors_10k_output_lsi}/kmeans/selection_data.csv ${authors_10k_output_lsi}/hdbscan/selection_data.csv ${authors_10k_output_lsi}/affinity/selection_data.csv +all:authors_tf_10k_lsi authors_tf_10k_lsi:${authors_tf_10k_output_lsi}/kmeans/selection_data.csv ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv ${authors_tf_10k_output_lsi}/affinity/selection_data.csv -${authors_10k_output}/kmeans/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py kmeans_clustering.py - $(srun_singularity) python3 kmeans_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/kmeans --savefile=${authors_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid) - -${terms_10k_output}/kmeans/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py kmeans_clustering.py - $(srun_singularity) python3 kmeans_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/kmeans --savefile=${terms_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid) - -${authors_tf_10k_output}/kmeans/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py kmeans_clustering.py - $(srun_singularity) python3 kmeans_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/kmeans --savefile=${authors_tf_10k_output}/kmeans/selection_data.csv $(kmeans_selection_grid) - -${authors_10k_output}/affinity/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py affinity_clustering.py - $(srun_singularity) python3 affinity_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/affinity --savefile=${authors_10k_output}/affinity/selection_data.csv $(affinity_selection_grid) - -${terms_10k_output}/affinity/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py affinity_clustering.py - $(srun_singularity) python3 affinity_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/affinity --savefile=${terms_10k_output}/affinity/selection_data.csv $(affinity_selection_grid) - -${authors_tf_10k_output}/affinity/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py affinity_clustering.py - $(srun_singularity) python3 affinity_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/affinity --savefile=${authors_tf_10k_output}/affinity/selection_data.csv $(affinity_selection_grid) - -${authors_10k_output}/hdbscan/selection_data.csv:selection.py ${authors_10k_input} clustering_base.py hdbscan_clustering.py - $(srun_singularity) python3 hdbscan_clustering.py --inpath=${authors_10k_input} --outpath=${authors_10k_output}/hdbscan --savefile=${authors_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid) - -${terms_10k_output}/hdbscan/selection_data.csv:selection.py ${terms_10k_input} clustering_base.py hdbscan_clustering.py - $(srun_singularity) python3 hdbscan_clustering.py --inpath=${terms_10k_input} --outpath=${terms_10k_output}/hdbscan --savefile=${terms_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid) - -${authors_tf_10k_output}/hdbscan/selection_data.csv:clustering.py ${authors_tf_10k_input} clustering_base.py hdbscan_clustering.py - $(srun_singularity) python3 hdbscan_clustering.py --inpath=${authors_tf_10k_input} --outpath=${authors_tf_10k_output}/hdbscan --savefile=${authors_tf_10k_output}/hdbscan/selection_data.csv $(hdbscan_selection_grid) - - ## LSI Models -${authors_10k_output_lsi}/kmeans/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py kmeans_clustering.py - $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/kmeans --savefile=${authors_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid) - -${terms_10k_output_lsi}/kmeans/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py kmeans_clustering.py - $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/kmeans --savefile=${terms_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid) - ${authors_tf_10k_output_lsi}/kmeans/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py kmeans_clustering.py - $(srun_singularity) python3 kmeans_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/kmeans --savefile=${authors_tf_10k_output_lsi}/kmeans/selection_data.csv $(kmeans_selection_grid) - -${authors_10k_output_lsi}/affinity/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py affinity_clustering.py - $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/affinity --savefile=${authors_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid) - -${terms_10k_output_lsi}/affinity/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py affinity_clustering.py - $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/affinity --savefile=${terms_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid) + $(srun_singularity) -c "source ~/.bashrc; python3 kmeans_clustering_lsi.py --inpath=${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)" ${authors_tf_10k_output_lsi}/affinity/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py affinity_clustering.py - $(srun_singularity) python3 affinity_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/affinity --savefile=${authors_tf_10k_output_lsi}/affinity/selection_data.csv $(affinity_selection_grid) - -${authors_10k_output_lsi}/hdbscan/selection_data.csv:selection.py ${authors_10k_input_lsi} clustering_base.py hdbscan_clustering.py - $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${authors_10k_input_lsi} --outpath=${authors_10k_output_lsi}/hdbscan --savefile=${authors_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid) - -${terms_10k_output_lsi}/hdbscan/selection_data.csv:selection.py ${terms_10k_input_lsi} clustering_base.py hdbscan_clustering.py - $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${terms_10k_input_lsi} --outpath=${terms_10k_output_lsi}/hdbscan --savefile=${terms_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid) + $(srun_singularity) -c "source ~/.bashrc; python3 affinity_clustering_lsi.py --inpath=${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)" ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv:clustering.py ${authors_tf_10k_input_lsi} clustering_base.py hdbscan_clustering.py - $(srun_singularity) python3 hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/hdbscan --savefile=${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv $(hdbscan_selection_grid) - -${authors_tf_10k_output_lsi}/umap_hdbscan/selection_data.csv:umap_hdbscan_clustering_lsi.py - $(srun_singularity) python3 umap_hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/umap_hdbscan --savefile=${authors_tf_10k_output_lsi}/umap_hdbscan/selection_data.csv $(umap_hdbscan_selection_grid) - - -${terms_10k_output_lsi}/best_hdbscan.feather:${terms_10k_output_lsi}/hdbscan/selection_data.csv pick_best_clustering.py - $(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2 + $(srun_singularity) -c "source ~/.bashrc; python3 hdbscan_clustering_lsi.py --inpath=${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) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2 - -${authors_tf_10k_output_lsi}/best_umap_hdbscan_2.feather:${authors_tf_10k_output_lsi}/umap_hdbscan/selection_data.csv pick_best_clustering.py - $(srun_singularity) python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2 - -best_umap_hdbscan.feather:${authors_tf_10k_output_lsi}/best_umap_hdbscan_2.feather - -# {'lsi_dimensions': 700, 'outpath': '/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/umap_hdbscan', 'silhouette_score': 0.27616957, 'name': 'mcs-2_ms-5_cse-0.05_csm-leaf_nn-15_lr-1.0_md-0.1_lc-1_lsi-700', 'n_clusters': 547, 'n_isolates': 2093, 'silhouette_samples': '/gscratch/comdata/output/reddit_clustering/subreddit_comment_authors-tf_10k_LSI/umap_hdbscan/silhouette_samples-mcs-2_ms-5_cse-0.05_csm-leaf_nn-15_lr-1.0_md-0.1_lc-1_lsi-700.feather', 'min_cluster_size': 2, 'min_samples': 5, 'cluster_selection_epsilon': 0.05, 'cluster_selection_method': 'leaf', 'n_neighbors': 15, 'learning_rate': 1.0, 'min_dist': 0.1, 'local_connectivity': 1, 'n_isolates_str': '2093', 'n_isolates_0': False} + $(srun_singularity) -c "source ~/.bashrc; python3 pick_best_clustering.py $< $@ --min_clusters=50 --max_isolates=5000 --min_cluster_size=2" -best_umap_grid=--min_cluster_sizes=[2] --min_samples=[5] --cluster_selection_epsilons=[0.05] --cluster_selection_methods=[leaf] --n_neighbors=[15] --learning_rate=[1] --min_dist=[0.1] --local_connectivity=[1] --save_step1=True +${authors_tf_10k_input_lsi}: + $(MAKE) -C ../similarities -umap_hdbscan_coords: - python3 umap_hdbscan_clustering_lsi.py --inpath=${authors_tf_10k_input_lsi} --outpath=${authors_tf_10k_output_lsi}/umap_hdbscan --savefile=/dev/null ${best_umap_grid} - -clean_affinity: - rm -f ${authors_10k_output}/affinity/selection_data.csv - rm -f ${authors_tf_10k_output}/affinity/selection_data.csv - rm -f ${terms_10k_output}/affinity/selection_data.csv - -clean_kmeans: - rm -f ${authors_10k_output}/kmeans/selection_data.csv - rm -f ${authors_tf_10k_output}/kmeans/selection_data.csv - rm -f ${terms_10k_output}/kmeans/selection_data.csv - -clean_hdbscan: - rm -f ${authors_10k_output}/hdbscan/selection_data.csv - rm -f ${authors_tf_10k_output}/hdbscan/selection_data.csv - rm -f ${terms_10k_output}/hdbscan/selection_data.csv - -clean_authors: - rm -f ${authors_10k_output}/affinity/selection_data.csv - rm -f ${authors_10k_output}/kmeans/selection_data.csv - rm -f ${authors_10k_output}/hdbscan/selection_data.csv - -clean_authors_tf: - rm -f ${authors_tf_10k_output}/affinity/selection_data.csv - rm -f ${authors_tf_10k_output}/kmeans/selection_data.csv - rm -f ${authors_tf_10k_output}/hdbscan/selection_data.csv - -clean_terms: - rm -f ${terms_10k_output}/affinity/selection_data.csv - rm -f ${terms_10k_output}/kmeans/selection_data.csv - rm -f ${terms_10k_output}/hdbscan/selection_data.csv - -clean_lsi_affinity: - rm -f ${authors_10k_output_lsi}/affinity/selection_data.csv - rm -f ${authors_tf_10k_output_lsi}/affinity/selection_data.csv - rm -f ${terms_10k_output_lsi}/affinity/selection_data.csv - -clean_lsi_kmeans: - rm -f ${authors_10k_output_lsi}/kmeans/selection_data.csv - rm -f ${authors_tf_10k_output_lsi}/kmeans/selection_data.csv - rm -f ${terms_10k_output_lsi}/kmeans/selection_data.csv - -clean_lsi_hdbscan: - rm -f ${authors_10k_output_lsi}/hdbscan/selection_data.csv - rm -f ${authors_tf_10k_output_lsi}/hdbscan/selection_data.csv - rm -f ${terms_10k_output_lsi}/hdbscan/selection_data.csv - -clean_lsi_authors: - rm -f ${authors_10k_output_lsi}/affinity/selection_data.csv - rm -f ${authors_10k_output_lsi}/kmeans/selection_data.csv - rm -f ${authors_10k_output_lsi}/hdbscan/selection_data.csv - -clean_lsi_authors_tf: +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 -clean_lsi_terms: - rm -f ${terms_10k_output_lsi}/affinity/selection_data.csv - rm -f ${terms_10k_output_lsi}/kmeans/selection_data.csv - rm -f ${terms_10k_output_lsi}/hdbscan/selection_data.csv - -clean: clean_affinity clean_kmeans clean_hdbscan - -PHONY: clean clean_affinity clean_kmeans clean_hdbscan clean_authors clean_authors_tf clean_terms terms_10k authors_10k authors_tf_10k best_umap_hdbscan.feather umap_hdbscan_coords - -# $(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 - -# $(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 - -# $(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 - - -# $(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 - -# $(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 - -# $(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