├── .gitignore ├── README.md └── thread_scaling ├── iotest ├── iotest.Rmd ├── iotest.cpp ├── iotest.hpp ├── iotest_lbm.sh ├── iotest_stampede2.csv ├── iotest_stampede2.sh └── refine.py ├── scripts ├── .gitignore ├── bt.tsv ├── bt2.tsv ├── bt2_base.tsv ├── bt2_batchhi.tsv ├── bt2_batchlo.tsv ├── bt2_inbuf.tsv ├── bt2_lustre.tsv ├── bt2_multiout.tsv ├── bt_base.tsv ├── bt_batchhi.tsv ├── bt_batchlo.tsv ├── bt_inbuf.tsv ├── bt_lustre.tsv ├── bt_multiout.tsv ├── bt_with_iot.tsv ├── bwa.tsv ├── check_blocked.py ├── common.sh ├── fstest.sh ├── get_reads.sh ├── hbb │ ├── .gitignore │ ├── Dockerfile │ ├── bbb_aligner.bash │ ├── bbb_aligner_build.sh │ ├── build_all.py │ ├── centos_aligner.bash │ └── centos_aligner_build.sh ├── ht.tsv ├── ht_base.tsv ├── ht_batchhi.tsv ├── ht_batchlo.tsv ├── ht_inbuf.tsv ├── ht_lustre.tsv ├── ht_multiout.tsv ├── marcc_lbm │ ├── .gitignore │ ├── README.md │ ├── all.sh │ ├── bt2_base_pe.sh │ ├── bt2_base_unp.sh │ ├── bt2_lustre_pe.sh │ ├── bt2_lustre_unp.sh │ ├── bt2_multiout_pe.sh │ ├── bt2_multiout_unp.sh │ ├── bt2_pe.sh │ ├── bt2_unp.sh │ ├── bt_base_pe.sh │ ├── bt_base_unp.sh │ ├── bt_lustre_pe.sh │ ├── bt_lustre_unp.sh │ ├── bt_multiout_pe.sh │ ├── bt_multiout_unp.sh │ ├── bt_pe.sh │ ├── bt_unp.sh │ ├── bwa_pe.sh │ ├── bwa_unp.sh │ ├── fstest.sh │ ├── ht_base_pe.sh │ ├── ht_base_unp.sh │ ├── ht_lustre_pe.sh │ ├── ht_lustre_unp.sh │ ├── ht_multiout_pe.sh │ ├── ht_multiout_unp.sh │ ├── ht_pe.sh │ ├── ht_unp.sh │ ├── lustre_temp_dir.txt │ ├── temp_dir.txt │ └── thread_series.txt ├── master.py ├── peak_res.py ├── peak_throughput_baseline.tex_snippet ├── peak_throughput_final.tex_snippet ├── peak_throughput_multi.tex_snippet ├── peak_throughput_parsing.tex_snippet ├── postprocess_peak_throughput.py ├── reads.py ├── reads.sh ├── reads_cat.sh ├── scaling_results.Rmd ├── scaling_results.sh ├── stampede_knl │ ├── .gitignore │ ├── README.md │ ├── all.sh │ ├── bt2_base_pe.sh │ ├── bt2_base_unp.sh │ ├── bt2_batchhi_pe.sh │ ├── bt2_batchhi_unp.sh │ ├── bt2_batchinbuf_pe.sh │ ├── bt2_batchinbuf_unp.sh │ ├── bt2_batchlo_pe.sh │ ├── bt2_batchlo_unp.sh │ ├── bt2_lustre_pe.sh │ ├── bt2_lustre_unp.sh │ ├── bt2_multiout_pe.sh │ ├── bt2_multiout_unp.sh │ ├── bt2_pe.sh │ ├── bt2_unp.sh │ ├── bt_base_pe.sh │ ├── bt_base_unp.sh │ ├── bt_batchhi_pe.sh │ ├── bt_batchhi_unp.sh │ ├── bt_batchinbuf_pe.sh │ ├── bt_batchinbuf_unp.sh │ ├── bt_batchlo_pe.sh │ ├── bt_batchlo_unp.sh │ ├── bt_lustre_pe.sh │ ├── bt_lustre_unp.sh │ ├── bt_multiout_pe.sh │ ├── bt_multiout_unp.sh │ ├── bt_pe.sh │ ├── bt_unp.sh │ ├── bwa_pe.sh │ ├── bwa_unp.sh │ ├── fstest.Rmd │ ├── fstest.csv │ ├── fstest.sh │ ├── fstest_nout_20180203.csv │ ├── fstest_results_20171223.csv │ ├── fstest_results_20171226.csv │ ├── fstest_results_20171227.csv │ ├── fstest_strace.csv │ ├── fstest_time.csv │ ├── ht_base_pe.sh │ ├── ht_base_unp.sh │ ├── ht_batchhi_pe.sh │ ├── ht_batchhi_unp.sh │ ├── ht_batchinbuf_pe.sh │ ├── ht_batchinbuf_unp.sh │ ├── ht_batchlo_pe.sh │ ├── ht_batchlo_unp.sh │ ├── ht_lustre_pe.sh │ ├── ht_lustre_unp.sh │ ├── ht_multiout_pe.sh │ ├── ht_multiout_unp.sh │ ├── ht_pe.sh │ ├── ht_unp.sh │ ├── lustre_temp_dir.txt │ ├── refine.py │ ├── runner.py │ ├── stampede_knl_bt2_pe_scale.txt │ ├── stampede_knl_bt2_unp_scale.txt │ ├── stampede_knl_bwa_pe_scale.txt │ ├── stampede_knl_bwa_unp_scale.txt │ ├── tabulate_fstest.py │ ├── tabulate_fstest_strace.sh │ ├── temp_dir.txt │ └── thread_series.txt ├── stampede_skx │ ├── .gitignore │ ├── all.sh │ ├── bt2_base_pe.sh │ ├── bt2_base_unp.sh │ ├── bt2_lustre_pe.sh │ ├── bt2_lustre_unp.sh │ ├── bt2_multiout_pe.sh │ ├── bt2_multiout_unp.sh │ ├── bt2_pe.sh │ ├── bt2_unp.sh │ ├── bt_base_pe.sh │ ├── bt_base_unp.sh │ ├── bt_lustre_pe.sh │ ├── bt_lustre_unp.sh │ ├── bt_multiout_pe.sh │ ├── bt_multiout_unp.sh │ ├── bt_pe.sh │ ├── bt_unp.sh │ ├── bt_with_iot_pe.sh │ ├── bt_with_iot_unp.sh │ ├── bwa_pe.sh │ ├── bwa_unp.sh │ ├── fstest.sh │ ├── ht_base_pe.sh │ ├── ht_base_unp.sh │ ├── ht_lustre_pe.sh │ ├── ht_lustre_unp.sh │ ├── 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