From b13c3e97fc510af6be1e82f37652533cff88b866 Mon Sep 17 00:00:00 2001 From: Sam Grayson Date: Sat, 7 Dec 2024 01:58:04 -0500 Subject: [PATCH] Add PROBE to macro-benchmarks (#43) --- benchmark/experiment.py | 42 +- benchmark/flake.lock | 129 +- benchmark/flake.nix | 6 +- benchmark/notebook/cross-val.ipynb | 4722 +++++++++++++++++++++++++- benchmark/prov_collectors.py | 13 + benchmark/result2 | 1 + benchmark/run_server_and_client.py | 6 +- benchmark/stats.py | 60 +- benchmark/stats2.py | 221 -- benchmark/tasks.md | 6 + benchmark/util.py | 12 +- benchmark/workloads.py | 64 +- flake.nix | 1 - probe_src/frontend/cli/src/record.rs | 8 +- probe_src/python/pyproject.toml | 1 - probe_src/tasks.md | 4 +- 16 files changed, 4961 insertions(+), 335 deletions(-) create mode 120000 benchmark/result2 delete mode 100644 benchmark/stats2.py create mode 100644 benchmark/tasks.md diff --git a/benchmark/experiment.py b/benchmark/experiment.py index 88044604..93b37aff 100644 --- a/benchmark/experiment.py +++ b/benchmark/experiment.py @@ -137,27 +137,27 @@ def run_experiments( # Extracting a minimal set of fields # So we don't have all ExperimentStats in memory at once for i, (prov_collector, workload, stats) in enumerate(result_list): - counter = collections.Counter( - op.type for op in stats.operations - ) if stats is not None else None - record = { - "collector": prov_collector.name, - "collector_method": prov_collector.method, - "collector_submethod": prov_collector.submethod, - "workload": workload.name, - "workload_kind": workload.kind, - "cputime": stats.cputime, - "walltime": stats.walltime, - "memory": stats.memory, - "storage": stats.provenance_size, - "n_ops": len(stats.operations), - # "n_unique_files": n_unique(itertools.chain( - # (op.target0 for op in stats.operations), - # (op.target1 for op in stats.operations), - # )), - "op_type_counts": counter, - } if stats is not None else None - records.append(record) + if stats is not None: + counter = collections.Counter( + op.type for op in stats.operations + ) + records[i] = { + "collector": prov_collector.name, + "collector_method": prov_collector.method, + "collector_submethod": prov_collector.submethod, + "workload": workload.name, + "workload_kind": workload.kind, + "cputime": stats.cputime, + "walltime": stats.walltime, + "memory": stats.memory, + "storage": stats.provenance_size, + "n_ops": len(stats.operations), + # "n_unique_files": n_unique(itertools.chain( + # (op.target0 for op in stats.operations), + # (op.target1 for op in stats.operations), + # )), + "op_type_counts": counter, + } results_df = ( pandas.DataFrame.from_records(list(filter(bool, records))) .assign(**{ diff --git a/benchmark/flake.lock b/benchmark/flake.lock index 22e55b10..b09b3e7d 100644 --- a/benchmark/flake.lock +++ b/benchmark/flake.lock @@ -1,5 +1,42 @@ { "nodes": { + "advisory-db": { + "flake": false, + "locked": { + "lastModified": 1721864173, + "narHash": "sha256-tQn2ZPLAH6u2nAfV8Ac/2HPS5giBi0iceCp4g9SqWAU=", + "owner": "rustsec", + "repo": "advisory-db", + "rev": "af0e1b678a23ebd04efa0d0f63f98ad46781077d", + "type": "github" + }, + "original": { + "owner": "rustsec", + "repo": "advisory-db", + "type": "github" + } + }, + "crane": { + "inputs": { + "nixpkgs": [ + "probe", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1721842668, + "narHash": "sha256-k3oiD2z2AAwBFLa4+xfU+7G5fisRXfkvrMTCJrjZzXo=", + "owner": "ipetkov", + "repo": "crane", + "rev": "529c1a0b1f29f0d78fa3086b8f6a134c71ef3aaf", + "type": "github" + }, + "original": { + "owner": "ipetkov", + "repo": "crane", + "type": "github" + } + }, "flake-utils": { "inputs": { "systems": "systems" @@ -18,6 +55,24 @@ "type": "github" } }, + "flake-utils_2": { + "inputs": { + "systems": "systems_2" + }, + "locked": { + "lastModified": 1710146030, + "narHash": "sha256-SZ5L6eA7HJ/nmkzGG7/ISclqe6oZdOZTNoesiInkXPQ=", + "owner": "numtide", + "repo": "flake-utils", + "rev": "b1d9ab70662946ef0850d488da1c9019f3a9752a", + "type": "github" + }, + "original": { + "owner": "numtide", + "repo": "flake-utils", + "type": "github" + } + }, "new-nixos": { "locked": { "lastModified": 1716219014, @@ -47,11 +102,68 @@ "type": "indirect" } }, + "nixpkgs_2": { + "locked": { + "lastModified": 1721782431, + "narHash": "sha256-UNDpwjYxNXQet/g3mgRLsQ9zxrbm9j2JEvP4ijF3AWs=", + "owner": "NixOS", + "repo": "nixpkgs", + "rev": "4f02464258baaf54992debfd010a7a3662a25536", + "type": "github" + }, + "original": { + "owner": "NixOS", + "ref": "nixpkgs-unstable", + "repo": "nixpkgs", + "type": "github" + } + }, + "probe": { + "inputs": { + "advisory-db": "advisory-db", + "crane": "crane", + "flake-utils": "flake-utils_2", + "nixpkgs": "nixpkgs_2", + "rust-overlay": "rust-overlay" + }, + "locked": { + "lastModified": 0, + "narHash": "sha256-Ycn7WZZj5VYqCX2qcodDS9swVfPgNSTOV5JaKodKbjY=", + "path": "/nix/store/q378gmsa439yqlyqll6lis9d8ryrd5wy-source", + "type": "path" + }, + "original": { + "path": "/nix/store/q378gmsa439yqlyqll6lis9d8ryrd5wy-source", + "type": "path" + } + }, "root": { "inputs": { "flake-utils": "flake-utils", "new-nixos": "new-nixos", - "nixpkgs": "nixpkgs" + "nixpkgs": "nixpkgs", + "probe": "probe" + } + }, + "rust-overlay": { + "inputs": { + "nixpkgs": [ + "probe", + "nixpkgs" + ] + }, + "locked": { + "lastModified": 1721928877, + "narHash": "sha256-bW2ClCWzGCytPbUnqZwU8P1YsLW07uEs80EfHEctc0Q=", + "owner": "oxalica", + "repo": "rust-overlay", + "rev": "8b81b8ed00b20fd57b24adcb390bd96ea81ecd90", + "type": "github" + }, + "original": { + "owner": "oxalica", + "repo": "rust-overlay", + "type": "github" } }, "systems": { @@ -68,6 +180,21 @@ "repo": "default", "type": "github" } + }, + "systems_2": { + "locked": { + "lastModified": 1681028828, + "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=", + "owner": "nix-systems", + "repo": "default", + "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e", + "type": "github" + }, + "original": { + "owner": "nix-systems", + "repo": "default", + "type": "github" + } } }, "root": "root", diff --git a/benchmark/flake.nix b/benchmark/flake.nix index 9fb1b5ee..284a94fb 100644 --- a/benchmark/flake.nix +++ b/benchmark/flake.nix @@ -3,10 +3,13 @@ # Use newer Nix to apply this bugfix # https://github.com/NixOS/nix/pull/10467 inputs.new-nixos.url = "github:NixOS/nixpkgs"; + + inputs.probe.url = "../"; outputs = { self, nixpkgs, flake-utils, + probe, ... } @ inputs: flake-utils.lib.eachDefaultSystem ( @@ -113,6 +116,7 @@ pypkgs.scikit-learn pypkgs.nbconvert jupyter-contrib-nbextensions + pypkgs.xgboost ])) ]; }; @@ -220,7 +224,6 @@ rev = "master"; hash = "sha256-HFgqYEHanlwA0FA/7kOSsmcPzcb8BLJ3lG74DV5RtBA="; }; - a = "hi"; patches = [./splash-3.diff]; nativeBuildInputs = [pkgs.m4 pkgs.binutils]; sourceRoot = "source/codes"; @@ -786,6 +789,7 @@ # proot provides tests with `make -C test` however they do not run in the sandbox doCheck = false; }; + probe-pkg = probe.packages.${system}.probe-bundled; lftp = pkgs.lftp; wget = pkgs.wget; libseccomp = pkgs.libseccomp.lib; diff --git a/benchmark/notebook/cross-val.ipynb b/benchmark/notebook/cross-val.ipynb index e8cfb873..06ffe12a 100644 --- a/benchmark/notebook/cross-val.ipynb +++ b/benchmark/notebook/cross-val.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": 2, "id": "3ceeae8f-ef7d-4b00-9f31-26785721d9e6", "metadata": {}, "outputs": [], @@ -18,7 +18,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 3, "id": "6f063cd7-a1e6-4f5a-bbd3-4dca8b111886", "metadata": {}, "outputs": [ @@ -60,7 +60,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "id": "b46abe58-2987-421e-9078-65a1752aeac1", "metadata": {}, "outputs": [], @@ -70,7 +70,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 5, "id": "327b2da9-fa4b-4e04-8a1c-25cec2322f84", "metadata": {}, "outputs": [], @@ -99,10 +99,4716 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 9, "id": "1c8cd970-9dee-409b-93cc-e073e1df0f35", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + " 0%| | 0/468 [00:00 pickle.loads PROBE fstat 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE fstat 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE fstat 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE fstat 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov cd 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov cd 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads 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}, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE hg_schema-validation 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE hg_schema-validation 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE hg_schema-validation 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE hg_schema-validation 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 1%|█▌ | 6/468 [00:00<00:28, 16.15it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Untar_v6_gzip 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_gzip 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + 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"output_type": "stream", + "text": [ + " > pickle.loads noprov cholesky 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov cholesky 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov cholesky 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov cholesky 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 3%|████ | 16/468 [00:00<00:27, 16.57it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov mmap 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov mmap 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov mmap 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": 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pickle.loads PROBE all 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE all 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE all 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE all 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE ls 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE ls 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE ls 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE ls 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 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"output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov letter 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Untar_v6_ 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_ 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Untar_v6_ 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_ 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 6%|███████▋ | 30/468 [00:01<00:27, 15.83it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov water-nsquared 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov water-nsquared 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov water-nsquared 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov water-nsquared 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE git_setuptools_scm 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE git_setuptools_scm 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE git_setuptools_scm 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE git_setuptools_scm 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 7%|████████▏ | 32/468 [00:01<00:27, 16.13it/s]\u001b[A" + ] 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running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE blastp 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE blastp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE blastp 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 10%|████████████▏ | 48/468 [00:02<00:26, 15.97it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov nginx 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov nginx 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov nginx 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov nginx 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_ 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_ 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_ 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_ 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 11%|████████████▋ | 50/468 [00:03<00:26, 15.70it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE volrend 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE volrend 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE volrend 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE volrend 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE tblastx 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE tblastx 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE tblastx 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE tblastx 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 11%|█████████████▏ | 52/468 [00:03<00:26, 15.59it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_gzip 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_gzip 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_gzip 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_gzip 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE nginx 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE nginx 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE nginx 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE nginx 0: 0.0s 0.0B (gc: 0.1s)\n", + 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0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE hello-threads 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 12%|██████████████▏ | 56/468 [00:03<00:27, 15.08it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE git_strace_500 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE git_strace_500 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE git_strace_500 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE git_strace_500 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov exec 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov exec 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov exec 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov exec 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 12%|██████████████▋ | 58/468 [00:03<00:26, 15.38it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE cp smaller 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE cp smaller 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE cp smaller 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE cp smaller 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE tblastn 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE tblastn 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE tblastn 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE tblastn 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 13%|███████████████▎ | 60/468 [00:03<00:26, 15.35it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE cd 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE cd 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads 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"output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_pbzip2 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Untar_v6_pbzip2 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_pbzip2 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov proftpd 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov proftpd 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov proftpd 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov proftpd 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 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[00:04<00:26, 14.62it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE water-spatial 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE water-spatial 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE water-spatial 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE water-spatial 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Tar_v6_gzip 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Tar_v6_gzip 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Tar_v6_gzip 0: 0.0s 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"DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_pigz 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Untar_v6_pigz 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_pigz 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 17%|███████████████████▊ | 78/468 [00:04<00:27, 14.43it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov select-file 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov select-file 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov select-file 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov select-file 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov shell-incr 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov shell-incr 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov shell-incr 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov shell-incr 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 17%|████████████████████▎ | 80/468 [00:05<00:27, 14.29it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE stat 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE stat 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": 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"name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov fft 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov fft 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov fft 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE fft 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE fft 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE fft 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE fft 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 18%|█████████████████████▎ | 84/468 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"name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_bzip2 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 18%|█████████████████████▊ | 86/468 [00:05<00:25, 14.86it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_lzop 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_lzop 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_lzop 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_lzop 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE radix 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + 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[ + " > pickle.loads noprov ftp-curl 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov ftp-curl 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov ftp-curl 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov ftp-curl 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE fs 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE fs 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE fs 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE fs 0: 0.0s 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pickle.loads noprov Tar_v6_xz 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Tar_v6_xz 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 21%|████████████████████████▍ | 96/468 [00:06<00:24, 15.00it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Tar_v6_bzip2 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Tar_v6_bzip2 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Tar_v6_bzip2 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Tar_v6_bzip2 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE hello 0: running\n" + ] + 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"DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_bzip2 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE blastn 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE blastn 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE blastn 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE blastn 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 21%|█████████████████████████▏ | 100/468 [00:06<00:25, 14.71it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov stat 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov stat 0: running\n" + ] + }, + { + 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0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE mega 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE mega 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE mega 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_pbzip2 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_pbzip2 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_pbzip2 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_pbzip2 0: 0.0s 0.0B (gc: 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" > pickle.loads PROBE hello-bin 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE hello-bin 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 23%|██████████████████████████▋ | 106/468 [00:06<00:25, 14.44it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov simplehttp 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov simplehttp 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov simplehttp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov simplehttp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov import-pandas 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov import-pandas 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov import-pandas 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov import-pandas 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 23%|███████████████████████████▏ | 108/468 [00:07<00:24, 14.49it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov protection-fault 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov protection-fault 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov protection-fault 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov protection-fault 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov bw_file_rd 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov bw_file_rd 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov bw_file_rd 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov bw_file_rd 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 24%|███████████████████████████▋ | 110/468 [00:07<00:24, 14.40it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov git_strace_500 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov git_strace_500 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov git_strace_500 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov git_strace_500 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE minihttp 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE minihttp 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE minihttp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE minihttp 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 24%|████████████████████████████▏ | 112/468 [00:07<00:24, 14.39it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov 0 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov 0 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov 0 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov 0 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov write 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov write 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov write 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov write 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 24%|████████████████████████████▋ | 114/468 [00:07<00:24, 14.39it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE acmart 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE acmart 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE acmart 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE acmart 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE ps 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE ps 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE ps 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE ps 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 25%|█████████████████████████████▏ | 116/468 [00:07<00:24, 14.53it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov cp linux 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov cp linux 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov cp linux 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov cp linux 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov lu 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov lu 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov lu 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov lu 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 25%|█████████████████████████████▊ | 118/468 [00:07<00:24, 14.45it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Untar_v6_xz 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_xz 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Untar_v6_xz 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Untar_v6_xz 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE import-pandas 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE import-pandas 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE import-pandas 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE import-pandas 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 26%|██████████████████████████████▎ | 120/468 [00:07<00:23, 14.90it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE raytrace 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE raytrace 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE raytrace 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE raytrace 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov git_setuptools_scm 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov git_setuptools_scm 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov git_setuptools_scm 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov git_setuptools_scm 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 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+ "DEBUG:charmonium.logger: > pickle.loads noprov blastp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE lighttpd 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE lighttpd 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE lighttpd 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE lighttpd 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 27%|████████████████████████████████▎ | 128/468 [00:08<00:22, 14.94it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov true 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov true 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov true 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov true 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov raytrace 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov raytrace 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov raytrace 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov raytrace 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 28%|████████████████████████████████▊ | 130/468 [00:08<00:21, 15.38it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov getppid 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov getppid 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov getppid 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov getppid 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov ftp-wget 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov ftp-wget 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov ftp-wget 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads 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"stream", + "text": [ + " > pickle.loads noprov shell-echo 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov shell-echo 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 29%|█████████████████████████████████▊ | 134/468 [00:08<00:21, 15.71it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE fork 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE fork 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE fork 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE fork 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE select-tcp 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE select-tcp 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE select-tcp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE select-tcp 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 29%|██████████████████████████████████▎ | 136/468 [00:08<00:21, 15.26it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov ps 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov ps 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov ps 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov ps 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE cholesky 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE cholesky 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE cholesky 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE cholesky 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 29%|██████████████████████████████████▊ | 138/468 [00:09<00:21, 15.54it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov all 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov all 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov all 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov all 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_xz 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_xz 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Tar_v6_xz 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Tar_v6_xz 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 30%|███████████████████████████████████▎ | 140/468 [00:09<00:20, 16.04it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE select-file 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE select-file 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE select-file 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE select-file 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Tar_v6_lzop 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Tar_v6_lzop 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov Tar_v6_lzop 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov Tar_v6_lzop 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 30%|███████████████████████████████████▊ | 142/468 [00:09<00:20, 16.20it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Untar_v6_lzop 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Untar_v6_lzop 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Untar_v6_lzop 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Untar_v6_lzop 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE water-nsquared 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE water-nsquared 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE water-nsquared 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE water-nsquared 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 31%|████████████████████████████████████▎ | 144/468 [00:09<00:20, 15.49it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov minihttp 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov minihttp 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov minihttp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov minihttp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE lftp 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE lftp 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE lftp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE lftp 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 31%|████████████████████████████████████▊ | 146/468 [00:09<00:21, 15.30it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov read 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov read 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov read 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov read 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov tblastx 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov tblastx 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov tblastx 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov tblastx 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 32%|█████████████████████████████████████▎ | 148/468 [00:09<00:20, 15.91it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE 1 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE 1 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE 1 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE 1 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov select-tcp 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov select-tcp 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov select-tcp 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov select-tcp 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 32%|█████████████████████████████████████▊ | 150/468 [00:09<00:19, 16.30it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov blastx 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov blastx 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov blastx 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov blastx 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov lighttpd 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov lighttpd 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov lighttpd 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov lighttpd 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 32%|██████████████████████████████████████▎ | 152/468 [00:09<00:19, 16.34it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Untar_v6_ 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Untar_v6_ 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE Untar_v6_ 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE Untar_v6_ 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE letter 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE letter 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads PROBE letter 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads PROBE letter 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 33%|██████████████████████████████████████▊ | 154/468 [00:10<00:19, 15.82it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov bw_pipe 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov bw_pipe 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov bw_pipe 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov bw_pipe 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov install-signal 0: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov install-signal 0: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov install-signal 0: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov install-signal 0: 0.0s 0.0B (gc: 0.1s)\n", + "\n", + " 33%|███████████████████████████████████████▎ | 156/468 [00:10<00:19, 16.24it/s]\u001b[A" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov volrend 1: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov volrend 1: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > pickle.loads noprov volrend 1: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > pickle.loads noprov volrend 1: 0.0s 0.0B (gc: 0.1s)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > Compiling Nix env for PROBE and io-bench-lmbench-page-fault: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > Compiling Nix env for PROBE and io-bench-lmbench-page-fault: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > Compiling Nix env for PROBE and io-bench-lmbench-page-fault: 1.8s\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > Compiling Nix env for PROBE and io-bench-lmbench-page-fault: 1.8s\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > setup io-bench-lmbench-page-fault: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > setup io-bench-lmbench-page-fault: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > setup io-bench-lmbench-page-fault: 0.0s\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > setup io-bench-lmbench-page-fault: 0.0s\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > setup PROBE: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > setup PROBE: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > setup PROBE: 0.0s\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > setup PROBE: 0.0s\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + " > run io-bench-lmbench-page-fault in PROBE: running\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > run io-bench-lmbench-page-fault in PROBE: running\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "('probe', 'record', '--output', '.workdir/log/0/probe_log', '--overwrite', 'env', 'ENOUGH=10000', 'lat_pagefault', '-N', '100', '.workdir/work/0/test_file') {'PATH': '/nix/store/khndnv11g1rmzhzymm1s5dw7l2ld45bc-coreutils-9.4/bin:/nix/store/02zzpbzg9q70lj51vx6h48hpw251s8c6-lmbench-3.0.a9/bin:/nix/store/2vf650affcy5xx7mjgi6h78s279p2nxp-probe-bundled-0.1.0/bin', 'PYTHONNOUSERSITE': 'true:true', 'LC_CTYPE': 'C.UTF-8:C.UTF-8'}\n", + " > run io-bench-lmbench-page-fault in PROBE: 0.0s (err)\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "DEBUG:charmonium.logger: > run io-bench-lmbench-page-fault in PROBE: 0.0s (err)\n" + ] + }, + { + "ename": "DBusBaseError", + "evalue": "[err -123]: Could not open a bus to DBus\nThis is DBusBaseError, a base error for DBus (i bet you did not see that coming) if you need a special error, enhance pystemd.sysdexc module!.", + "output_type": "error", + "traceback": [ + "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", + "\u001b[0;31mDBusBaseError\u001b[0m Traceback (most recent call last)", + "Cell \u001b[0;32mIn[9], line 17\u001b[0m\n\u001b[1;32m 15\u001b[0m ignore_failures \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[1;32m 16\u001b[0m rerun \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mFalse\u001b[39;00m\n\u001b[0;32m---> 17\u001b[0m df \u001b[38;5;241m=\u001b[39m \u001b[43mget_results\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 18\u001b[0m \u001b[43m \u001b[49m\u001b[43mcollectors\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 19\u001b[0m \u001b[43m \u001b[49m\u001b[43mworkloads\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 20\u001b[0m \u001b[43m \u001b[49m\u001b[43miterations\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43miterations\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 21\u001b[0m \u001b[43m \u001b[49m\u001b[43mseed\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 22\u001b[0m \u001b[43m \u001b[49m\u001b[43mignore_failures\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mignore_failures\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 23\u001b[0m \u001b[43m \u001b[49m\u001b[43mrerun\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mrerun\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 24\u001b[0m \u001b[43m \u001b[49m\u001b[43mparallelism\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\n\u001b[1;32m 25\u001b[0m \u001b[43m)\u001b[49m\n", + "File \u001b[0;32m~/box/PROBE/benchmark/experiment.py:62\u001b[0m, in \u001b[0;36mget_results\u001b[0;34m(prov_collectors, workloads, iterations, seed, ignore_failures, rerun, parallelism)\u001b[0m\n\u001b[1;32m 60\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m expect_type(pandas\u001b[38;5;241m.\u001b[39mDataFrame, pickle\u001b[38;5;241m.\u001b[39mload(key_file))\n\u001b[1;32m 61\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m---> 62\u001b[0m results_df \u001b[38;5;241m=\u001b[39m \u001b[43mrun_experiments\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 63\u001b[0m \u001b[43m \u001b[49m\u001b[43mprov_collectors\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 64\u001b[0m \u001b[43m \u001b[49m\u001b[43mworkloads\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 65\u001b[0m \u001b[43m \u001b[49m\u001b[43mcache_dir\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 66\u001b[0m \u001b[43m \u001b[49m\u001b[43mbig_temp_dir\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 67\u001b[0m \u001b[43m \u001b[49m\u001b[43miterations\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 68\u001b[0m \u001b[43m \u001b[49m\u001b[43msize\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 69\u001b[0m \u001b[43m \u001b[49m\u001b[43mseed\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 70\u001b[0m \u001b[43m \u001b[49m\u001b[43mignore_failures\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 71\u001b[0m \u001b[43m \u001b[49m\u001b[43mrerun\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 72\u001b[0m \u001b[43m \u001b[49m\u001b[43mparallelism\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 73\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 74\u001b[0m key\u001b[38;5;241m.\u001b[39mwrite_bytes(pickle\u001b[38;5;241m.\u001b[39mdumps(results_df))\n\u001b[1;32m 75\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m results_df\n", + "File \u001b[0;32m~/box/PROBE/benchmark/experiment.py:139\u001b[0m, in \u001b[0;36mrun_experiments\u001b[0;34m(prov_collectors, workloads, cache_dir, big_temp_dir, iterations, size, seed, ignore_failures, rerun, parallelism)\u001b[0m\n\u001b[1;32m 135\u001b[0m records: \u001b[38;5;28mlist\u001b[39m[\u001b[38;5;28mdict\u001b[39m[\u001b[38;5;28mstr\u001b[39m, \u001b[38;5;28mobject\u001b[39m] \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m] \u001b[38;5;241m=\u001b[39m [\u001b[38;5;28;01mNone\u001b[39;00m] \u001b[38;5;241m*\u001b[39m (\u001b[38;5;28mlen\u001b[39m(prov_collectors) \u001b[38;5;241m*\u001b[39m \u001b[38;5;28mlen\u001b[39m(workloads) \u001b[38;5;241m*\u001b[39m iterations)\n\u001b[1;32m 136\u001b[0m \u001b[38;5;66;03m# Loop through each one at a time\u001b[39;00m\n\u001b[1;32m 137\u001b[0m \u001b[38;5;66;03m# Extracting a minimal set of fields\u001b[39;00m\n\u001b[1;32m 138\u001b[0m \u001b[38;5;66;03m# So we don't have all ExperimentStats in memory at once\u001b[39;00m\n\u001b[0;32m--> 139\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m i, (prov_collector, workload, stats) \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28menumerate\u001b[39m(result_list):\n\u001b[1;32m 140\u001b[0m counter \u001b[38;5;241m=\u001b[39m collections\u001b[38;5;241m.\u001b[39mCounter(\n\u001b[1;32m 141\u001b[0m op\u001b[38;5;241m.\u001b[39mtype \u001b[38;5;28;01mfor\u001b[39;00m op \u001b[38;5;129;01min\u001b[39;00m stats\u001b[38;5;241m.\u001b[39moperations\n\u001b[1;32m 142\u001b[0m ) \u001b[38;5;28;01mif\u001b[39;00m stats \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 143\u001b[0m record \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m 144\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcollector\u001b[39m\u001b[38;5;124m\"\u001b[39m: prov_collector\u001b[38;5;241m.\u001b[39mname,\n\u001b[1;32m 145\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcollector_method\u001b[39m\u001b[38;5;124m\"\u001b[39m: prov_collector\u001b[38;5;241m.\u001b[39mmethod,\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 158\u001b[0m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mop_type_counts\u001b[39m\u001b[38;5;124m\"\u001b[39m: counter,\n\u001b[1;32m 159\u001b[0m } \u001b[38;5;28;01mif\u001b[39;00m stats \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n", + "File \u001b[0;32m~/box/PROBE/benchmark/experiment.py:111\u001b[0m, in \u001b[0;36m\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 108\u001b[0m \u001b[38;5;28;01massert\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(inputs)\n\u001b[1;32m 109\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m parallelism \u001b[38;5;241m==\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m 110\u001b[0m result_list \u001b[38;5;241m=\u001b[39m (\n\u001b[0;32m--> 111\u001b[0m (prov_collector, workload, \u001b[43mrun_one_experiment_cached\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 112\u001b[0m \u001b[43m 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\u001b[38;5;129;01min\u001b[39;00m tqdm\u001b[38;5;241m.\u001b[39mtqdm(inputs)\n\u001b[1;32m 117\u001b[0m )\n\u001b[1;32m 118\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 119\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mdask\u001b[39;00m\n", + "File \u001b[0;32m~/box/PROBE/benchmark/experiment.py:207\u001b[0m, in \u001b[0;36mrun_one_experiment_cached\u001b[0;34m(cache_dir, iteration, prov_collector, workload, work_dir, log_dir, temp_dir, artifacts_dir, size, ignore_failures, rerun)\u001b[0m\n\u001b[1;32m 205\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 206\u001b[0m delete_children(temp_dir)\n\u001b[0;32m--> 207\u001b[0m stats \u001b[38;5;241m=\u001b[39m \u001b[43mrun_one_experiment\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 208\u001b[0m \u001b[43m \u001b[49m\u001b[43miteration\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mprov_collector\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mworkload\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mwork_dir\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlog_dir\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 209\u001b[0m \u001b[43m \u001b[49m\u001b[43mtemp_dir\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43martifacts_dir\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43msize\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mignore_failures\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 210\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 211\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m stats \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 212\u001b[0m cache_dir\u001b[38;5;241m.\u001b[39mmkdir(exist_ok\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m, parents\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)\n", + "File \u001b[0;32m~/box/PROBE/benchmark/experiment.py:287\u001b[0m, in \u001b[0;36mrun_one_experiment\u001b[0;34m(iteration, prov_collector, workload, work_dir, log_dir, temp_dir, artifacts_dir, size, ignore_failures)\u001b[0m\n\u001b[1;32m 285\u001b[0m full_env \u001b[38;5;241m=\u001b[39m merge_env_vars(workload_env, collector_env)\n\u001b[1;32m 286\u001b[0m \u001b[38;5;28mprint\u001b[39m(cmd, full_env)\n\u001b[0;32m--> 287\u001b[0m stats \u001b[38;5;241m=\u001b[39m \u001b[43mrun_exec\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 288\u001b[0m \u001b[43m \u001b[49m\u001b[43mcmd\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcmd\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 289\u001b[0m \u001b[43m \u001b[49m\u001b[43menv\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfull_env\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 290\u001b[0m \u001b[43m \u001b[49m\u001b[43mdir_modes\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m{\u001b[49m\n\u001b[1;32m 291\u001b[0m \u001b[43m \u001b[49m\u001b[43mwork_dir\u001b[49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mDirMode\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mFULL_ACCESS\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 292\u001b[0m \u001b[43m \u001b[49m\u001b[43mlog_dir\u001b[49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mDirMode\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mFULL_ACCESS\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 293\u001b[0m \u001b[43m \u001b[49m\u001b[43mpathlib\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mPath\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mDirMode\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mREAD_ONLY\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 294\u001b[0m \u001b[43m \u001b[49m\u001b[43mpathlib\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mPath\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43m/nix/store\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43mDirMode\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mREAD_ONLY\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 295\u001b[0m \u001b[43m \u001b[49m\u001b[43m}\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 296\u001b[0m \u001b[43m \u001b[49m\u001b[43mnetwork_access\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mworkload\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mnetwork_access\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 297\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 299\u001b[0m prov_collector\u001b[38;5;241m.\u001b[39mstop(collector_env)\n\u001b[1;32m 301\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m stats\u001b[38;5;241m.\u001b[39msuccess:\n", + "File \u001b[0;32m~/box/PROBE/benchmark/run_exec_wrapper.py:118\u001b[0m, in \u001b[0;36mrun_exec\u001b[0;34m(cmd, cwd, env, dir_modes, time_limit, mem_limit, network_access)\u001b[0m\n\u001b[1;32m 115\u001b[0m \u001b[38;5;66;03m# https://github.com/sosy-lab/benchexec/blob/2c56e08d5f0f44b3073f9c82a6c5f166a12b45e7/benchexec/runexecutor.py#L304\u001b[39;00m\n\u001b[1;32m 116\u001b[0m \u001b[38;5;66;03m# https://github.com/sosy-lab/benchexec/blob/2c56e08d5f0f44b3073f9c82a6c5f166a12b45e7/benchexec/containerexecutor.py#L297\u001b[39;00m\n\u001b[1;32m 117\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m dont_add_handler():\n\u001b[0;32m--> 118\u001b[0m run_executor \u001b[38;5;241m=\u001b[39m \u001b[43mRunExecutor\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 119\u001b[0m \u001b[43m \u001b[49m\u001b[38;5;66;43;03m# use_namespaces=False,\u001b[39;49;00m\n\u001b[1;32m 120\u001b[0m \u001b[43m \u001b[49m\u001b[43muse_namespaces\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 121\u001b[0m \u001b[43m \u001b[49m\u001b[43mdir_modes\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdir_modes_processed\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 122\u001b[0m \u001b[43m \u001b[49m\u001b[43mcontainer_system_config\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 123\u001b[0m \u001b[43m \u001b[49m\u001b[43mcontainer_tmpfs\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;28;43;01mTrue\u001b[39;49;00m\u001b[43m,\u001b[49m\n\u001b[1;32m 124\u001b[0m \u001b[43m \u001b[49m\u001b[43mnetwork_access\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnetwork_access\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 125\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 126\u001b[0m \u001b[38;5;66;03m# Runexec appears to install its own logging handlers, but we might already have one\u001b[39;00m\n\u001b[1;32m 127\u001b[0m caught_signal_number: Signal \u001b[38;5;241m|\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n", + "File \u001b[0;32m/nix/store/wx8jmp7hbqpw3rfrgf9gq0mv5sqml5sy-python3-3.10.13-env/lib/python3.10/site-packages/benchexec/runexecutor.py:335\u001b[0m, in \u001b[0;36mRunExecutor.__init__\u001b[0;34m(self, cleanup_temp_dir, additional_cgroup_subsystems, *args, **kwargs)\u001b[0m\n\u001b[1;32m 329\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cgroup_subsystems \u001b[38;5;241m=\u001b[39m additional_cgroup_subsystems\n\u001b[1;32m 331\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_energy_measurement \u001b[38;5;241m=\u001b[39m (\n\u001b[1;32m 332\u001b[0m intel_cpu_energy\u001b[38;5;241m.\u001b[39mEnergyMeasurement\u001b[38;5;241m.\u001b[39mcreate_if_supported()\n\u001b[1;32m 333\u001b[0m )\n\u001b[0;32m--> 335\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_init_cgroups\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n", + "File \u001b[0;32m/nix/store/wx8jmp7hbqpw3rfrgf9gq0mv5sqml5sy-python3-3.10.13-env/lib/python3.10/site-packages/benchexec/runexecutor.py:341\u001b[0m, in \u001b[0;36mRunExecutor._init_cgroups\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 337\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_init_cgroups\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[1;32m 338\u001b[0m \u001b[38;5;250m \u001b[39m\u001b[38;5;124;03m\"\"\"\u001b[39;00m\n\u001b[1;32m 339\u001b[0m \u001b[38;5;124;03m This function initializes the cgroups for the limitations and measurements.\u001b[39;00m\n\u001b[1;32m 340\u001b[0m \u001b[38;5;124;03m \"\"\"\u001b[39;00m\n\u001b[0;32m--> 341\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcgroups \u001b[38;5;241m=\u001b[39m \u001b[43mCgroups\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43minitialize\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 342\u001b[0m critical_cgroups \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mset\u001b[39m()\n\u001b[1;32m 344\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m subsystem \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_cgroup_subsystems:\n", + "File \u001b[0;32m/nix/store/wx8jmp7hbqpw3rfrgf9gq0mv5sqml5sy-python3-3.10.13-env/lib/python3.10/site-packages/benchexec/cgroups.py:89\u001b[0m, in \u001b[0;36mCgroups.initialize\u001b[0;34m(allowed_versions)\u001b[0m\n\u001b[1;32m 86\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m version \u001b[38;5;241m==\u001b[39m CGROUPS_V2:\n\u001b[1;32m 87\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mcgroupsv2\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m initialize\n\u001b[0;32m---> 89\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43minitialize\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 91\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m Cgroups\u001b[38;5;241m.\u001b[39mdummy()\n", + "File \u001b[0;32m/nix/store/wx8jmp7hbqpw3rfrgf9gq0mv5sqml5sy-python3-3.10.13-env/lib/python3.10/site-packages/benchexec/cgroupsv2.py:112\u001b[0m, in \u001b[0;36minitialize\u001b[0;34m()\u001b[0m\n\u001b[1;32m 105\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(cgroup\u001b[38;5;241m.\u001b[39mget_all_tasks()) \u001b[38;5;241m==\u001b[39m [os\u001b[38;5;241m.\u001b[39mgetpid()]:\n\u001b[1;32m 106\u001b[0m \u001b[38;5;66;03m# If we are the only process, somebody prepared a cgroup for us. Use it.\u001b[39;00m\n\u001b[1;32m 107\u001b[0m \u001b[38;5;66;03m# We might be able to relax this check and for example allow child processes,\u001b[39;00m\n\u001b[1;32m 108\u001b[0m \u001b[38;5;66;03m# but then we would also have to move them to another cgroup,\u001b[39;00m\n\u001b[1;32m 109\u001b[0m \u001b[38;5;66;03m# which might not be a good idea.\u001b[39;00m\n\u001b[1;32m 110\u001b[0m logging\u001b[38;5;241m.\u001b[39mdebug(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mBenchExec was started in its own cgroup: \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[38;5;124m\"\u001b[39m, cgroup)\n\u001b[0;32m--> 112\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[43m_create_systemd_scope_for_us\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m:\n\u001b[1;32m 113\u001b[0m \u001b[38;5;66;03m# If we can create a systemd scope for us and move ourselves in it,\u001b[39;00m\n\u001b[1;32m 114\u001b[0m \u001b[38;5;66;03m# we have a usable cgroup afterwards.\u001b[39;00m\n\u001b[1;32m 115\u001b[0m cgroup \u001b[38;5;241m=\u001b[39m CgroupsV2\u001b[38;5;241m.\u001b[39mfrom_system()\n\u001b[1;32m 117\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 118\u001b[0m \u001b[38;5;66;03m# No usable cgroup. We might still be able to continue if we actually\u001b[39;00m\n\u001b[1;32m 119\u001b[0m \u001b[38;5;66;03m# do not require cgroups for benchmarking. So we do not fail here\u001b[39;00m\n\u001b[1;32m 120\u001b[0m \u001b[38;5;66;03m# but return an instance that will on produce an error later.\u001b[39;00m\n", + "File \u001b[0;32m/nix/store/wx8jmp7hbqpw3rfrgf9gq0mv5sqml5sy-python3-3.10.13-env/lib/python3.10/site-packages/benchexec/cgroupsv2.py:162\u001b[0m, in \u001b[0;36m_create_systemd_scope_for_us\u001b[0;34m()\u001b[0m\n\u001b[1;32m 159\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpystemd\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mdbusexc\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m DBusFileNotFoundError\n\u001b[1;32m 160\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mpystemd\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01msystemd1\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m Manager, Unit\n\u001b[0;32m--> 162\u001b[0m \u001b[38;5;28;01mwith\u001b[39;00m DBus(user_mode\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m) \u001b[38;5;28;01mas\u001b[39;00m bus, Manager(bus\u001b[38;5;241m=\u001b[39mbus) \u001b[38;5;28;01mas\u001b[39;00m manager:\n\u001b[1;32m 163\u001b[0m unit_params \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m 164\u001b[0m \u001b[38;5;66;03m# workaround for not declared parameters, remove in the future\u001b[39;00m\n\u001b[1;32m 165\u001b[0m \u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m_custom\u001b[39m\u001b[38;5;124m\"\u001b[39m: (\u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mPIDs\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mau\u001b[39m\u001b[38;5;124m\"\u001b[39m, [os\u001b[38;5;241m.\u001b[39mgetpid()]),\n\u001b[0;32m (...)\u001b[0m\n\u001b[1;32m 168\u001b[0m \u001b[38;5;124mb\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mDelegate\u001b[39m\u001b[38;5;124m\"\u001b[39m: \u001b[38;5;28;01mTrue\u001b[39;00m,\n\u001b[1;32m 169\u001b[0m }\n\u001b[1;32m 171\u001b[0m random_suffix \u001b[38;5;241m=\u001b[39m secrets\u001b[38;5;241m.\u001b[39mtoken_urlsafe(\u001b[38;5;241m8\u001b[39m)\n", + "File \u001b[0;32m/nix/store/wx8jmp7hbqpw3rfrgf9gq0mv5sqml5sy-python3-3.10.13-env/lib/python3.10/site-packages/pystemd/dbuslib.pyx:287\u001b[0m, in \u001b[0;36mpystemd.dbuslib.DBus.__enter__\u001b[0;34m()\u001b[0m\n", + "File \u001b[0;32m/nix/store/wx8jmp7hbqpw3rfrgf9gq0mv5sqml5sy-python3-3.10.13-env/lib/python3.10/site-packages/pystemd/dbuslib.pyx:305\u001b[0m, in \u001b[0;36mpystemd.dbuslib.DBus.open\u001b[0;34m()\u001b[0m\n", + "\u001b[0;31mDBusBaseError\u001b[0m: [err -123]: Could not open a bus to DBus\nThis is DBusBaseError, a base error for DBus (i bet you did not see that coming) if you need a special error, enhance pystemd.sysdexc module!." + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "\n", + " 33%|███████████████████████████████████████▎ | 156/468 [00:20<00:19, 16.24it/s]\u001b[A" + ] + } + ], "source": [ "from experiment import get_results\n", "from workloads import WORKLOAD_GROUPS\n", @@ -111,11 +4817,11 @@ "\n", "collectors = list(flatten1([\n", " PROV_COLLECTOR_GROUPS[collector_name]\n", - " for collector_name in [\"working\"]\n", + " for collector_name in [\"PROBE\", \"noprov\"]\n", "]))\n", "workloads = list(flatten1([\n", " WORKLOAD_GROUPS[workload_name]\n", - " for workload_name in [\"working-low-mem\"]\n", + " for workload_name in [\"working\"]\n", "]))\n", "iterations = 3\n", "ignore_failures = False\n", diff --git a/benchmark/prov_collectors.py b/benchmark/prov_collectors.py index 8159b715..f3926f2d 100644 --- a/benchmark/prov_collectors.py +++ b/benchmark/prov_collectors.py @@ -754,6 +754,18 @@ def count(self, log: Path, exe: Path) -> tuple[ProvOperation, ...]: ) +class PROBE(ProvCollector): + method = "lib instrm." + submethod = "lib instrm." + name = "PROBE" + + nix_packages = [".#probe-pkg"] + + def run(self, cmd: Sequence[CmdArg], log: Path, size: int) -> Sequence[CmdArg]: + (log / "probe").mkdir() + return ("probe", "record", "--overwrite", "--no-transcribe", "--output", f"{log}/probe/", *cmd) + + PROV_COLLECTORS: list[ProvCollector] = [ NoProv(), STrace(), @@ -769,6 +781,7 @@ def count(self, log: Path, exe: Path) -> tuple[ProvOperation, ...]: SpadeAuditd(), Darshan(), BPFTrace(), + PROBE(), ] PROV_COLLECTOR_GROUPS: Mapping[str, list[ProvCollector]] = { diff --git a/benchmark/result2 b/benchmark/result2 new file mode 120000 index 00000000..3e235e4a --- /dev/null +++ b/benchmark/result2 @@ -0,0 +1 @@ +/nix/store/mdh4izsr947x093jfpp5qlz3zq1cm2ra-notebook-env \ No newline at end of file diff --git a/benchmark/run_server_and_client.py b/benchmark/run_server_and_client.py index b9795808..1d8ffbb4 100755 --- a/benchmark/run_server_and_client.py +++ b/benchmark/run_server_and_client.py @@ -5,8 +5,6 @@ import subprocess import sys import signal -import pathlib -sys.stderr.write(sys.executable) import psutil shell = "bash" @@ -27,10 +25,12 @@ sleeped = False if check_prog is not None: + n_successes = 0 for check in range(50): print("Check", check, "$", check_prog) proc = subprocess.run([shell, "-c", check_prog], check=False) - if proc.returncode == 0: + n_successes += int(proc.returncode == 0) + if n_successes > 3: break time.sleep(0.1) sleeped = True diff --git a/benchmark/stats.py b/benchmark/stats.py index 8b471ed0..48cb4c03 100644 --- a/benchmark/stats.py +++ b/benchmark/stats.py @@ -34,7 +34,7 @@ def output_features(df: pandas.DataFrame) -> None: }, "op_type_counts_sum": pandas.NamedAgg( "op_type_counts", - lambda op_type_freqs: functools.reduce(operator.add, op_type_freqs, collections.Counter()), + lambda op_type_counts: functools.reduce(operator.add, op_type_counts, collections.Counter()), ), "count": pandas.NamedAgg("walltime", lambda walltimes: len(walltimes)), "workload_kind": pandas.NamedAgg( @@ -44,6 +44,7 @@ def output_features(df: pandas.DataFrame) -> None: }) .assign(**{ "rel_slowdown": lambda df: df["walltime_mean"] / df.loc["noprov"]["walltime_mean"], + "slowdown_diff": lambda df: df["walltime_mean"] - df.loc["noprov"]["walltime_mean"], }) .assign(**{ "log_rel_slowdown": lambda df: numpy.log(df["rel_slowdown"]), @@ -52,49 +53,32 @@ def output_features(df: pandas.DataFrame) -> None: agged.to_pickle(output / "agged.pkl") collectors = df["collector"].unique() - if "strace" in collectors and "noprov" in collectors: - all_syscalls = collections.Counter[str]() - for counter in df[df["collector"] == "strace"]["op_type_counts"]: - all_syscalls += counter - syscall_groups = { - "socket": {"accept4", "connect", "bind", "accept"}, - "file": {"newfstatat", "readlink", "access", "chmod", "fchmod", "mkdir", "rmdir", "mkdirat", "rename", "unlink", "link", "symlink"}, - "fd": {"creat", "open", "openat"}, - "exec": {"execve", "clone", "clone3", "vfork"}, - } - syscall_groups["other"] = { - syscall - for syscall in all_syscalls - if not any(syscall in group for group in syscall_groups.values()) - } - noprov = agged.loc["noprov"] + if "strace" in collectors: strace = agged.loc["strace"] - features_df = pandas.DataFrame({ - "cputime_per_sec": noprov["cputime_mean"] / noprov["walltime_mean"], - "memory_mean": noprov["memory_mean"], - **{ - group_name + "_syscalls_per_sec": strace["op_type_counts_sum"].map(lambda op_type_counts: sum( - op_type_counts[syscall_name] - for syscall_name in syscall_names - )) / (noprov["walltime_mean"] * noprov["count"]) - for group_name, syscall_names in syscall_groups.items() - }, - "n_ops_per_sec": strace["n_ops_mean"] / noprov["walltime_mean"], - }) - features_df.to_pickle(output / "features_df.pkl") - - tmp_df = agged.reset_index().pivot(index="collector", columns="workload", values="log_rel_slowdown") + all_syscalls = set[str]() + for counter in strace["op_type_counts_sum"]: + all_syscalls |= counter.keys() + benchmarks_by_features = pandas.DataFrame({ + syscall_group: [ + counter[syscall_group] + for counter in strace["op_type_counts_sum"] + ] + for syscall_group in all_syscalls + }).set_index(strace.index) + benchmarks_by_features.to_pickle(output / "benchmarks_by_features.pkl") + + systems_by_benchmarks = ( + agged + .reset_index() + .pivot(index="collector", columns="workload", values="slowdown_diff") + ) + systems_by_benchmarks.to_pickle(output / "systems_by_benchmarks.pkl") assert all( workload0 == workload1 - for workload0, workload1 in zip(tmp_df.columns, features_df.index) + for workload0, workload1 in zip(systems_by_benchmarks.columns, benchmarks_by_features.index) ) - numpy.save(output / "systems_by_benchmarks", tmp_df.values) - numpy.save(output / "benchmarks_by_features", features_df.values) - (output / "systems.txt").write_text("\n".join(agged.index.levels[0])) - (output / "benchmarks.txt").write_text("\n".join(agged.index.levels[1])) - (output / "features.txt").write_text("\n".join(features_df.columns)) @charmonium.time_block.decor() def performance(df: pandas.DataFrame) -> None: diff --git a/benchmark/stats2.py b/benchmark/stats2.py deleted file mode 100644 index 77c6b3d0..00000000 --- a/benchmark/stats2.py +++ /dev/null @@ -1,221 +0,0 @@ -import os -import pandas -import pathlib -import numpy -import collections -import abc -import numpy.typing - -import pandas -import functools -from typing import Mapping, Callable -from util import flatten1 -from prov_collectors import PROV_COLLECTORS -from workloads import WORKLOADS -import operator - -rel_qois = ["cputime", "walltime", "memory"] -abs_qois = ["storage", "n_ops", "n_unique_files"] -tmp_output = pathlib.Path("output") -tmp_output.mkdir(exist_ok=True) -output_dir = pathlib.Path("../docs/benchmark_suite/generated") -output_dir.mkdir() - -print("The following appear to have failed") -print(df[df["walltime"] < 0.001]) - - -df = ( - df - # Get rid of unused columns - # They just soak up memory - .drop(columns=[col for col in ["collector_method", "collector_submethod"] if col in df.columns]) - - # Get rid of "failure" runs which have walltime == 0.0 - [lambda df: df["walltime"] != 0.0] - - # Sciunits runs out of memory on some benchmarks (without failing) - [lambda df: df["collector"] != "sciunit"] - - # We can refer to the 1st or 2nd run of X workload in Y collector - .assign(iter=lambda df: df.groupby(["collector", "workload"], observed=True).cumcount()) -) - -# Rename the benchmarks to match their names in the paper. -df_with_balanced_clusters = ( - df_with_balanced_clusters - .assign( - workload_triple=lambda df: [ - { - "notebook": lambda: ( - "Data science", "Notebook", {"a-data-sci": "nb-1", "comprehens": "nb-2", "titanic-da": "nb-3"}[name], - ), - "archive": lambda: ("Tar", "Archive", name.split(' ')[-1].replace(" archive", "raw").strip()), - "unarchive": lambda: ("Tar", "Unarchive", name.split(' ')[-1].replace(" unarchive", "raw").strip()), - "http_server": lambda: ("HTTP", "srv/traffic", name.replace('python http.server', 'simplehttp')), - "http_client": lambda: ("HTTP", "srv/client", name), - "ftp_server": lambda: ("FTP", "srv/traffic", name), - "ftp_client": lambda: ("FTP", "srv/client", name.split('-')[-1].strip()), - "blast": lambda: ("BLAST", "", "mega" if name == "megablast" else name), - "shell": lambda: ("Utils", "bash", name), - "lmbench": lambda: ("IO bench", "lmbench", name.replace('lm-', '').strip()), - "copy": lambda: ("cp", "", name.split(' ')[-1].strip()), - "simple": lambda: ("Utils", "", name.strip()), - "vcs": lambda: ("VCS checkout", "", name.replace('schema-validation', 'hg-repo-1').replace('setuptools_scm', 'git-repo-1').strip()), - "postmark": lambda: ("IO bench", "postmark", "main"), - "pdflatex": lambda: ("Compile", "w/latex", name.replace('latex-', '').replace('test2', 'doc2').replace('test', 'doc1').strip()), - "splash-3": lambda: ("CPU bench", "SPLASH-3", name.split(' ')[-1].split('-')[-1].strip()), - "spack": lambda: ("Compile", "w/Spack", name.split(' ')[-1].split("~")[0].strip()), - "gcc": lambda: ("Compile", "w/gcc", name.split(' ')[-1].replace('gcc-', '').strip()), - "python": lambda: ("Data science", "python", name.strip()), - }[kind]() - for kind, name in df[["workload_kind", "workload"]].values - ], - collector=lambda df: [ - { - "care": "CARE", - "fsatrace": "fsatrace", - "noprov": "(none)", - "reprozip": "ReproZip", - "rr": "RR", - "strace": "strace", - "sciunit": "Sciunit", - }[collector] - for collector in df["collector"] - ], - ) - .assign( - workload_kind=lambda df: [f"{a} {b}" for a, b, c in df.workload_triple], - workload_shortname=lambda df: [c for a, b, c in df.workload_triple], - workload=lambda df: [f"{a} {b} ({c})" for a, b, c in df.workload_triple], - ) - .assign( - workload_kind=lambda df: df["workload_kind"].astype("category"), - workload_shortname=lambda df: df["workload_shortname"].astype("category"), - workload=lambda df: df["workload"].astype("category"), - collector=lambda df: df["collector"].astype("category"), - ) -) -collector_order = [ - "(none)", - "fsatrace", - "CARE", - "strace", - "RR", - "ReproZip", -] -agged = ( - df_with_balanced_clusters - .groupby(["collector", "workload"], observed=True, as_index=True) - .agg(**{ - **{ - f"{qoi}_std": pandas.NamedAgg(qoi, "std") - for qoi in abs_qois + rel_qois - }, - **{ - f"{qoi}_mean": pandas.NamedAgg(qoi, "mean") - for qoi in abs_qois + rel_qois - }, - **{ - f"{qoi}_low": pandas.NamedAgg(qoi, lambda data: numpy.percentile(data, 5)) - for qoi in abs_qois + rel_qois - }, - **{ - f"{qoi}_high": pandas.NamedAgg(qoi, lambda data: numpy.percentile(data, 95)) - for qoi in abs_qois + rel_qois - }, - **{ - f"{qoi}_sorted": pandas.NamedAgg(qoi, lambda data: list(sorted(data))) - for qoi in abs_qois + rel_qois - }, - "op_type_counts_sum": pandas.NamedAgg( - "op_type_counts", - lambda op_type_freqs: functools.reduce(operator.add, op_type_freqs, collections.Counter()), - ), - "count": pandas.NamedAgg("walltime", lambda walltimes: len(walltimes)), - "workload_kind": pandas.NamedAgg("workload_kind", lambda workload_kinds: workload_kinds.iloc[0]), - "workload_shortname": pandas.NamedAgg("workload_shortname", lambda workload_shortnames: workload_shortnames.iloc[0]), - }) - .assign(**{ - **{ - f"{qoi}_rel": lambda df, qoi=qoi: df[f"{qoi}_std"] / df[f"{qoi}_mean"] - for qoi in abs_qois + rel_qois - }, - "rel_slowdown": lambda df: df["walltime_mean"] / df.loc["(none)"]["walltime_mean"], - # workload_kind gets set to a String/PyObj in the previous aggregation. This convert it back to categorical - "workload_kind": lambda df: df["workload_kind"].astype(df_with_balanced_clusters["workload_kind"].dtype), - "workload_shortname": lambda df: df["workload_shortname"].astype(df_with_balanced_clusters["workload_shortname"].dtype), - }) - .assign(**{ - "log_rel_slowdown": lambda df: numpy.log(df["rel_slowdown"]), - }) - .loc[collector_order] -) - -assert df["collector"].nunique() == len(collector_order), "not all collectors in df are specified in collector_order" - -print(f"Check {tmp_output} for best and worst slowdowns; sometimes that indicates there is an error") -for collector in agged.index.levels[0]: - fig = matplotlib.figure.Figure() - ax = fig.add_subplot(1, 1, 1) - ax = agged.loc[collector]["rel_slowdown"].nlargest(20).plot.bar(ax=ax) - ax.set_title(f"{collector} worst slowdown") - ax.set_ylabel("Slowdown ratio") - fig.savefig(tmp_output / "worst_slowdowns_{collector}.png") - -for collector in agged.index.levels[0]: - fig = matplotlib.figure.Figure() - ax = fig.add_subplot(1, 1, 1) - ax = agged.loc[collector]["rel_slowdown"].nsmallest(20).plot.bar(ax=ax) - ax.set_title(f"{collector} best slowdown") - ax.set_ylabel("Slowdown ratio") - fig.savefig(tmp_output / "best_slowdowns_{collector}.png") - -print("All benchmarks:", ", ".join(agged.index.levels[1])) - -log_to_human_readable = lambda series: r"{:.0f}".format( - 100 * (numpy.exp(numpy.mean(series)) - 1), - # 100 * ( - # (numpy.exp(numpy.mean(series) + numpy.std(series)) - numpy.exp(numpy.mean(series) - numpy.std(series))) - # / 2 - # ), -) - -file = output_dir / "benchmark_groups_by_slowdown.tex" -print(f"Writing {file}") -file.write_text( - agged - .reset_index() - .groupby(["collector", "workload_kind"], observed=True) - .agg({"log_rel_slowdown": "mean"}) - .assign(**{ - "gmean": lambda df: [ - log_to_human_readable(x) - for x in df.log_rel_slowdown - ], - }) - .reset_index() - .pivot(index="collector", columns="workload_kind", values="gmean") - .pipe(lambda df: (df.index.__setattr__("name", None), df)[1]) - .pipe(lambda df: (df.columns.__setattr__("name", None), df)[1]) - .loc[collector_order] - .transpose() - .to_latex() - .replace("\\bottomrule", "\n".join([ - r"\midrule", - "Total (gmean) & " + " & ".join(list( - agged - .groupby(level=0, observed=True) - .agg(**{ - "gmean": pandas.NamedAgg("log_rel_slowdown", log_to_human_readable), - }) - .transpose() - [collector_order] - .loc["gmean"] - )) + r" \\", - r"\bottomrule", - ])) -) - - - diff --git a/benchmark/tasks.md b/benchmark/tasks.md new file mode 100644 index 00000000..811e4ae6 --- /dev/null +++ b/benchmark/tasks.md @@ -0,0 +1,6 @@ +- [ ] Change provenance_collectors.py -> PROBE to have a count() function. count() should transcribe and dump the provenance log. It should import `probe_py.generated.parser`. We should convert the Ops to ProvOperation, and return a tuple of them from count(). +- [ ] We should change stats.py -> output_features() to use the `op_type_freqs` from PROBE instead of from strace. Unlike with strace, grouping is not required. +- [ ] We should do a linear regression from `${x}_syscalls_per_sec` to `log_rel_overhead`. Compute the R^2 and mean squared error. +- [ ] Do a PCA on `${x}_syscalls_per_sec`. Emit a formula for the first principle component. Compute the percent of explained variance. +- [ ] Make a plot showing each trial. Show the first principle component on the x-axis, walltime on the y-axis, each dot is one trial. Also overlay a line which is the linear regression (as a function) applied to the first principle component (assuming the other components are zero). +- [ ] As much as possible, seek to script the answer to the previous questions, so that when we get new data, the analysis can be repeated on the new data. diff --git a/benchmark/util.py b/benchmark/util.py index 277f1673..ab9cc9d3 100644 --- a/benchmark/util.py +++ b/benchmark/util.py @@ -262,11 +262,15 @@ def n_unique(it: Iterable[Hashable]) -> int: return len(set(it)) -_system_nix_path = shutil.which("nix") -if _system_nix_path is None: - raise ValueError("Please add `nix` to the $PATH") +_system_nix_path_str = shutil.which("nix") +if _system_nix_path_str is None: + _system_nix_path = pathlib.Path(__file__).resolve().parent / "result/bin/nix" + if not _system_nix_path.exists(): + raise ValueError("Please add nix to the $PATH or run `nix build .#env`") +else: + _system_nix_path = pathlib.Path(_system_nix_path_str) _project_nix_path = check_returncode(subprocess.run( - [_system_nix_path, "shell", ".#which", ".#nix", "--command", "which", "nix"], + [str(_system_nix_path), "shell", ".#which", ".#nix", "--command", "which", "nix"], env=cast(Mapping[str, str], {}), capture_output=True, text=True, diff --git a/benchmark/workloads.py b/benchmark/workloads.py index c53cf1d0..b1484df1 100644 --- a/benchmark/workloads.py +++ b/benchmark/workloads.py @@ -1256,34 +1256,34 @@ def repeat(n: int, cmd: tuple[CmdArg, ...], no_stdout: bool = False) -> tuple[Cm ), name="0", ), - KaggleNotebook( - "ldfreeman3/a-data-science-framework-to-achieve-99-accuracy", - "competitions/titanic", - replace=( - ( - "from sklearn.preprocessing import Imputer , Normalizer", - ( - "from sklearn.impute import SimpleImputer as Imputer; " - "from sklearn.preprocessing import Normalizer" - ), - ), - ( - "from pandas.tools.plotting import scatter_matrix", - "from pandas.plotting import scatter_matrix", - ), - ("sns.factorplot(", "sns.catplot("), - (".corr()", ".corr(numeric_only=True)"), - ( - "data2.set_value(index, 'Random_Predict', 0)", - "data2.loc[index, 'Random_Predict'] = 0", - ), - ( - "data2.set_value(index, 'Random_Predict', 1)", - "data2.loc[index, 'Random_Predict'] = 1", - ), - ), - name="1", - ), + # KaggleNotebook( + # "ldfreeman3/a-data-science-framework-to-achieve-99-accuracy", + # "competitions/titanic", + # replace=( + # ( + # "from sklearn.preprocessing import Imputer , Normalizer", + # ( + # "from sklearn.impute import SimpleImputer as Imputer; " + # "from sklearn.preprocessing import Normalizer" + # ), + # ), + # ( + # "from pandas.tools.plotting import scatter_matrix", + # "from pandas.plotting import scatter_matrix", + # ), + # ("sns.factorplot(", "sns.catplot("), + # (".corr()", ".corr(numeric_only=True)"), + # ( + # "data2.set_value(index, 'Random_Predict', 0)", + # "data2.loc[index, 'Random_Predict'] = 0", + # ), + # ( + # "data2.set_value(index, 'Random_Predict', 1)", + # "data2.loc[index, 'Random_Predict'] = 1", + # ), + # ), + # name="1", + # ), # KaggleNotebook( # "yassineghouzam/titanic-top-4-with-ensemble-modeling", # "competitions/titanic", @@ -1437,12 +1437,16 @@ def repeat(n: int, cmd: tuple[CmdArg, ...], no_stdout: bool = False) -> tuple[Cm "working": [ workload for workload in WORKLOADS - if workload.kind != "w/Spack" and workload.name != "Linux" + if workload.kind != "w/Spack" and workload.name != "Linux" and workload.kind != "lmbench" ], "fast": [ workload for workload in WORKLOADS - if workload.name not in {"postmark", "titanic-to", "select-tcp", "spack spack-repo.mpich"} and workload.kind not in {"spack", "http_server", "splash3"} + if ( + workload.name not in {"postmark", "titanic-to", "select-tcp", "spack spack-repo.mpich", "Linux"} + and workload.kind not in {"w/Spack", "Linux", "http_server", "splash3"} + and workload.superkind not in {"Un/archive", "BLAST"} + ) ], "superfast": [ workload diff --git a/flake.nix b/flake.nix index a23e277d..0d8e3d9f 100644 --- a/flake.nix +++ b/flake.nix @@ -194,7 +194,6 @@ (python.withPackages (pypkgs: [ # probe_py.manual runtime requirements pypkgs.networkx - pypkgs.pygraphviz pypkgs.pydot pypkgs.rich pypkgs.typer diff --git a/probe_src/frontend/cli/src/record.rs b/probe_src/frontend/cli/src/record.rs index 0a0e113c..7c999e3c 100644 --- a/probe_src/frontend/cli/src/record.rs +++ b/probe_src/frontend/cli/src/record.rs @@ -24,11 +24,9 @@ pub fn record_no_transcribe( ) -> Result<()> { let output = match output { Some(x) => fs::canonicalize(x).wrap_err("Failed to canonicalize record directory path")?, - None => { - let mut output = std::env::current_dir().wrap_err("Failed to get CWD")?; - output.push("probe_record"); - output - } + None => std::env::current_dir() + .wrap_err("Failed to get CWD")? + .join("probe_record"), }; if overwrite { diff --git a/probe_src/python/pyproject.toml b/probe_src/python/pyproject.toml index 5b0d08b5..09bbf201 100644 --- a/probe_src/python/pyproject.toml +++ b/probe_src/python/pyproject.toml @@ -15,7 +15,6 @@ dynamic = ["version", "description"] dependencies = [ "probe_py.generated", "networkx", - "pygraphviz", "pydot", "rich", "typer", diff --git a/probe_src/tasks.md b/probe_src/tasks.md index 4bdec56e..4ed00ec3 100644 --- a/probe_src/tasks.md +++ b/probe_src/tasks.md @@ -130,9 +130,11 @@ Performance issues: - [ ] Test high mem - [ ] Put magic bytes in arena - - [ ] Use lock-free implementation of InodeTable +- [ ] Try to break it. Jenna has some input on this. + - [ ] In one terminal execute: `probe record --overwrite --no-transcribe --output .workdir/log/0/probe/ python -m http.server 54123 --directory .workdir/work/0/simple'`. In another, execute `hey -n 50000 http://localhost:54123/test'`. Notice `__arena_reinstantiate: openat: Too many open files`. + Documentation: - [ ] Make the CLI better. You shouldn't need to give `-f` to make repeated applications work. You shouldn't need to give `--input`.