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Sort experiment summarize #249

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merged 2 commits into from
Dec 13, 2023
Merged

Sort experiment summarize #249

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01f624c
Improve mardown for experiment summarize
ksuderman Dec 13, 2023
c371f14
Add --sort-by option to experiment.summarize
ksuderman Dec 13, 2023
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132 changes: 96 additions & 36 deletions abm/lib/experiment.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
import argparse
import json
import logging
import os
import threading
import traceback
from datetime import timedelta
from pprint import pprint
from time import perf_counter

import benchmark
Expand Down Expand Up @@ -119,35 +121,68 @@ def summarize(context: Context, args: list):
input_dirs = []
make_row = make_table_row
header_row = "Run,Cloud,Job Conf,Workflow,History,Inputs,Tool,Tool Version,State,Slots,Memory,Runtime (Sec),CPU,Memory Limit (Bytes),Memory Max usage (Bytes)"
for arg in args:
if arg in ['-t', '--tsv']:
if separator is not None or markdown:
print('ERROR: The output format is specified more than once')
return
print('tsv')
separator = '\t'
elif arg in ['-c', '--csv']:
if separator is not None or markdown:
print('ERROR: The output format is specified more than once')
return
separator = ','
print('csv')
elif arg in ['-m', '--model']:
if separator is not None or markdown:
print('ERROR: The output format is specified more than once')
return
print('making a model')
separator = ','
make_row = make_model_row
header_row = "job_id,tool_id,tool_version,state,memory.max_usage_in_bytes,cpuacct.usage,process_count,galaxy_slots,runtime_seconds,ref_data_size,input_data_size_1,input_data_size_2"
elif arg == '--markdown':
if separator is not None or markdown:
print('ERROR: The output format is specified more than once')
return
markdown = True
else:
# print(f"Input dir {arg}")
input_dirs.append(arg)
# for arg in args:
# if arg in ['-t', '--tsv']:
# if separator is not None or markdown:
# print('ERROR: The output format is specified more than once')
# return
# print('tsv')
# separator = '\t'
# elif arg in ['-c', '--csv']:
# if separator is not None or markdown:
# print('ERROR: The output format is specified more than once')
# return
# separator = ','
# print('csv')
# elif arg in ['-m', '--model']:
# if separator is not None or markdown:
# print('ERROR: The output format is specified more than once')
# return
# print('making a model')
# separator = ','
# make_row = make_model_row
# header_row = "job_id,tool_id,tool_version,state,memory.max_usage_in_bytes,cpuacct.usage,process_count,galaxy_slots,runtime_seconds,ref_data_size,input_data_size_1,input_data_size_2"
# elif arg == '--markdown':
# if separator is not None or markdown:
# print('ERROR: The output format is specified more than once')
# return
# markdown = True
# else:
# # print(f"Input dir {arg}")
# input_dirs.append(arg)

parser = argparse.ArgumentParser()
parser.add_argument('dirs', nargs='*')
parser.add_argument('-c', '--csv', action='store_true')
parser.add_argument('-t', '--tsv', action='store_true')
parser.add_argument('-m', '--model', action='store_true')
parser.add_argument('--markdown', action='store_true')
parser.add_argument('-s', '--sort-by', choices=['cpu', 'runtime', 'memory'])
argv = parser.parse_args(args)

count = 0
if argv.csv:
separator = ','
count += 1
if argv.tsv:
separator = '\t'
count += 1
if argv.model:
separator = ','
make_row = make_model_row
count += 1
if argv.markdown:
markdown = True
count += 1

if count == 0:
print("ERROR: no output format selected")
return
if count > 1:
print("ERROR: multiple output formats selected")
return

input_dirs = argv.dirs

if len(input_dirs) == 0:
input_dirs.append('metrics')
Expand All @@ -156,10 +191,13 @@ def summarize(context: Context, args: list):
separator = ','

if markdown:
print("|Run|Job Conf|Tool|Tool Version|State|Runtime (Sec)|CPU|Max Memory|")
print("|---|---|---|---|---|---|---|---|")
print("|Run|Job Conf|Tool|State|Runtime (Sec)|CPU (Sec) |Max Memory (GB)|")
print("|---|---|---|---|---:|---:|---:|")
else:
print(header_row)

table = list()
GB = float(1073741824)
for input_dir in input_dirs:
for file in os.listdir(input_dir):
input_path = os.path.join(input_dir, file)
Expand All @@ -172,18 +210,40 @@ def summarize(context: Context, args: list):
# print('Ignoring upload tool')
continue
row = make_row(data)
if markdown:
line = ' | '.join(row[i] for i in [0,2,6,7,8,11,12,14])
print(f'| {line} |')
else:
print(separator.join([str(x) for x in row]))
table.append(row)
except Exception as e:
# Silently fail to allow the remainder of the table to be generated.
print(f"Unable to process {input_path}")
print(e)
traceback.print_exc()
# pass

def comparator(row):
print('key', row[key])
print('type', type(row[key]))
return row[key]

if argv.sort_by:
key = 0
if argv.sort_by == 'runtime':
key = 10
elif argv.sort_by == 'cpu':
key = 11
elif argv.sort_by == 'memory':
key = 13
table.sort(key=lambda row: -1 if row[key] == '' else float(row[key]), reverse=True)

if markdown:
for row in table:
runtime = '' if len(row[10]) == 0 else f"{float(row[10]):4.1f}"
cpu = '' if len(row[11]) == 0 else f"{float(row[11])/10**9:4.1f}"
memory = '' if len(row[13]) == 0 else f"{float(row[13])/GB:4.3f}"
# memory = float(row[13]) / GB
print(f"| {row[0]} | {row[2]} | {row[6]} | {row[7]} | {runtime} | {cpu} | {memory} |")
else:
for row in table:
print(separator.join([str(x) for x in row]))


accept_metrics = [
'galaxy_slots',
Expand Down