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[WIP] Don't use gc in pandas join benchmark. #84

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[WIP] Don't use gc in pandas join benchmark. #84

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a5f3071
[WIP] Don't use gc in pandas join benchmark.
trivialfis May 3, 2019
4cc4bbb
Replace run parameter.
trivialfis May 3, 2019
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67 changes: 25 additions & 42 deletions pandas/join-pandas.py
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Original file line number Diff line number Diff line change
@@ -1,12 +1,10 @@
#!/usr/bin/env python

print("# join-pandas.py")

#!/usr/bin/env python3
import os
import gc
import timeit
import pandas as pd
# import pydoop.hdfs as hd
import sys
import argparse

exec(open("./helpers.py").read())

Expand All @@ -23,9 +21,9 @@
fun = "merge"
cache = "TRUE"

if os.path.basename(src_x)=="X1e9_2c.csv":
print("# join with pandas skipped for 1e9 x 1e9 (20GB x 20GB) due to memory error on 125GB mem machine")
exit(0)
if os.path.basename(src_x) == "X1e9_2c.csv":
print("# join with pandas skipped for 1e9 x 1e9 (20GB x 20GB) due to memory error on 125GB mem machine")
sys.exit(0)

print("loading datasets...")

Expand All @@ -39,40 +37,25 @@

print("joining...")

gc.collect()
t_start = timeit.default_timer()
ans = x.merge(y, how='inner', on='KEY')
print(ans.shape)
t = timeit.default_timer() - t_start
m = memory_usage()
t_start = timeit.default_timer()
chk = [ans['X2'].sum(), ans['Y2'].sum()]
chkt = timeit.default_timer() - t_start
write_log(task=task, data=data_name, in_rows=x.shape[0], question=question, out_rows=ans.shape[0], out_cols=ans.shape[1], solution=solution, version=ver, git=git, fun=fun, run=1, time_sec=t, mem_gb=m, cache=cache, chk=make_chk(chk), chk_time_sec=chkt)
del ans
def run_benchmark(run: int):
'''Run benchark for join operation.

run: The iteration number of current run.
'''
t_start = timeit.default_timer()
ans = x.merge(y, how='inner', on='KEY')
print('Shape:', ans.shape)
m = memory_usage()
t_start = timeit.default_timer()
chk = [ans['X2'].sum(), ans['Y2'].sum()]
chkt = timeit.default_timer() - t_start
write_log(task=task, data=data_name, in_rows=x.shape[0], question=question, out_rows=ans.shape[0], out_cols=ans.shape[1], solution=solution, version=ver, git=git, fun=fun, run=run, time_sec=t, mem_gb=m, cache=cache, chk=make_chk(chk), chk_time_sec=chkt)

gc.collect()
t_start = timeit.default_timer()
ans = x.merge(y, how='inner', on='KEY')
print(ans.shape)
t = timeit.default_timer() - t_start
m = memory_usage()
t_start = timeit.default_timer()
chk = [ans['X2'].sum(), ans['Y2'].sum()]
chkt = timeit.default_timer() - t_start
write_log(task=task, data=data_name, in_rows=x.shape[0], question=question, out_rows=ans.shape[0], out_cols=ans.shape[1], solution=solution, version=ver, git=git, fun=fun, run=2, time_sec=t, mem_gb=m, cache=cache, chk=make_chk(chk), chk_time_sec=chkt)
del ans

gc.collect()
t_start = timeit.default_timer()
ans = x.merge(y, how='inner', on='KEY')
print(ans.shape)
t = timeit.default_timer() - t_start
m = memory_usage()
t_start = timeit.default_timer()
chk = [ans['X2'].sum(), ans['Y2'].sum()]
chkt = timeit.default_timer() - t_start
write_log(task=task, data=data_name, in_rows=x.shape[0], question=question, out_rows=ans.shape[0], out_cols=ans.shape[1], solution=solution, version=ver, git=git, fun=fun, run=3, time_sec=t, mem_gb=m, cache=cache, chk=make_chk(chk), chk_time_sec=chkt)
del ans
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Run pandas join operation.')
parser.add_argument('--run', type=int, required=True)
args = parser.parse_args()

exit(0)
run_benchmark(args.run)
sys.exit(0)