forked from bellwether/minerva
improved run_cluster.py; touching up the dask test; upgrade pyarrow dependency for security patch
This commit is contained in:
Ari Brown
parent
c6280a3826
commit
210e7ebd92
3 changed files with 99 additions and 40 deletions
106
dask_test.py
106
dask_test.py
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@ -2,64 +2,112 @@ import sys
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import minerva
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from minerva.timing import Timing
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import dask
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import dask.distributed
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from dask.distributed import Client
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import dask.dataframe as dd
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import time
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m = minerva.Minerva("hay")
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print(f"connecting to {sys.argv[1]}")
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client = Client(sys.argv[1])
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#client = Client()
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manifest_files = ['s3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_0934fdc9-1bc7-4dae-a371-c3f58f3b31fc',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_7011b49a-bf6c-42d0-9852-85aa10a3ad37',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_8ca98d70-74c2-4d17-b059-83cd25e398c0',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_61265893-e992-4026-8b69-e60a4641dd10',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_d4318a64-7fc0-4b59-8f85-8b1790e72a70',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_4e2e19a8-b360-49fe-9b82-f66a1e23ad3e',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_c5a77760-f078-432c-aaf5-6d99fb0cee0c',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_db5f90f3-9fc0-4b86-98da-d840bb9b5423',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_2472c560-1113-448b-ae18-e23032d3f3d8',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_551944ef-47f4-475d-a575-e209ca1ee7b4',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_67569166-18f9-40bd-9845-20f069f8dc8a',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_8a81dca0-767d-43bf-b0aa-a087f98d41c5',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_c9dd6a02-0f92-4202-ba70-77fda02d4acf',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_9f094026-03f4-4ec2-a348-0498eeb6b04d',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_2c20c942-1e2c-4f37-86ec-4adce83edbea',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_237d6c26-8372-4584-ae15-9f693d2295a6',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_cf41cbf5-eb46-4bb9-b904-f1518affbefa',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_420f8434-5a71-4af8-91b5-d5364c941ded',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_f155616d-39bc-483e-b19a-56da9fbae685',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_ef8a7770-43b7-44bb-9dde-f92ed8faae9b',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_8aa7de20-91ee-4ada-8f48-c7a5b313572f',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_7c265580-ada5-4b94-b818-5cebdb4bb6c6',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_13562caf-4578-4e36-83fe-8b7a5eabc7e8',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_b0f80cd3-4aa5-40ac-a0c8-632c763f8969',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_2f1e190b-621c-4638-91f1-e961ba674714',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_5dcd43e4-67bd-41ba-b3cd-7e8f8da9b1f9',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_293c6916-4f22-4ca0-a240-078ebe48368b',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_80e8c47e-f254-47c4-80af-d744885e8174',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_6b1ba112-0545-4c3f-9321-dbf597d98bc1',
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's3://haystac-pmo-athena/results/0.12892323498922598/20231127_175506_00007_3735a_0b3dd1a8-72ef-4852-bf1d-f7091629d3b6']
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def full_s3(obj):
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return "s3://" + obj.bucket_name + "/" + obj.key
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try:
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# Practice with a big array
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# https://matthewrocklin.com/blog/work/2017/01/12/dask-dataframes
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#import numpy as np
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#import dask.array as da
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import dask.dataframe as dd
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import time
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# https://stackoverflow.com/questions/43796774/loading-local-file-from-client-onto-dask-distributed-cluster
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athena = m.athena("s3://haystac-pmo-athena/")
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records = 1_000_000_000
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# Iteratively load files and scatter them to the cluster
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with Timing("athena query"):
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query = athena.execute("select * from trajectories.kitware limit 1000000", format='csv')
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query.finish()
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df = dd.read_csv(query.info_cache['ResultConfiguration']['OutputLocation'])
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with Timing("read parquet from athena"):
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# Delta Table
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#files = m.s3.ls("s3://haystac-archive-phase1.trial1/ta1.kitware/ta1/simulation/train/")
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#parqs = [full_s3(o) for o in files if o.key.endswith('.parquet')]
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#query = athena.query("select * from trajectories.kitware limit 100000000")
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# 20 partitions at a time, concat 20 at a time
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#df = dd.read_parquet(parqs[0:20])#.astype({"agent": "category",
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# # "timestamp": "datetime64[ns, UTC]"})
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#for i in range(20, len(parqs), 20):
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# new = dd.read_parquet(parqs[i:i + 20])#.astype({"agent": "category",
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# # "timestamp": "datetime64[ns, UTC]"})
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# df = df.concat(new)
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# 20 partitions at a time, concat all at once
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#df = dd.concat([dd.read_parquet(parqs[i:i + 20], engine='fastparquet') for i in range(0, len(parqs), 20)])
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# All partitions at once
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#df = dd.read_parquet(parqs, engine='fastparquet')
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# Single CSV file
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#query = athena.execute(f"select * from trajectories.kitware limit {records}", format="csv")
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#query.finish()
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#df = dd.read_csv(query.info_cache['ResultConfiguration']['OutputLocation'])
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# Unload to Parquet files
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#query = athena.query(f"select * from trajectories.kitware limit {records}")
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#df = dd.read_parquet(query.manifest_files())
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#df = query.distribute_results(client, size=10000)
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df = dd.read_parquet(manifest_files)
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print("distributed")
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with Timing("partitioning"):
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#df = df.categorize('agent')
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#df['agent'] = df['agent'].cat.as_ordered()
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#partitions = df.describe(include=['category']).compute().iloc[0][0]
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#df = df.set_index('agent', npartitions=partitions)
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divisions = list(range(0, 10001))
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df = df.set_index('agent', divisions=divisions)
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with Timing("persisting"):
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dp = df.persist()
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import IPython
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IPython.embed()
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#import IPython
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#IPython.embed()
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with Timing("count()"):
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print(dp.count().visualize(filename='count.svg'))
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print(dp.count().compute())
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with Timing("mean latitude"):
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print(dp.groupby(dp.index).latitude.mean().visualize(filename='latitude.svg'))
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print(dp.groupby(dp.index).latitude.mean().compute())
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with Timing("mean longitude"):
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print(dp.groupby(dp.index).longitude.mean().visualize(filename='longitude.svg'))
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with Timing("count()"):
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print(dp.count().compute())
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#with Timing("mean longitude"):
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# print(dp.groupby(dp.index).longitude.mean().compute())
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finally:
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########## FIN #######################
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print("closing client")
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client.close()
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print("end")
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input()
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#print("end")
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#input()
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@ -18,7 +18,7 @@ minerva-console = "minerva.console:main"
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[tool.poetry.dependencies]
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python = ">3.9, <3.12"
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boto3 = "^1.26.161"
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pyarrow = "^12.0.1"
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pyarrow = "^14.0.1"
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joblib = "^1.1.0"
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fabric = "^3.0.0"
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s3fs = "2023.9.2"
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s3fs = "2023.6.0"
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@ -4,9 +4,12 @@ from minerva.pier import Pier
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########### PREP ############################
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# modin base (built on dask base)
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DASK_BASE = "ami-0a8b05658a4f00e52" # dask on ubuntu 22.04 x86
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def worker(pier, n):
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mach = pier.machine(ami = "ami-0a3df8365ed416816", # dask on ubuntu 22.04 x86
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instance_type = "t3.medium",
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mach = pier.machine(ami = DASK_BASE,
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instance_type = "r5.xlarge",
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username = "ubuntu",
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name = f"dask-worker-{n}",
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variables = {"type": "worker",
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@ -15,8 +18,8 @@ def worker(pier, n):
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return mach
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def scheduler(pier):
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mach = pier.machine(ami = "ami-0a3df8365ed416816", # dask on ubuntu 22.04 x86
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instance_type = "t3.medium",
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mach = pier.machine(ami = DASK_BASE,
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instance_type = "r5.xlarge",
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username = "ubuntu",
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name = f"dask-scheduler",
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variables = {"type": "scheduler"},
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@ -35,9 +38,17 @@ pier = m.pier(subnet_id = "subnet-05eb26d8649a093e1", # project-subnet-public
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cluster = pier.cluster(scheduler, worker, num_workers=int(sys.argv[1]))
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cluster.start()
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print(cluster.public_location)
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print("press enter to terminate cluster")
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input()
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print()
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print(f"dashboard: http://{cluster.scheduler.public_ip}:8787/")
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print(f"cluster: {cluster.public_location}")
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print()
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print("type `exit()` to terminate the cluster")
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print()
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import IPython
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IPython.embed()
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cluster.terminate()
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