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Merge pull request hail-is#31 from Nealelab/liam-add-custom-python-pa…
…ckages removed Anaconda from notebook init; added --pkgs option to cluster s…
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,165 +1,143 @@ | ||
| #!/usr/bin/env python | ||
|
|
||
| #!/usr/bin/python | ||
| import os | ||
| import json | ||
| import time | ||
| from subprocess import call, check_output | ||
| from subprocess import check_output, call | ||
|
|
||
| # get role of machine (master or worker) | ||
| role = check_output(['/usr/share/google/get_metadata_value', 'attributes/dataproc-role']) | ||
|
|
||
| # initialization actions to perform on master machine only | ||
| if role == 'Master': | ||
|
|
||
| # download Anaconda Python 2.7 installation script | ||
| call(['wget', '-P', '/home/anaconda2/', 'https://repo.continuum.io/archive/Anaconda2-4.3.1-Linux-x86_64.sh']) | ||
|
|
||
| # install Anaconda in /home/anaconda2/ | ||
| call(['bash', '/home/anaconda2/Anaconda2-4.3.1-Linux-x86_64.sh', '-b', '-f', '-p', '/home/anaconda2/']) | ||
| os.chmod('/home/anaconda2/', 0777) | ||
|
|
||
| # additional packages to install | ||
| pkgs = [ | ||
| 'lxml', | ||
| 'jupyter-spark', | ||
| 'jgscm' | ||
| ] | ||
|
|
||
| # use pip to install packages | ||
| for pkg in pkgs: | ||
| call(['/home/anaconda2/bin/pip', 'install', pkg]) | ||
|
|
||
| # get Hail hash and Spark version to use for Jupyter notebook, if set through cluster startup metadata | ||
| spark = check_output(['/usr/share/google/get_metadata_value', 'attributes/SPARK']) | ||
| hail_version = check_output(['/usr/share/google/get_metadata_value', 'attributes/HAIL_VERSION']) | ||
| hash_name = check_output(['/usr/share/google/get_metadata_value', 'attributes/HASH']) | ||
|
|
||
| # default to Spark 2.0.2 if not otherwise specified through metadata | ||
| if not spark: | ||
| spark = '2.0.2' | ||
|
|
||
| # default to version 0.1 | ||
| if not hail_version: | ||
| hail_version = '0.1' | ||
|
|
||
| # default to latest Hail build if none specified through metadata | ||
| if not hash_name: | ||
| hash_name = check_output(['gsutil', 'cat', 'gs://hail-common/builds/{0}/latest-hash-spark-{1}.txt'.format(hail_version, spark)]).strip() | ||
|
|
||
| # Hail jar | ||
| try: | ||
| custom_jar = check_output(['/usr/share/google/get_metadata_value', 'attributes/JAR']) | ||
| except: | ||
| hail_jar = 'hail-{0}-{1}-Spark-{2}.jar'.format(hail_version, hash_name, spark) | ||
| jar_path = 'gs://hail-common/builds/{0}/jars/{1}'.format(hail_version, hail_jar) | ||
| else: | ||
| hail_jar = custom_jar.rsplit('/')[-1] | ||
| jar_path = custom_jar | ||
|
|
||
| # Hail zip | ||
| try: | ||
| custom_zip = check_output(['/usr/share/google/get_metadata_value', 'attributes/ZIP']) | ||
| except: | ||
| hail_zip = 'hail-{0}-{1}.zip'.format(hail_version, hash_name) | ||
| zip_path = 'gs://hail-common/builds/{0}/python/{1}'.format(hail_version, hail_zip) | ||
| else: | ||
| hail_zip = custom_zip.rsplit('/')[-1] | ||
| zip_path = custom_zip | ||
|
|
||
| # make directory for Hail and Jupyter notebook related files | ||
| if not os.path.isdir('/home/hail/'): | ||
| os.mkdir('/home/hail/') | ||
| os.chmod('/home/hail/', 0777) | ||
|
|
||
| # copy Hail jar and zip to local directory on master node | ||
| call(['gsutil', 'cp', jar_path, '/home/hail/']) | ||
| call(['gsutil', 'cp', zip_path, '/home/hail/']) | ||
|
|
||
| # create Jupyter kernel spec file | ||
| kernel = { | ||
| 'argv': [ | ||
| '/home/anaconda2/bin/python', | ||
| '-m', | ||
| 'ipykernel', | ||
| '-f', | ||
| '{connection_file}' | ||
| ], | ||
| 'display_name': 'Hail', | ||
| 'language': 'python', | ||
| 'env': { | ||
| 'PYTHONHASHSEED': '0', | ||
| 'SPARK_HOME': '/usr/lib/spark/', | ||
| 'SPARK_CONF_DIR': '/home/hail/conf/', | ||
| 'PYTHONPATH': '/usr/lib/spark/python/:/usr/lib/spark/python/lib/py4j-0.10.3-src.zip:/home/hail/{}'.format(hail_zip) | ||
| } | ||
| } | ||
|
|
||
| # write kernel spec file to default Jupyter kernel directory | ||
| os.makedirs('/home/anaconda2/share/jupyter/kernels/hail/') | ||
| with open('/home/anaconda2/share/jupyter/kernels/hail/kernel.json', 'wb') as f: | ||
| json.dump(kernel, f) | ||
|
|
||
| # make directory for custom Spark conf | ||
| os.mkdir('/home/hail/conf') | ||
|
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||
| # copy conf files to custom directory | ||
| call(['cp', '/etc/spark/conf/spark-defaults.conf', '/home/hail/conf/spark-defaults.conf']) | ||
| call(['cp', '/etc/spark/conf/spark-env.sh', '/home/hail/conf/spark-env.sh']) | ||
|
|
||
| # modify custom Spark conf file to reference Hail jar and zip | ||
| with open('/home/hail/conf/spark-defaults.conf', 'ab') as f: | ||
| opts = [ | ||
| 'spark.files=/home/hail/{}'.format(hail_jar), | ||
| 'spark.submit.pyFiles=/home/hail/{}'.format(hail_zip), | ||
| 'spark.driver.extraClassPath=./{}'.format(hail_jar), | ||
| 'spark.executor.extraClassPath=./{}'.format(hail_jar) | ||
| ] | ||
| f.write('\n'.join(opts)) | ||
|
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| # add Spark variable designating Anaconda Python executable as the default on driver, in both custom and default conf files | ||
| with open('/home/hail/conf/spark-env.sh', 'ab') as f_custom, open('/etc/spark/conf/spark-env.sh', 'ab') as f_default: | ||
| f_custom.write('PYSPARK_DRIVER_PYTHON=/home/anaconda2/bin/python' + '\n') | ||
| f_default.write('PYSPARK_DRIVER_PYTHON=/home/anaconda2/bin/python' + '\n') | ||
|
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||
| # create Jupyter configuration file | ||
| call(['mkdir', '-p', '/home/anaconda2/etc/jupyter/']) | ||
| with open('/home/anaconda2/etc/jupyter/jupyter_notebook_config.py', 'wb') as f: | ||
| opts = [ | ||
| 'c.Application.log_level = "DEBUG"', | ||
| 'c.NotebookApp.ip = "127.0.0.1"', | ||
| 'c.NotebookApp.open_browser = False', | ||
| 'c.NotebookApp.port = 8123', | ||
| 'c.NotebookApp.token = ""', | ||
| 'c.NotebookApp.contents_manager_class = "jgscm.GoogleStorageContentManager"' | ||
| ] | ||
| f.write('\n'.join(opts) + '\n') | ||
|
|
||
| # setup jupyter-spark extension | ||
| call(['/home/anaconda2/bin/jupyter', 'serverextension', 'enable', '--user', '--py', 'jupyter_spark']) | ||
| call(['/home/anaconda2/bin/jupyter', 'nbextension', 'install', '--user', '--py', 'jupyter_spark']) | ||
| call(['/home/anaconda2/bin/jupyter', 'nbextension', 'enable', '--user', '--py', 'jupyter_spark']) | ||
| call(['/home/anaconda2/bin/jupyter', 'nbextension', 'enable', '--user', '--py', 'widgetsnbextension']) | ||
|
|
||
| # create systemd service file for Jupyter notebook server process | ||
| with open('/lib/systemd/system/jupyter.service', 'wb') as f: | ||
| opts = [ | ||
| '[Unit]', | ||
| 'Description=Jupyter Notebook', | ||
| 'After=hadoop-yarn-resourcemanager.service', | ||
| '[Service]', | ||
| 'Type=simple', | ||
| 'User=root', | ||
| 'Group=root', | ||
| 'WorkingDirectory=/home/hail/', | ||
| 'ExecStart=/home/anaconda2/bin/python /home/anaconda2/bin/jupyter notebook', | ||
| 'Restart=always', | ||
| 'RestartSec=1', | ||
| '[Install]', | ||
| 'WantedBy=multi-user.target' | ||
| ] | ||
| f.write('\n'.join(opts) + '\n') | ||
|
|
||
| # add Jupyter service to autorun and start it | ||
| call(['systemctl', 'daemon-reload']) | ||
| call(['systemctl', 'enable', 'jupyter']) | ||
| call(['service', 'jupyter', 'start']) | ||
| # install pip | ||
| call(['apt-get', 'update']) | ||
| call(['apt-get', 'install', '-y', 'python-dev']) | ||
| call(['apt-get', 'install', '-y', 'python-pip']) | ||
| call(['pip', 'install', '--upgrade', 'pip']) | ||
|
|
||
| # additional packages to install | ||
| pkgs = [ | ||
| 'decorator', | ||
| 'jupyter', | ||
| 'lxml', | ||
| 'jupyter-spark', | ||
| 'jgscm' | ||
| ] | ||
|
|
||
| # add user-requested packages | ||
| try: | ||
| user_pkgs = check_output(['/usr/share/google/get_metadata_value', 'attributes/PKGS']) | ||
| except: | ||
| pass | ||
| else: | ||
| pkgs.extend(user_pkgs.split(',')) | ||
|
|
||
| # use pip to install packages | ||
| for pkg in pkgs: | ||
| call(['pip', 'install', '--upgrade', pkg]) | ||
|
|
||
| # get Hail hash and Spark version to use for Jupyter notebook, if set through cluster startup metadata | ||
| spark = check_output(['/usr/share/google/get_metadata_value', 'attributes/SPARK']) | ||
| hail_version = check_output(['/usr/share/google/get_metadata_value', 'attributes/HAIL_VERSION']) | ||
| hash_name = check_output(['/usr/share/google/get_metadata_value', 'attributes/HASH']) | ||
|
|
||
| # Hail jar | ||
| try: | ||
| custom_jar = check_output(['/usr/share/google/get_metadata_value', 'attributes/JAR']) | ||
| except: | ||
| hail_jar = 'hail-{0}-{1}-Spark-{2}.jar'.format(hail_version, hash_name, spark) | ||
| jar_path = 'gs://hail-common/builds/{0}/jars/{1}'.format(hail_version, hail_jar) | ||
| else: | ||
| hail_jar = custom_jar.rsplit('/')[-1] | ||
| jar_path = custom_jar | ||
|
|
||
| # Hail zip | ||
| try: | ||
| custom_zip = check_output(['/usr/share/google/get_metadata_value', 'attributes/ZIP']) | ||
| except: | ||
| hail_zip = 'hail-{0}-{1}.zip'.format(hail_version, hash_name) | ||
| zip_path = 'gs://hail-common/builds/{0}/python/{1}'.format(hail_version, hail_zip) | ||
| else: | ||
| hail_zip = custom_zip.rsplit('/')[-1] | ||
| zip_path = custom_zip | ||
|
|
||
| # copy Hail jar and zip to local directory on master node | ||
| call(['gsutil', 'cp', jar_path, '/usr/lib/spark/jars/']) | ||
| call(['gsutil', 'cp', zip_path, '/usr/lib/spark/python/']) | ||
|
|
||
| # modify custom Spark conf file to reference Hail jar and zip | ||
| with open('/etc/spark/conf/spark-defaults.conf', 'a') as f: | ||
| opts = [ | ||
| 'spark.files=/usr/lib/spark/jars/{}'.format(hail_jar), | ||
| 'spark.submit.pyFiles=/usr/lib/spark/python/{}'.format(hail_zip), | ||
| 'spark.driver.extraClassPath=./{}'.format(hail_jar), | ||
| 'spark.executor.extraClassPath=./{}'.format(hail_jar) | ||
| ] | ||
| f.write('\n'.join(opts)) | ||
|
|
||
| # create Jupyter kernel spec file | ||
| kernel = { | ||
| 'argv': [ | ||
| '/usr/bin/python', | ||
| '-m', | ||
| 'ipykernel', | ||
| '-f', | ||
| '{connection_file}' | ||
| ], | ||
| 'display_name': 'Hail', | ||
| 'language': 'python', | ||
| 'env': { | ||
| 'PYTHONHASHSEED': '0', | ||
| 'SPARK_HOME': '/usr/lib/spark/', | ||
| 'SPARK_CONF_DIR': '/etc/spark/conf/', | ||
| 'PYTHONPATH': '/usr/lib/spark/python/:/usr/lib/spark/python/lib/py4j-0.10.3-src.zip:/usr/lib/spark/python/{}'.format(hail_zip) | ||
| } | ||
| } | ||
|
|
||
| # write kernel spec file to default Jupyter kernel directory | ||
| os.mkdir('/usr/local/share/jupyter/kernels/hail/') | ||
| with open('/usr/local/share/jupyter/kernels/hail/kernel.json', 'w') as f: | ||
| json.dump(kernel, f) | ||
|
|
||
| # create Jupyter configuration file | ||
| os.mkdir('/usr/local/etc/jupyter/') | ||
| with open('/usr/local/etc/jupyter/jupyter_notebook_config.py', 'w') as f: | ||
| opts = [ | ||
| 'c.Application.log_level = "DEBUG"', | ||
| 'c.NotebookApp.ip = "127.0.0.1"', | ||
| 'c.NotebookApp.open_browser = False', | ||
| 'c.NotebookApp.port = 8123', | ||
| 'c.NotebookApp.token = ""', | ||
| 'c.NotebookApp.contents_manager_class = "jgscm.GoogleStorageContentManager"' | ||
| ] | ||
| f.write('\n'.join(opts) + '\n') | ||
|
|
||
| # setup jupyter-spark extension | ||
| call(['/usr/local/bin/jupyter', 'serverextension', 'enable', '--user', '--py', 'jupyter_spark']) | ||
| call(['/usr/local/bin/jupyter', 'nbextension', 'install', '--user', '--py', 'jupyter_spark']) | ||
| call(['/usr/local/bin/jupyter', 'nbextension', 'enable', '--user', '--py', 'jupyter_spark']) | ||
| call(['/usr/local/bin/jupyter', 'nbextension', 'enable', '--user', '--py', 'widgetsnbextension']) | ||
|
|
||
| # create systemd service file for Jupyter notebook server process | ||
| with open('/lib/systemd/system/jupyter.service', 'w') as f: | ||
| opts = [ | ||
| '[Unit]', | ||
| 'Description=Jupyter Notebook', | ||
| 'After=hadoop-yarn-resourcemanager.service', | ||
| '[Service]', | ||
| 'Type=simple', | ||
| 'User=root', | ||
| 'Group=root', | ||
| 'WorkingDirectory=/usr/local/', | ||
| 'ExecStart=/usr/bin/python /usr/local/bin/jupyter notebook --allow-root', | ||
| 'Restart=always', | ||
| 'RestartSec=1', | ||
| '[Install]', | ||
| 'WantedBy=multi-user.target' | ||
| ] | ||
| f.write('\n'.join(opts) + '\n') | ||
|
|
||
| # add Jupyter service to autorun and start it | ||
| call(['systemctl', 'daemon-reload']) | ||
| call(['systemctl', 'enable', 'jupyter']) | ||
| call(['service', 'jupyter', 'start']) |
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