community/pbs/scripts/startup-script.py

#!/usr/bin/python # -*- coding: utf-8 -*- # Copyright 2018 Google Inc. All Rights Reserved. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # # Configure PBS Pro Open Source Edition cluster on GCP (https://www.pbspro.org/) # Create deployment: "gcloud deployment-manager deployments --project=<project-name> create <deployment-name> --config pbs-cluster.yaml" # Clean-up (delete) deployment: "gcloud deployment-manager deployments delete --project=<project-name> <deployment-name>" # import httplib import os import shlex import subprocess import time import urllib import urllib2 import socket CLUSTER_NAME = '@CLUSTER_NAME@' MACHINE_TYPE = '@MACHINE_TYPE@' # e.g. n1-standard-1, n1-starndard-2 INSTANCE_TYPE = '@INSTANCE_TYPE@' #'controller' #'@INSTANCE_TYPE@' # e.g. controller or compute PROJECT = '@PROJECT@' ZONE = '@ZONE@' APPS_DIR = '/apps' PBS_VERSION = '@PBS_VERSION@' STATIC_NODE_COUNT = @STATIC_NODE_COUNT@ COMPUTE_PUBLIC_IPS = @COMPUTE_PUBLIC_IPS@ PBS_PREFIX = APPS_DIR + '/pbs/pbs-' + PBS_VERSION INSTANCE_NAME_PREFIX = '@INSTANCE_NAME_PREFIX@' MOTD_HEADER = ''' ********* PBS PRO ********* qsub submit a pbs job qdel delete pbs batch job qhold hold pbs batch jobs qrls release hold on pbs batch jobs qstat -q list all queues qstat -a list all jobs qstat -u userid list jobs for userid qstat -r list running jobs qstat -f job_id list full information about job_id qstat -Qf queue list full information about queue qstat -B list summary status of the job server pbsnodes -a list status of all compute nodes tracejob Extracts job info from log files sudo /etc/init.d/pbs restart Restart PBS export PATH=$PATH:/opt/pbs/bin/ ''' NodeName="" def add_pbs_user(): PBS_UID = str(992) subprocess.call(['groupadd', '-g', PBS_UID, 'pbs']) subprocess.call(['useradd', '-m', '-c', 'PBS Workload Manager', '-d', '/var/lib/pbs', '-u', PBS_UID, '-g', 'pbs', '-s', '/bin/bash', 'pbs']) # END add_pbs_user() def start_motd(): msg = MOTD_HEADER + """ *** PBS is currently being installed/configured in the background. *** A terminal broadcast will announce when installation and configuration is complete. You can check startup log messages in /var/log/messages To run startup script again: sudo google_metadata_script_runner --script-type startup More info: https://cloud.google.com/compute/docs/startupscript#rerunthescript """ if INSTANCE_TYPE != "controller": msg += """/home on the controller will be mounted over the existing /home. Any changes in /home will be hidden. Please wait until the installation is complete before making changes in your home directory. """ f = open('/etc/motd', 'w') f.write(msg) f.close() # END start_motd() def end_motd(): f = open('/etc/motd', 'w') f.write(MOTD_HEADER) f.close() subprocess.call(['wall', '-n', '*** PBS ' + INSTANCE_TYPE + ' daemon installation complete ***']) if INSTANCE_TYPE != "controller": subprocess.call(['wall', '-n', """ /home on the controller was mounted over the existing /home. Either log out and log back in or cd into ~. """]) #END start_motd() def have_internet(): conn = httplib.HTTPConnection("www.google.com", timeout=1) try: conn.request("HEAD", "/") conn.close() return True except: conn.close() return False #END have_internet() def install_packages(): packages = [ 'munge', 'munge-devel', 'munge-libs', 'wget', 'gcc', 'make', 'rpm-build', 'libtool', 'hwloc-devel', 'libX11-devel', 'libXt-devel', 'libedit-devel', 'libical-devel', 'ncurses-devel', 'perl', 'postgresql-devel', 'python-devel', 'tcl-devel', 'tk-devel', 'swig', 'expat-devel', 'openssl-devel', 'libXext', 'libXft', 'expat', 'libedit', 'postgresql-server', 'python', 'sendmail', 'sudo', 'tcl', 'tk', 'libical', 'unzip', 'nfs-utils', 'nfs-utils-lib' ] while subprocess.call(['yum', 'install', '-y'] + packages): print "yum failed to install packages. Trying again in 5 seconds" time.sleep(5) #END install_packages() def setup_nfs_exports(): f = open('/etc/exports', 'w') f.write(""" /home *(rw,sync,no_subtree_check,no_root_squash) %s *(rw,sync,no_subtree_check,no_root_squash) """ % APPS_DIR) f.close() subprocess.call(shlex.split("exportfs -a")) #END setup_nfs_exports() def expand_machine_type(): # Force re-evaluation of site-packages so that namespace packages (such # as google-auth) are importable. This is needed because we install the # packages while this script is running and do not have the benefit of # restarting the interpreter for it to do it's usual startup sequence to # configure import magic. import sys import site for path in [x for x in sys.path if 'site-packages' in x]: site.addsitedir(path) import googleapiclient.discovery # Assume sockets is 1. Currently, no instances with multiple sockets # Assume hyper-threading is on and 2 threads per core machine = {'sockets': 1, 'cores': 1, 'threads': 1, 'memory': 1} try: compute = googleapiclient.discovery.build('compute', 'v1', cache_discovery=False) type_resp = compute.machineTypes().get(project=PROJECT, zone=ZONE, machineType=MACHINE_TYPE).execute() if type_resp: tot_cpus = type_resp['guestCpus'] if tot_cpus > 1: machine['cores'] = tot_cpus / 2 machine['threads'] = 2 # Because the actual memory on the host will be different than what # is configured (e.g. kernel will take it). From experiments, about # 16 MB per GB are used (plus about 400 MB buffer for the first # couple of GB's. Using 30 MB to be safe. gb = type_resp['memoryMb'] / 1024; machine['memory'] = type_resp['memoryMb'] - (400 + (gb * 30)) except Exception, e: print "Failed to get MachineType '%s' from google api (%s)" % (MACHINE_TYPE, str(e)) return machine #END expand_machine_type() def install_pbs(): #Ex. Source http://wpc.23a7.iotacdn.net/8023A7/origin2/rl/PBS-Open/pbspro_18.1.2.centos7.zip #Ex2: https://s3.amazonaws.com/pbspro/pbspro-server-18.1.1-0.x86_64.rpm #Ex3: https://github.com/PBSPro/pbspro/releases/download/v18.1.3/pbspro_18.1.3.centos7.zip BASE_URL = 'https://github.com/PBSPro/pbspro/releases/download/' file = 'v' + PBS_VERSION + '/pbspro_' + PBS_VERSION + '.centos7.zip' print "Will download %s to /tmp/ directory" % file urllib.urlretrieve(BASE_URL + file, '/tmp/pbs.zip') prev_path = os.getcwd() os.chdir('/tmp') pkgPbs = "/tmp/" + file subprocess.call(['unzip', '-o', 'pbs.zip']) os.chdir('/tmp/pbspro_' + PBS_VERSION + '.centos7') subprocess.call(['yum', 'install', '-y', 'pbspro-server-' + PBS_VERSION + '-0.x86_64.rpm']) #END install_pbs() def install_pbs_tmpfile(): run_dir = '/var/run/pbs' f = open('/etc/tmpfiles.d/pbs.conf', 'w') f.write(""" d %s 0755 pbs pbs - """ % run_dir) f.close() if not os.path.exists(run_dir): os.makedirs(run_dir) os.chmod(run_dir, 0o755) subprocess.call(['chown', 'pbs:', run_dir]) #END install_pbs_tmpfile() def install_controller_service_scripts(): install_pbs_tmpfile() # pbsctld.service f = open('/usr/lib/systemd/system/pbsctld.service', 'w') f.write(""" [Unit] Description=PBS controller daemon After=network.target munge.service ConditionPathExists={prefix}/etc/pbs.conf [Service] Type=forking EnvironmentFile=-/etc/sysconfig/pbsctld ExecStart={prefix}/sbin/pbsctld $PBSCTLD_OPTIONS ExecReload=/bin/kill -HUP $MAINPID PIDFile=/var/run/pbs/pbsctld.pid [Install] WantedBy=multi-user.target """.format(prefix = PBS_PREFIX)) f.close() os.chmod('/usr/lib/systemd/system/pbsctld.service', 0o644) # pbsdbd.service f = open('/usr/lib/systemd/system/pbsdbd.service', 'w') f.write(""" [Unit] Description=PPS DBD accounting daemon After=network.target munge.service ConditionPathExists={prefix}/etc/pbsdbd.conf [Service] Type=forking EnvironmentFile=-/etc/sysconfig/pbsdbd ExecStart={prefix}/sbin/pbsdbd $PBSDBD_OPTIONS ExecReload=/bin/kill -HUP $MAINPID PIDFile=/var/run/pbs/pbsdbd.pid [Install] WantedBy=multi-user.target """.format(prefix = APPS_DIR + "/pbs/current")) f.close() os.chmod('/usr/lib/systemd/system/pbsdbd.service', 0o644) #END install_controller_service_scripts() def install_compute_service_scripts(): install_pbs_tmpfile() #config {test} f = open('/etc/pbs.conf', 'w') f.write(""" PBS_EXEC=/opt/pbs PBS_SERVER={instance_prefix}controller PBS_START_SERVER=0 PBS_START_SCHED=0 PBS_START_COMM=1 PBS_START_MOM=1 PBS_HOME=/var/spool/pbs PBS_CORE_LIMIT=unlimited PBS_SCP=/bin/scp """.format(instance_prefix = INSTANCE_NAME_PREFIX)) f.close() # pbsd.service f = open('/usr/lib/systemd/system/pbsd.service', 'w') f.write(""" [Unit] Description=pbs node daemon After=network.target munge.service ConditionPathExists={prefix}/etc/pbs.conf [Service] Type=forking EnvironmentFile=-/etc/sysconfig/pbsd ExecStart={prefix}/sbin/pbsd $PBSD_OPTIONS ExecReload=/bin/kill -HUP $MAINPID PIDFile=/var/run/pbs/pbsd.pid KillMode=process LimitNOFILE=51200 LimitMEMLOCK=infinity LimitSTACK=infinity [Install] WantedBy=multi-user.target """.format(prefix = APPS_DIR + "/pbs/current")) f.close() os.chmod('/usr/lib/systemd/system/pbsd.service', 0o644) #END install_compute_service_scripts() def setup_bash_profile(): f = open('/etc/profile.d/pbs.sh', 'w') f.write(""" S_PATH=/opt/pbs PATH=$PATH:$S_PATH/bin """) f.close() #END setup_bash_profile() def mount_nfs_vols(): f = open('/etc/fstab', 'a') f.write(""" {1}controller:{0} {0} nfs rw,sync,hard,intr 0 0 {1}controller:/home /home nfs rw,sync,hard,intr 0 0 """.format(APPS_DIR, INSTANCE_NAME_PREFIX)) f.close() while subprocess.call(['mount', '-a']): print "Waiting for " + APPS_DIR + " and /home to be mounted" time.sleep(5) #END mount_nfs_vols() def test_pbs(): urllib.urlretrieve('https://s3.amazonaws.com/pbspro/test.zip', '/tmp/test.zip') os.chdir('/tmp') subprocess.call(['unzip', '-o', 'test.zip']) #install pip urllib.urlretrieve('https://bootstrap.pypa.io/get-pip.py', '/tmp/get-pip.py') subprocess.call(['python', 'get-pip.py']) os.chdir('/tmp/test/fw') subprocess.call(shlex.split('pip install -r requirements.txt .')) subprocess.call(shlex.split('pbs_config --make-ug')) os.chdir('/tmp/test/tests') subprocess.call(shlex.split('pbs_benchpress -l INFOCLI2 -o ptl.txt')) #END test_pbs() def register_compute_nodes(): host = socket.gethostname(); for node_id in range(1, STATIC_NODE_COUNT+1): cmd_create_node = "/opt/pbs/bin/qmgr -c 'create node " + INSTANCE_NAME_PREFIX + "compute" + str(node_id) + "'" print "will execute: " + cmd_create_node subprocess.call(shlex.split(cmd_create_node)) #END create_node() def main(): # Disable SELinux subprocess.call(shlex.split('setenforce 0')) print "ARGUMENT STATIC_NODE_COUNT: @STATIC_NODE_COUNT@" #if ((INSTANCE_TYPE == "controller") and not COMPUTE_PUBLIC_IPS): if (INSTANCE_TYPE == "controller"): # Setup a NAT gateway for the compute instances to get internet from. subprocess.call(shlex.split("sysctl -w net.ipv4.ip_forward=1")) subprocess.call(shlex.split("firewall-cmd --direct --add-rule ipv4 nat POSTROUTING 0 -o eth0 -j MASQUERADE")) subprocess.call(shlex.split("firewall-cmd --reload")) subprocess.call(shlex.split("echo net.ipv4.ip_forward=1 >> /etc/sysctl.conf")) if INSTANCE_TYPE == "compute": while not have_internet(): print "Waiting for internet connection" add_pbs_user() start_motd() print "Installing packages..." install_packages() if not os.path.exists(APPS_DIR + '/pbs'): os.makedirs(APPS_DIR + '/pbs') if INSTANCE_TYPE != "controller": mount_nfs_vols() if INSTANCE_TYPE == "controller": print "Installing PBS on controller node..." install_pbs() print "Installing PBS service scripts..." install_controller_service_scripts() print "Starting PBS process..." subprocess.call(shlex.split('/etc/init.d/pbs start')) print "Registering compute nodes ..." register_compute_nodes() # Export at the end to signal that everything is up subprocess.call(shlex.split('systemctl enable nfs-server')) subprocess.call(shlex.split('systemctl start nfs-server')) setup_nfs_exports() elif INSTANCE_TYPE == "compute": print "Installing PBS on compute node..." install_pbs() install_compute_service_scripts() subprocess.call(shlex.split('systemctl enable pbsd')) subprocess.call(shlex.split('systemctl start pbsd')) print "Installed additional components on compute node" end_motd() print "Setting up bash profile..." setup_bash_profile() print "Restarting PBS to get activate new configuration..." subprocess.call(shlex.split("/etc/init.d/pbs restart")) subprocess.call(["wall", "Completed PBS installation"]) #test_pbs() print "Completed PBS installation on " + INSTANCE_TYPE # END main() if __name__ == '__main__': main()

community/pbs/scripts/startup-script.py (260 lines of code) (raw):