-
Notifications
You must be signed in to change notification settings - Fork 2
/
scidbplugin.py
293 lines (237 loc) · 13.6 KB
/
scidbplugin.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
import os
import time
import random
import string
from starcluster.clustersetup import DefaultClusterSetup
from starcluster.exception import RemoteCommandFailed
from starcluster.logger import log
SCIDB_VERSION = 14.8
SCIDB_REVISION = 8628
POSTGRES_VERSION = '9.1'
#SCIDB_INSTALL_PATH = '/opt/scidb/$SCIDB_VER'
DEFAULT_USERNAME = 'scidb'
DEFAULT_REPOSITORY = 'https://github.com/BrandonHaynes/scidb.git'
DEFAULT_BRANCH = None
DEFAULT_SHIM_PACKAGE_URI = 'https://paradigm4.github.io/shim/shim_14.8_amd64.deb'
DEFAULT_DIRECTORY = '/mnt/scidb'
DEFAULT_CLIENTS = '0.0.0.0/0'
DEFAULT_BUILD_TYPE = 'RelWithDebInfo'
DEFAULT_BUILD_THREADS = 4
DEFAULT_REDUNDANCY = 0
DEFAULT_INSTANCES_PER_NODE = 1
# http://www.scidb.org/forum/viewtopic.php?f=11&t=530
# Documentation specified Postgres 8.4; I moved to 9.1
REQUIRED_PACKAGES = ['build-essential', 'cmake', 'libboost1.48-all-dev',
'postgresql-9.1', 'libpqxx-3.1', 'libpqxx3-dev',
'libprotobuf7', 'libprotobuf-dev', 'protobuf-compiler',
'doxygen', 'flex', 'bison', 'libxerces-c-dev',
'libxerces-c3.1', 'liblog4cxx10', 'liblog4cxx10-dev',
'libcppunit-1.12-1', 'libcppunit-dev', 'libbz2-dev',
'postgresql-contrib-9.1', 'libconfig++8',
'libconfig++8-dev', 'libconfig8-dev', 'subversion',
'libreadline6-dev', 'libreadline6', 'python-paramiko',
'python-crypto', 'xsltproc', 'liblog4cxx10-dev',
'subversion', 'expect', 'openssh-server', 'openssh-client',
'git-svn', 'gdebi'] # Shim uses gdebi
class SciDBInstaller(DefaultClusterSetup):
def __init__(self,
username=DEFAULT_USERNAME,
password=''.join(random.sample(string.lowercase+string.digits, 20)),
repository=DEFAULT_REPOSITORY,
branch=DEFAULT_BRANCH,
shim_uri=DEFAULT_SHIM_PACKAGE_URI,
directory=DEFAULT_DIRECTORY,
clients=DEFAULT_CLIENTS,
build_type=DEFAULT_BUILD_TYPE,
build_threads=DEFAULT_BUILD_THREADS,
redundancy=DEFAULT_REDUNDANCY,
instances_per_node=DEFAULT_INSTANCES_PER_NODE):
super(SciDBInstaller, self).__init__()
self.username = username
self.password = password
self.repository = repository
self.branch = branch
self.shim_uri = shim_uri
self.directory = directory
self.clients = clients
self.build_type = build_type
self.build_threads = build_threads
self.redundancy = redundancy
self.instances_per_node = instances_per_node
def _set_up_node(self, master, node):
log.info("1 Begin configuration {}".format(node.alias))
log.info('* Removing source deb http://www.cs.wisc.edu/condor/debian/development lenny contrib')
node.ssh.execute('sed -i "s/deb http:\/\/www.cs.wisc.edu\/condor\/debian\/development lenny contrib/#deb http:\/\/www.cs.wisc.edu\/condor\/debian\/development lenny contrib/g" /etc/apt/sources.list')
log.info('* Adding SciDB directory "{}"'.format(self.directory))
self._add_directory(node, self.directory)
time.sleep(30)
log.info('2.1 Installing packages')
node.apt_install(' '.join(REQUIRED_PACKAGES))
log.info('2.2 Configure and start the SSH server')
node.ssh.execute('sudo service ssh restart')
def _set_ownership(self, master, node):
log.info('* Setting home directory owner to scidb on node {}'.format(node.alias))
try:
node.ssh.execute('chown -R scidb /home/scidb')
node.ssh.execute('chmod 700 /home/scidb/.ssh')
except RemoteCommandFailed as e:
if node != master:
pass
else:
raise e
def run(self, nodes, master, user, user_shell, volumes):
super(SciDBInstaller, self).run(nodes, master, user, user_shell, volumes)
aliases = ' '.join(map(lambda node: node.alias, nodes))
log.info('Beginning SciDB cluster configuration')
log.info('* Adding SciDB user "{}"'.format(self.username))
self._add_user(master, nodes)
time.sleep(90)
[self.pool.simple_job(self._set_up_node, (master, node), jobid=node.alias) for node in nodes]
self.pool.wait(len(nodes))
[self.pool.simple_job(self._set_ownership, (master, node), jobid=node.alias) for node in nodes]
self.pool.wait(len(nodes))
log.info('3 Cloning repository {}'.format(self.repository))
master.ssh.execute('cd {} && su scidb -c "git clone {} {} {}"'.format(
self.directory, self.repository, self.directory,
'--branch {}'.format(self.branch) if self.branch else ''))
# I guess the Paradigm4 source for Ubuntu 12.04 now requres HTTPS?
log.info('* Fixing register_3rdparty_scidb_repository.sh')
master.ssh.execute('sed -i "s/http:\/\/downloads.paradigm4.com/https:\/\/downloads.paradigm4.com/g" {}/deployment/common/register_3rdparty_scidb_repository.sh'.format(self.directory))
#log.info('4.1 Configure passwordless SSH to all the cluster nodes')
#self._execute(master, '''su scidb -c "deployment/deploy.sh access scidb '{password}' '' {}"'''.format(aliases, password=self.password))
log.info('4.2 N/A')
log.info('4.3 Toolchain')
time.sleep(60)
self._execute(master, 'deployment/deploy.sh prepare_toolchain {}'.format(master.alias))
log.info('4.4 Coordinator')
self._add_swapfile(master)
self._execute(master, 'deployment/deploy.sh prepare_coordinator {}'.format(master.alias))
log.info('End SciDB node configuration')
log.info('4.5 N/A')
log.info('4.6 N/A')
log.info('5.1 Install Postgres')
self._execute(master, 'deployment/deploy.sh prepare_postgresql postgres postgres {} {}'.format(
self.clients, master.alias))
log.info('5.2 Enable the postgres user to access scidb source code')
master.ssh.execute('sudo usermod -G scidb -a postgres')
master.ssh.execute('chmod -R g+rx {}'.format(self.directory))
log.info('6.1 Environment Variables')
self._add_environment(master, '/root/.bashrc')
self._add_environment(master, '/home/scidb/.bashrc')
log.info('6.2 Build')
#TODO can probably remove now that we've committed revision
self._ensure_revision(master)
log.info(' * Setup')
self._execute(master, 'su scidb -c "./run.py setup -f"')
log.info(' * Build')
self._execute(master, 'su scidb -c "./run.py make -j{}"'.format(self.build_threads))
log.info('6.3 N/A') # Local Development')
#self._execute(master, './run.py install -f')
log.info('6.4 Cluster Development')
log.info(' * Package')
self._execute(master, 'su scidb -c "./run.py make_packages /tmp/packages -f"')
log.info(' * Distribute Libraries')
[self.pool.simple_job(self._distribute_libraries, (master, node), jobid=node.alias) for node in nodes]
self.pool.wait(len(nodes))
log.info(' * Install')
self._execute(master, 'deployment/deploy.sh scidb_install /tmp/packages {}'.format(aliases))
log.info(' * Redistribute Deployment')
[self.pool.simple_job(self._copy_deployment, (master, node), jobid=node.alias) for node in nodes]
self.pool.wait(len(nodes))
log.info(' * Tweak Root SSH Configuration')
self._set_root_ssh_config(master)
log.info(' * Tweak Root SSH Permissions')
master.ssh.execute('chmod 700 /root/.ssh')
master.ssh.execute('chmod 600 /root/.ssh/*')
master.ssh.execute('''sed -i "s/scidb_prepare_node \\"/ssh root@\$\{{hostname\}} 'chmod 600 \/root\/.ssh\/\* \/home\/scidb\/.ssh\/*' \&\& scidb_prepare_node \\"/" {}/deployment/deploy.sh'''.format(self.directory))
time.sleep(30)
log.info(' * Prepare')
self._execute(master, 'deployment/deploy.sh scidb_prepare scidb "{password}" mydb mydb mydb {directory}/db {instances} default {redundancy} {aliases}'.format(
instances=self.instances_per_node,
redundancy=self.redundancy,
password=self.password,
directory=self.directory,
aliases=aliases))
log.info('* Set Postgres Listener')
[self.pool.simple_job(self._set_postgres_listener, (node, '*'), jobid=node.alias) for node in nodes]
self.pool.wait(len(nodes))
[self.pool.simple_job(self._add_host_authentication, (node, 'host all all 0.0.0.0/0 md5'), jobid=node.alias) for node in nodes]
self.pool.wait(len(nodes))
log.info('7 Start SciDB')
log.info(' * Initialize Catalogs')
self._execute(master, '/opt/scidb/14.8/bin/scidb.py initall mydb -f')
log.info(' * Start All')
self._execute(master, '/opt/scidb/14.8/bin/scidb.py startall mydb')
log.info('A Install Shim')
self._execute(master, 'wget {}'.format(self.shim_uri))
self._execute(master, 'ldconfig {}/stage/install/lib'.format(self.directory))
self._execute(master, 'gdebi --n shim*.deb')
log.info('B Install SciDB-Py')
master.ssh.execute('pip install requests')
master.ssh.execute('pip install --upgrade scidb-py')
log.info('End SciDB cluster configuration')
def _add_user(self, master, nodes):
uid, gid = self._get_new_user_id(self.username)
map(lambda node: self.pool.simple_job(self.__add_user_to_node, (uid, gid, node), jobid=node.alias), nodes)
self.pool.wait(numtasks=len(nodes))
#self._setup_cluster_user(self.username)
master.generate_key_for_user(self.username, auth_new_key=True, auth_conn_key=True)
master.add_to_known_hosts(self.username, nodes)
def __add_user_to_node(self, uid, gid, node):
node.add_user(self.username, uid, gid, '/bin/bash')
node.ssh.execute('echo -e "{username}:{password}" | chpasswd'.format(
username=self.username, password=self.password))
def _add_directory(self, node, path):
node.ssh.execute('mkdir {}'.format(path))
node.ssh.execute('chown {username} {path}'.format(username=self.username, path=path))
node.ssh.execute('chgrp {username} {path}'.format(username=self.username, path=path))
def _add_swapfile(self, node):
node.ssh.execute('sudo dd if=/dev/zero of=/mnt/swapfile bs=1024 count=2048k')
node.ssh.execute('sudo mkswap /mnt/swapfile')
node.ssh.execute('sudo swapon /mnt/swapfile')
def _add_environment(self, node, path):
with node.ssh.remote_file(path, 'a') as descriptor:
descriptor.write('export SCIDB_VER={}\n'.format(SCIDB_VERSION))
#descriptor.write('export SCIDB_INSTALL_PATH={}\n'.format(SCIDB_INSTALL_PATH))
#descriptor.write('export PATH=$SCIDB_INSTALL_PATH/bin:$PATH\n')
descriptor.write('export PATH={}/stage/install/bin:$PATH\n'.format(self.directory))
descriptor.write('export LD_LIBRARY_PATH={}/stage/install/lib:$LD_LIBRARY_PATH\n'.format(self.directory))
descriptor.write('export SCIDB_BUILD_TYPE={}\n'.format(self.build_type))
def _ensure_revision(self, node):
self._execute(node, 'mv .git temp.git') #TODO
with node.ssh.remote_file(os.path.join(self.directory, 'revision'), 'w') as descriptor:
descriptor.write(str(SCIDB_REVISION))
def _distribute_libraries(self, master, node):
# Awesome! SciDB has hardcoded paths (/opt/scidb/*)
node.ssh.execute('mkdir -p /opt/scidb/{}'.format(SCIDB_VERSION))
master.ssh.execute('scp -r {directory}/stage/build/debian/scidb-{version}-plugins{directory}/stage/install/* {alias}:/opt/scidb/{version}'.format(
directory=self.directory,
alias=node.alias,
version=SCIDB_VERSION))
def _copy_deployment(self, master, node):
master.ssh.execute('scp -r {}/stage/install/* {}:/opt/scidb/{}'.format(self.directory, node.alias, SCIDB_VERSION))
def _set_root_ssh_config(self, node, path='/root/.ssh/config'):
with node.ssh.remote_file(path, 'w') as descriptor:
descriptor.write('Host *\n'
' StrictHostKeyChecking no\n'
' UserKnownHostsFile=/dev/null\n'
' IdentityFile ~/.ssh/id_rsa\n'
' User root\n'
'\n'
'Host *\n'
' StrictHostKeyChecking no\n'
' UserKnownHostsFile=/dev/null\n'
' IdentityFile /home/scidb/.ssh/id_rsa\n'
' User scidb\n')
node.ssh.execute('chmod 600 {}'.format(path))
def _set_postgres_listener(self, node, listeners, path='/etc/postgresql/{version}/main/postgresql.conf', version=POSTGRES_VERSION):
node.ssh.execute(r'sed -i "s/^\s*\#\?\s*listen_addresses\s*=\s*''.*\?''/listen_addresses = \'{listeners}\'/ig" {path}'.format(
listeners=listeners,
path=path.format(version=version)))
node.ssh.execute('sudo service postgresql restart')
def _add_host_authentication(self, node, authentication, path='/etc/postgresql/{version}/main/pg_hba.conf', version=POSTGRES_VERSION):
with node.ssh.remote_file(path.format(version=version), 'a') as descriptor:
descriptor.write(authentication + '\n')
node.ssh.execute('sudo service postgresql restart')
def _execute(self, node, command):
node.ssh.execute('cd {} && {}'.format(self.directory, command))