-
Notifications
You must be signed in to change notification settings - Fork 12
/
start-mspass.sh
323 lines (305 loc) · 14.3 KB
/
start-mspass.sh
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
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
#!/bin/bash
# If running with docker use /home, else use pwd to store all data and logs
if grep "docker/containers" /proc/self/mountinfo -qa; then
MSPASS_WORKDIR=/home
elif [[ -z ${MSPASS_WORK_DIR} ]]; then
MSPASS_WORKDIR=`pwd`
else
MSPASS_WORKDIR=$MSPASS_WORK_DIR
fi
# define SLEEP_TIME
if [[ -z $MSPASS_SLEEP_TIME ]]; then
MSPASS_SLEEP_TIME=15
fi
# This sets defaults for this set of env variables
if [[ -z ${MSPASS_DB_DIR} ]]; then
MSPASS_DB_DIR=${MSPASS_WORKDIR}/db
fi
if [[ -z ${MSPASS_LOG_DIR} ]]; then
MSPASS_LOG_DIR=${MSPASS_WORKDIR}/logs
fi
if [[ -z ${MSPASS_WORKER_DIR} ]]; then
MSPASS_WORKER_DIR=${MSPASS_WORKDIR}/work
fi
# Note that only log is required for all roles. Other dirs will be created later when needed.
[[ -d $MSPASS_LOG_DIR ]] || mkdir -p $MSPASS_LOG_DIR
MONGO_DATA=${MSPASS_DB_DIR}/data
MONGO_LOG=${MSPASS_LOG_DIR}/mongo_log
export SPARK_WORKER_DIR=${MSPASS_WORKER_DIR}
export SPARK_LOG_DIR=${MSPASS_LOG_DIR}
if [ $# -eq 0 ] || [ $1 = "--batch" ]; then
function start_mspass_frontend {
BATCH_MODE_ARGS="--to notebook --inplace --execute $1"
NOTEBOOK_ARGS="--notebook-dir=${MSPASS_WORKDIR} --port=${JUPYTER_PORT} --no-browser --ip=0.0.0.0 --allow-root"
# if MSPASS_JUPYTER_PWD is not set, notebook will generate a default token
if [[ ! -z ${MSPASS_JUPYTER_PWD+x} ]]; then
# we rely on jupyter's python function to hash the password
MSPASS_JUPYTER_PWD_HASHED=$(python3 -c "from notebook.auth import passwd; print(passwd('${MSPASS_JUPYTER_PWD}'))")
NOTEBOOK_ARGS="${NOTEBOOK_ARGS} --NotebookApp.password=${MSPASS_JUPYTER_PWD_HASHED}"
fi
if [ "$MSPASS_SCHEDULER" = "spark" ]; then
export PYSPARK_DRIVER_PYTHON=jupyter
if [ -z $1 ]; then
export PYSPARK_DRIVER_PYTHON_OPTS="lab ${NOTEBOOK_ARGS}"
else
export PYSPARK_DRIVER_PYTHON_OPTS="nbconvert ${BATCH_MODE_ARGS}"
fi
pyspark \
--conf "spark.mongodb.input.uri=mongodb://${MSPASS_DB_ADDRESS}:${MONGODB_PORT}/test.misc" \
--conf "spark.mongodb.output.uri=mongodb://${MSPASS_DB_ADDRESS}:${MONGODB_PORT}/test.misc" \
--conf "spark.master=spark://${MSPASS_SCHEDULER_ADDRESS}:${SPARK_MASTER_PORT}" \
--packages org.mongodb.spark:mongo-spark-connector_2.12:3.0.0
else # if [ "$MSPASS_SCHEDULER" = "dask" ]
export DASK_SCHEDULER_ADDRESS=${MSPASS_SCHEDULER_ADDRESS}:${DASK_SCHEDULER_PORT}
if [ -z $1 ]; then
jupyter lab ${NOTEBOOK_ARGS}
else
jupyter nbconvert ${BATCH_MODE_ARGS}
fi
fi
}
function clean_up_single_node {
# ---------------------- clean up workflow -------------------------
# stop mongodb
mongosh --port $MONGODB_PORT admin --eval "db.shutdownServer({force:true})"
sleep 5
# copy shard data to scratch
if [ "$MSPASS_DB_PATH" = "tmp" ]; then
echo "standalone: copy shard data to scratch"
# copy data
scp -r /tmp/db/data ${MSPASS_DB_DIR}
# copy log
scp -r /tmp/logs/mongo_log ${MSPASS_LOG_DIR}
fi
sleep ${MSPASS_SLEEP_TIME}
}
function clean_up_multiple_nodes {
# ---------------------- clean up workflow -------------------------
# stop mongos routers
mongosh --port $MONGODB_PORT admin --eval "db.shutdownServer({force:true})"
sleep 5
# stop each shard replica set
for i in ${MSPASS_SHARD_ADDRESS[@]}; do
ssh -o "StrictHostKeyChecking no" ${i} "kill -2 \$(pgrep mongo)"
sleep 5
done
# stop config servers
mongosh --port $(($MONGODB_PORT+1)) admin --eval "db.shutdownServer({force:true})"
# copy the shard data to scratch if the shards are deployed in /tmp
if [ "$MSPASS_DB_PATH" = "tmp" ]; then
echo "distributed: copy shard data to scratch"
# copy data
for i in ${MSPASS_SHARD_DB_PATH[@]}; do
scp -r -o StrictHostKeyChecking=no ${i} ${MSPASS_DB_DIR}
done
# copy log
for i in ${MSPASS_SHARD_LOGS_PATH[@]}; do
scp -r -o StrictHostKeyChecking=no ${i} ${MSPASS_LOG_DIR}
done
fi
sleep ${MSPASS_SLEEP_TIME}
}
function start_db_scratch {
[[ -d $MONGO_DATA ]] || mkdir -p $MONGO_DATA
mongod --port $MONGODB_PORT --dbpath $MONGO_DATA --logpath $MONGO_LOG --bind_ip_all &
}
function start_db_tmp {
# create db and log dirs if not exists
[[ -d /tmp/db ]] || mkdir -p /tmp/db
[[ -d /tmp/logs ]] || mkdir -p /tmp/logs && touch /tmp/logs/mongo_log
# copy all data on scratch to the local tmp folder
if [[ -d ${MSPASS_DB_DIR}/data ]]; then
cp -r ${MSPASS_DB_DIR}/data /tmp/db
else
mkdir -p /tmp/db/data
fi
# copy dfiles to /tmp
if [[ -d $MSPASS_SCRATCH_DATA_DIR ]]; then
cp -r $MSPASS_SCRATCH_DATA_DIR /tmp
fi
# start mongodb on /tmp
mongod --port $MONGODB_PORT --dbpath /tmp/db/data --logpath /tmp/logs/mongo_log --bind_ip_all &
}
MY_ID=$(cat /dev/urandom | tr -dc 'a-zA-Z0-9' | fold -w 12 | head -n 1)
if [ "$MSPASS_SCHEDULER" = "spark" ]; then
MSPASS_SCHEDULER_CMD='$SPARK_HOME/sbin/start-master.sh'
MSPASS_WORKER_CMD='$SPARK_HOME/sbin/start-slave.sh spark://$MSPASS_SCHEDULER_ADDRESS:$SPARK_MASTER_PORT'
else # if [ "$MSPASS_SCHEDULER" = "dask" ]
MSPASS_SCHEDULER_CMD='dask-scheduler --port $DASK_SCHEDULER_PORT > ${MSPASS_LOG_DIR}/dask-scheduler_log_${MY_ID} 2>&1 & sleep 5'
MSPASS_WORKER_CMD='dask-worker ${MSPASS_WORKER_ARG} --local-directory $MSPASS_WORKER_DIR tcp://$MSPASS_SCHEDULER_ADDRESS:$DASK_SCHEDULER_PORT > ${MSPASS_LOG_DIR}/dask-worker_log_${MY_ID} 2>&1 &'
fi
if [ "$MSPASS_ROLE" = "db" ]; then
if [ "$MSPASS_DB_PATH" = "tmp" ]; then
start_db_tmp
else
start_db_scratch
fi
elif [ "$MSPASS_ROLE" = "dbmanager" ]; then
# config server configuration
MONGODB_CONFIG_PORT=$(($MONGODB_PORT+1))
if [ -d ${MONGO_DATA}_config ]; then
echo "restore config server $HOSTNAME cluster"
# start a mongod instance
mongod --port $MONGODB_CONFIG_PORT --dbpath ${MONGO_DATA}_config --logpath ${MONGO_LOG}_config --bind_ip_all &
sleep ${MSPASS_SLEEP_TIME}
# drop the local database
echo "drop local database for config server $HOSTNAME"
mongosh --port $MONGODB_CONFIG_PORT local --eval "db.dropDatabase()"
sleep ${MSPASS_SLEEP_TIME}
# update config.shards collections
echo "update shard host names for config server $HOSTNAME"
# if using ${!MSPASS_SHARD_LIST[@]} style for loop, it doesn't work. Not sure why it doesn't work.
ITER=0
for i in ${MSPASS_SHARD_LIST[@]}; do
echo "update rs${ITER} with host ${i}"
mongosh --port $MONGODB_CONFIG_PORT config --eval "db.shards.updateOne({\"_id\": \"rs${ITER}\"}, {\$set: {\"host\": \"${i}\"}})"
((ITER++))
sleep ${MSPASS_SLEEP_TIME}
done
echo "restart the config server $HOSTNAME as a replica set"
# restart the mongod as a new single-node replica set
mongosh --port $MONGODB_CONFIG_PORT admin --eval "db.shutdownServer()"
sleep ${MSPASS_SLEEP_TIME}
mongod --port $MONGODB_CONFIG_PORT --configsvr --replSet configserver --dbpath ${MONGO_DATA}_config --logpath ${MONGO_LOG}_config --bind_ip_all &
sleep ${MSPASS_SLEEP_TIME}
# initiate the new replica set
mongosh --port $MONGODB_CONFIG_PORT --eval \
"rs.initiate({_id: \"configserver\", configsvr: true, version: 1, members: [{ _id: 0, host : \"$HOSTNAME:$MONGODB_CONFIG_PORT\" }]})"
sleep ${MSPASS_SLEEP_TIME}
# start a mongos router server
mongos --port $MONGODB_PORT --configdb configserver/$HOSTNAME:$MONGODB_CONFIG_PORT --logpath ${MONGO_LOG}_router --bind_ip_all &
sleep ${MSPASS_SLEEP_TIME}
else
# create a config dir
mkdir -p ${MONGO_DATA}_config
echo "dbmanager config server $HOSTNAME replicaSet is initialized"
# start a config server
mongod --port $MONGODB_CONFIG_PORT --configsvr --replSet configserver --dbpath ${MONGO_DATA}_config --logpath ${MONGO_LOG}_config --bind_ip_all &
sleep ${MSPASS_SLEEP_TIME}
mongosh --port $MONGODB_CONFIG_PORT --eval \
"rs.initiate({_id: \"configserver\", configsvr: true, version: 1, members: [{ _id: 0, host : \"$HOSTNAME:$MONGODB_CONFIG_PORT\" }]})"
sleep ${MSPASS_SLEEP_TIME}
# start a mongos router server
mongos --port $MONGODB_PORT --configdb configserver/$HOSTNAME:$MONGODB_CONFIG_PORT --logpath ${MONGO_LOG}_router --bind_ip_all &
# add shard clusters
for i in ${MSPASS_SHARD_LIST[@]}; do
echo "add shard with host ${i}"
sleep ${MSPASS_SLEEP_TIME}
mongosh --host $HOSTNAME --port $MONGODB_PORT --eval "sh.addShard(\"${i}\")"
done
fi
# enable database sharding
echo "enable database $MSPASS_SHARD_DATABASE sharding"
mongosh --host $HOSTNAME --port $MONGODB_PORT --eval "sh.enableSharding(\"${MSPASS_SHARD_DATABASE}\")"
sleep ${MSPASS_SLEEP_TIME}
# shard collection(using hashed)
for i in ${MSPASS_SHARD_COLLECTIONS[@]}; do
echo "shard collection $MSPASS_SHARD_DATABASE.${i%%:*} and shard key is ${i##*:}"
mongosh --host $HOSTNAME --port $MONGODB_PORT --eval "sh.shardCollection(\"$MSPASS_SHARD_DATABASE.${i%%:*}\", {${i##*:}: \"hashed\"})"
sleep ${MSPASS_SLEEP_TIME}
done
tail -f /dev/null
elif [ "$MSPASS_ROLE" = "shard" ]; then
[[ -n $MSPASS_SHARD_ID ]] || MSPASS_SHARD_ID=$MY_ID
# Note that we have to create a one-member replica set here
# because certain pymongo API will use "retryWrites=true"
# and thus trigger an error.
if [ "$MSPASS_DB_PATH" = "tmp" ]; then
echo "store shard data in tmp for shard server $HOSTNAME"
# create db and log dirs if not exists
[[ -d /tmp/db ]] || mkdir -p /tmp/db
[[ -d /tmp/logs ]] || mkdir -p /tmp/logs && touch /tmp/logs/mongo_log_shard_${MSPASS_SHARD_ID}
# copy all the shard data to the local tmp folder
if [[ -d ${MSPASS_DB_DIR}/data_shard_${MSPASS_SHARD_ID} ]]; then
scp -r -o StrictHostKeyChecking=no ${MSPASS_DB_DIR}/data_shard_${MSPASS_SHARD_ID} /tmp/db
else
mkdir -p /tmp/db/data_shard_${MSPASS_SHARD_ID}
fi
# reconfig the shard replica set
if [ -d ${MONGO_DATA}_shard_${MSPASS_SHARD_ID} ]; then
# restore the shard replica set
mongod --port $MONGODB_PORT --dbpath /tmp/db/data_shard_${MSPASS_SHARD_ID} --logpath /tmp/logs/mongo_log_shard_${MSPASS_SHARD_ID} --bind_ip_all &
sleep ${MSPASS_SLEEP_TIME}
# drop local database
echo "drop local database for shard server $HOSTNAME"
mongosh --port $MONGODB_PORT local --eval "db.dropDatabase()"
sleep ${MSPASS_SLEEP_TIME}
# update shard metadata in each shard's identity document
echo "update config server host names for shard server $HOSTNAME"
mongosh --port $MONGODB_PORT admin --eval "db.system.version.updateOne({\"_id\": \"shardIdentity\"}, {\$set: {\"configsvrConnectionString\": \"${MSPASS_CONFIG_SERVER_ADDR}\"}})"
sleep ${MSPASS_SLEEP_TIME}
# restart the mongod as a new single-node replica set
echo "restart the shard server $HOSTNAME as a replica set"
mongosh --port $MONGODB_PORT admin --eval "db.shutdownServer()"
sleep ${MSPASS_SLEEP_TIME}
mongod --port $MONGODB_PORT --shardsvr --replSet "rs${MSPASS_SHARD_ID}" --dbpath /tmp/db/data_shard_${MSPASS_SHARD_ID} --logpath /tmp/logs/mongo_log_shard_${MSPASS_SHARD_ID} --bind_ip_all &
else
# store the shard data in the /tmp folder in local machine
mongod --port $MONGODB_PORT --shardsvr --replSet "rs${MSPASS_SHARD_ID}" --dbpath /tmp/db/data_shard_${MSPASS_SHARD_ID} --logpath /tmp/logs/mongo_log_shard_${MSPASS_SHARD_ID} --bind_ip_all &
fi
else
echo "store shard data in scratch for shard server $HOSTNAME"
if [ -d ${MONGO_DATA}_shard_${MSPASS_SHARD_ID} ]; then
# restore the shard replica set
mongod --port $MONGODB_PORT --dbpath ${MONGO_DATA}_shard_${MSPASS_SHARD_ID} --logpath ${MONGO_LOG}_shard_${MSPASS_SHARD_ID} --bind_ip_all &
sleep ${MSPASS_SLEEP_TIME}
# drop local database
echo "drop local database for shard server $HOSTNAME"
mongosh --port $MONGODB_PORT local --eval "db.dropDatabase()"
sleep ${MSPASS_SLEEP_TIME}
# update shard metadata in each shard's identity document
echo "update config server host names for shard server $HOSTNAME"
mongosh --port $MONGODB_PORT admin --eval "db.system.version.updateOne({\"_id\": \"shardIdentity\"}, {\$set: {\"configsvrConnectionString\": \"${MSPASS_CONFIG_SERVER_ADDR}\"}})"
sleep ${MSPASS_SLEEP_TIME}
# restart the mongod as a new single-node replica set
echo "restart the shard server $HOSTNAME as a replica set"
mongosh --port $MONGODB_PORT admin --eval "db.shutdownServer()"
sleep ${MSPASS_SLEEP_TIME}
mongod --port $MONGODB_PORT --shardsvr --replSet "rs${MSPASS_SHARD_ID}" --dbpath ${MONGO_DATA}_shard_${MSPASS_SHARD_ID} --logpath ${MONGO_LOG}_shard_${MSPASS_SHARD_ID} --bind_ip_all &
else
# initialize the shard replica set
mkdir -p ${MONGO_DATA}_shard_${MSPASS_SHARD_ID}
mongod --port $MONGODB_PORT --shardsvr --replSet "rs${MSPASS_SHARD_ID}" --dbpath ${MONGO_DATA}_shard_${MSPASS_SHARD_ID} --logpath ${MONGO_LOG}_shard_${MSPASS_SHARD_ID} --bind_ip_all &
fi
fi
sleep ${MSPASS_SLEEP_TIME}
# shard server configuration
echo "shard server $HOSTNAME replicaSet is initialized"
mongosh --port $MONGODB_PORT --eval \
"rs.initiate({_id: \"rs${MSPASS_SHARD_ID}\", version: 1, members: [{ _id: 0, host : \"$HOSTNAME:$MONGODB_PORT\" }]})"
tail -f /dev/null
elif [ "$MSPASS_ROLE" = "scheduler" ]; then
eval $MSPASS_SCHEDULER_CMD
tail -f /dev/null
elif [ "$MSPASS_ROLE" = "worker" ]; then
[[ -d $MSPASS_WORKER_DIR ]] || mkdir -p $MSPASS_WORKER_DIR
eval $MSPASS_WORKER_CMD
# copy dfiles to /tmp
if [[ -d $MSPASS_SCRATCH_DATA_DIR ]]; then
cp -r $MSPASS_SCRATCH_DATA_DIR /tmp
fi
tail -f /dev/null
elif [ "$MSPASS_ROLE" = "frontend" ]; then
start_mspass_frontend $2
if [ "$MSPASS_DB_MODE" = "shard" ]; then
clean_up_multiple_nodes
else
clean_up_single_node
fi
else # if [ "$MSPASS_ROLE" = "all" ]
MSPASS_DB_ADDRESS=$HOSTNAME
MSPASS_SCHEDULER_ADDRESS=$HOSTNAME
eval $MSPASS_SCHEDULER_CMD
eval $MSPASS_WORKER_CMD
if [ "$MSPASS_DB_PATH" = "tmp" ]; then
start_db_tmp
else
start_db_scratch
fi
start_mspass_frontend $2
clean_up_single_node
fi
wait
else
docker-entrypoint.sh $@
fi