forked from vcellmike/Biosimulators_VCell
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathDockerfile-master_NOTUSED
138 lines (126 loc) · 5.44 KB
/
Dockerfile-master_NOTUSED
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
FROM maven:3.5-jdk-8-alpine as build
COPY . /app/
WORKDIR /app
RUN mvn clean install dependency:copy-dependencies
FROM schaff/vtk-openjdk-alpine:latest
RUN mkdir -p /usr/local/app && \
apk update && \
apk add openssh-client && \
apk add screen
WORKDIR /usr/local/app
COPY --from=build \
/app/vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
/app/vcell-server/target/maven-jars/*.jar \
/app/vcell-oracle/target/vcell-oracle-0.0.1-SNAPSHOT.jar \
/app/vcell-oracle/target/maven-jars/*.jar \
/app/ojdbc6/src/ojdbc6.jar \
/app/ucp/src/ucp.jar \
./lib/
COPY --from=build /app/pythonScripts ./pythonScripts
COPY --from=build /app/nativelibs/linux64 ./nativelibs/linux64
COPY --from=build /app/docker/vcell-master.log4j.xml .
ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
serverid=SITE \
dburl="db-url-not-set" \
dbdriver="db-driver-not-set" \
dbuser="db-user-not-set" \
jmshost_internal=activemq \
jmsport_internal=61616 \
jmsrestport_internal=8161 \
jmsuser=clientUser \
jmshost_external="jms-host-external-not-set" \
jmsport_external="jms-port-external-not-set" \
jmsrestport_external="jms-restport-external-not-set" \
mongodb_host_internal=mongodb \
mongodb_port_internal=27017 \
mongodb_database=test \
mongodb_host_external="mongodb-host-external-not-set" \
mongodb_port_external="mongodb-port-external-not-set" \
export_baseurl="export-baseurl-not-set" \
simdatadir_external=/path/to/external/simdata/ \
simdatadir_parallel_external=/path/to/external/parallel/simdata/ \
htclogdir_internal=/path/to/internal/htclogs/ \
htclogdir_external=/path/to/external/htclogs/ \
nativesolverdir_external=/path/to/external/nativesolvers/ \
htcnodelist="" \
singularity_imagefile=/path/to/external/singularity.img \
docker_name="repo/namespace/vcell-batch:tag" \
batchhost="batch-host-not-set" \
batchuser="batch-user-not-set" \
slurm_cmd_sbatch=sbatch \
slurm_cmd_sacct=sacct \
slurm_cmd_scancel=scancel \
slurm_cmd_squeue=squeue \
slurm_partition=vcell \
slurm_tmpdir="slurm-tmpdir-not-set" \
maxJobsPerScan=max-jobs-per-scan-not-set \
maxJobsPerSite=max-jobs-per-site-not-set \
maxOdeJobsPerUser=max-ode-jobs-per-user-not-set \
maxPdeJobsPerUser=max-pde-jobs-per-user-not-set \
jmsblob_minsize=100000 \
simdataCacheSize=simdata-cache-size-not-set
ENV dbpswdfile=/run/secrets/dbpswd \
jmspswdfile=/run/secrets/jmspswd \
batchuserkeyfile=/run/secrets/batchuserkeyfile
VOLUME /simdata
VOLUME /exportdir
VOLUME /htclogs
EXPOSE 8000
ENTRYPOINT java \
-Xdebug -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=n \
-XX:+UnlockExperimentalVMOptions -XX:+UseCGroupMemoryLimitForHeap -XX:MaxRAMFraction=1 -Xms64M \
-Djava.awt.headless=true \
-Dvcell.softwareVersion="${softwareVersion}" \
-Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager \
-Dlog4j.configurationFile=/usr/local/app/vcell-master.log4j.xml \
-Dvcell.server.id="${serverid}" \
-Dvcell.python.executable=/usr/bin/python \
-Dvcell.primarySimdatadir.internal=/simdata \
-Dvcell.simdataCacheSize="${simdataCacheSize}" \
-Dvcell.primarySimdatadir.external="${simdatadir_external}" \
-Dvcell.parallelDatadir.external="${simdatadir_parallel_external}" \
-Dvcell.nativesolverdir.external="${nativesolverdir_external}" \
-Dvcell.export.baseDir.internal=/exportdir/ \
-Dvcell.export.baseURL="${export_baseurl}" \
-Dvcell.htc.user="${batchuser}" \
-Dvcell.htc.logdir.internal=/htclogs \
-Dvcell.htc.logdir.external="${htclogdir_external}" \
-Dvcell.htc.nodelist="${htcnodelist}" \
-Dvcell.slurm.cmd.sbatch="${slurm_cmd_sbatch}" \
-Dvcell.slurm.cmd.sacct="${slurm_cmd_sacct}" \
-Dvcell.slurm.cmd.squeue="${slurm_cmd_squeue}" \
-Dvcell.slurm.cmd.scancel="${slurm_cmd_scancel}" \
-Dvcell.slurm.partition="${slurm_partition}" \
-Dvcell.slurm.tmpdir="${slurm_tmpdir}" \
-Dvcell.batch.singularity.image="${singularity_imagefile}" \
-Dvcell.batch.docker.name="${docker_name}" \
-Dvcell.simulation.postprocessor=JavaPostprocessor64 \
-Dvcell.simulation.preprocessor=JavaPreprocessor64 \
-Dvcell.javaSimulation.executable=JavaSimExe64 \
-Dvcell.installDir=/usr/local/app \
-Dvcell.server.dbConnectURL="${dburl}" \
-Dvcell.server.dbDriverName="${dbdriver}" \
-Dvcell.server.dbUserid="${dbuser}" \
-Dvcell.db.pswdfile="${dbpswdfile}" \
-Dvcell.jms.host.internal="${jmshost_internal}" \
-Dvcell.jms.port.internal="${jmsport_internal}" \
-Dvcell.jms.restport.internal="${jmsrestport_internal}" \
-Dvcell.jms.host.external="${jmshost_external}" \
-Dvcell.jms.port.external="${jmsport_external}" \
-Dvcell.jms.restport.external="${jmsrestport_external}" \
-Dvcell.jms.blobMessageUseMongo=true \
-Dvcell.jms.blobMessageMinSize="${jmsblob_minsize}" \
-Dvcell.jms.user="${jmsuser}" \
-Dvcell.jms.pswdfile="${jmspswdfile}" \
-Dvcell.mongodb.host.internal=${mongodb_host_internal} \
-Dvcell.mongodb.port.internal=${mongodb_port_internal} \
-Dvcell.mongodb.host.external=${mongodb_host_external} \
-Dvcell.mongodb.port.external=${mongodb_port_external} \
-Dvcell.mongodb.database=${mongodb_database} \
-Dvcell.server.maxJobsPerScan=${maxJobsPerScan} \
-Dvcell.server.maxJobsPerSite=${maxJobsPerSite} \
-Dvcell.server.maxOdeJobsPerUser=${maxOdeJobsPerUser} \
-Dvcell.server.maxPdeJobsPerUser=${maxPdeJobsPerUser} \
-Dvcell.limit.jobMemoryMB=2000 \
-cp "./lib/*" cbit.vcell.message.server.combined.VCellServices \
"${batchhost}" "${batchuser}" "${batchuserkeyfile}"