-
Notifications
You must be signed in to change notification settings - Fork 20
/
Dockerfile-submit-dev
181 lines (165 loc) · 8.12 KB
/
Dockerfile-submit-dev
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
FROM eclipse-temurin:17 as jre-build
# Create a custom Java runtime
RUN $JAVA_HOME/bin/jlink \
--add-modules ALL-MODULE-PATH \
--strip-debug \
--no-man-pages \
--no-header-files \
--compress=2 \
--output /javaruntime
# Define base image and copy in jlink created minimal Java 17 environment
FROM debian:buster-slim
ENV JAVA_HOME=/opt/java/openjdk
ENV PATH "${JAVA_HOME}/bin:${PATH}"
COPY --from=jre-build /javaruntime $JAVA_HOME
RUN mkdir -p /usr/local/app && \
apt-get -y update && \
apt-get -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
RUN unlink /etc/localtime || true
RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
# Create a user with UID 10001 and GID 10000
RUN groupadd -g 10000 vcellgroup && \
useradd -rm -d /home/vcell -s /bin/bash -u 10001 -g vcellgroup vcell
USER vcell
RUN mkdir -p ~vcell/.ssh && \
chmod 700 ~vcell/.ssh
WORKDIR /usr/local/app
COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
./vcell-server/target/maven-jars/*.jar \
./lib/
COPY ./docker/build/vcell-submit.log4j.xml .
ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
serverid=SITE \
jmshost_int_internal=activemqint \
jmsport_int_internal=61616 \
jmshost_sim_internal=activemqsim \
jmsport_sim_internal=61616 \
jmsuser=clientUser \
jmshost_sim_external="jms-host-sim-external-not-set" \
jmsport_sim_external="jms-port-sim-external-not-set" \
jmsrestport_sim_external="jms-restport-sim-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_secondary_external=/path/to/external/secondary/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="batch-host-not-set" \
htc_vcellfvsolver_docker_name="htc-vcellfvsolver-docker-name-not-set" \
htc_vcellfvsolver_solver_list="htc-vcellfvsolver-solver-list-not-set" \
htc_vcellsolvers_docker_name="htc-vcellsolvers-docker-name-not-set" \
htc_vcellsolvers_solver_list="htc-vcellsolvers-solver-list-not-set" \
htc_vcellbatch_docker_name="htc-vcellbatch-docker-name-not-set" \
htc_vcellbatch_solver_list="htc-vcellbatch-solver-list-not-set" \
htc_vcellopt_docker_name="htc-vcellopt-docker-name-not-set" \
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="slurm-partition-not-set" \
slurm_reservation="slurm_reservation-not-set" \
slurm_qos="slurm_qos-not-set" \
slurm_partition_pu="slurm_partition_pu-not-set" \
slurm_reservation_pu="slurm_reservation_pu-not-set" \
slurm_qos_pu="slurm_qos_pu-not-set" \
slurm_tmpdir="slurm-tmpdir-not-set" \
slurm_singularity_cachedir="slurm_singularity_cachedir-not-set" \
slurm_singularity_pullfolder="slurm_singularity_pullfolder-not-set" \
slurm_singularity_module_name="slurm_singularity_module_name-not-set" \
jmsblob_minsize=100000 \
vcell_ssh_cmd_cmdtimeout="cmdSrvcSshCmdTimeoutMS-not-set" \
vcell_ssh_cmd_restoretimeout="cmdSrvcSshCmdRestoreTimeoutFactor-not-set" \
simdatadir_archive_external="simdatadir_archive_external-not-set" \
simdatadir_archive_internal="simdatadir_archive_internal-not-set" \
htcMinMemoryMB="htc-min-memory-not-set" \
htcMaxMemoryMB="htc-max-memory-not-set" \
htcPowerUserMemoryFloorMB="htc-power-user-memory-floor-not-set" \
htcPowerUserMemoryMaxMB="htc-power-user-memory-max-not-set"
ENV jmspswdfile=/run/secrets/jmspswd \
jmsrestpswdfile=/run/secrets/jmsrestpswd \
batchuserkeyfile=/run/secrets/batchuserkeyfile
VOLUME /simdata
VOLUME /simdata_secondary
VOLUME /htclogs
EXPOSE 8000
ENTRYPOINT java \
-Xdebug -agentlib:jdwp=transport=dt_socket,address=*:8000,server=y,suspend=n \
-XX:MaxRAMPercentage=80 \
# -XX:+PrintFlagsFinal -XshowSettings:vm \
-Djava.awt.headless=true \
-Dvcell.softwareVersion="${softwareVersion}" \
-Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager \
-Dlog4j.configurationFile=/usr/local/app/vcell-submit.log4j.xml \
-Dvcell.server.id="${serverid}" \
-Dvcell.primarySimdatadir.internal=/simdata \
-Dvcell.secondarySimdatadir.external="${simdatadir_secondary_external}" \
-Dvcell.secondarySimdatadir.internal=/simdata_secondary \
-Dvcell.primarySimdatadir.external="${simdatadir_external}" \
-Dvcell.parallelDatadir.external="${simdatadir_parallel_external}" \
-Dvcell.nativesolverdir.external="${nativesolverdir_external}" \
-Dvcell.htc.user="${batchuser}" \
-Dvcell.htc.hosts="${batchhost}" \
-Dvcell.htc.userkeyfile="${batchuserkeyfile}" \
-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="${slurm_partition}" \
-Dvcell.slurm.reservation="${slurm_reservation}" \
-Dvcell.slurm.qos="${slurm_qos}" \
-Dvcell.slurm.partitionpu="${slurm_partition_pu}" \
-Dvcell.slurm.reservationpu="${slurm_reservation_pu}" \
-Dvcell.slurm.qospu="${slurm_qos_pu}" \
-Dvcell.slurm.tmpdir="${slurm_tmpdir}" \
-Dvcell.slurm.singularity.cachedir="${slurm_singularity_cachedir}" \
-Dvcell.slurm.singularity.pullfolder="${slurm_singularity_pullfolder}" \
-Dvcell.slurm.singularity.module.name="${slurm_singularity_module_name}" \
-Dvcell.htc.vcellfvsolver.docker.name="${htc_vcellfvsolver_docker_name}" \
-Dvcell.htc.vcellfvsolver.solver.list="${htc_vcellfvsolver_solver_list}" \
-Dvcell.htc.vcellsolvers.docker.name="${htc_vcellsolvers_docker_name}" \
-Dvcell.htc.vcellsolvers.solver.list="${htc_vcellsolvers_solver_list}" \
-Dvcell.htc.vcellbatch.docker.name="${htc_vcellbatch_docker_name}" \
-Dvcell.htc.vcellbatch.solver.list="${htc_vcellbatch_solver_list}" \
-Dvcell.htc.vcellopt.docker.name="${htc_vcellopt_docker_name}" \
-Dvcell.simulation.postprocessor=JavaPostprocessor64 \
-Dvcell.simulation.preprocessor=JavaPreprocessor64 \
-Dvcell.javaSimulation.executable=JavaSimExe64 \
-Dvcell.installDir=/usr/local/app \
-Dvcell.jms.int.host.internal="${jmshost_int_internal}" \
-Dvcell.jms.int.port.internal="${jmsport_int_internal}" \
-Dvcell.jms.sim.host.internal="${jmshost_sim_internal}" \
-Dvcell.jms.sim.port.internal="${jmsport_sim_internal}" \
-Dvcell.jms.sim.host.external="${jmshost_sim_external}" \
-Dvcell.jms.sim.port.external="${jmsport_sim_external}" \
-Dvcell.jms.sim.restport.external="${jmsrestport_sim_external}" \
-Dvcell.jms.blobMessageUseMongo=true \
-Dvcell.jms.blobMessageMinSize="${jmsblob_minsize}" \
-Dvcell.jms.user="${jmsuser}" \
-Dvcell.jms.pswdfile="${jmspswdfile}" \
-Dvcell.jms.rest.pswdfile="${jmsrestpswdfile}" \
-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=${mongodb_database} \
-Dvcell.simdatadir.archive.internal=${simdatadir_archive_internal} \
-Dvcell.simdatadir.archive.external=${simdatadir_archive_external} \
-Dvcell.ssh.cmd.cmdtimeout=${vcell_ssh_cmd_cmdtimeout} \
-Dvcell.ssh.cmd.restoretimeout=${vcell_ssh_cmd_restoretimeout} \
-Dvcell.htc.memory.min.mb=${htcMinMemoryMB} \
-Dvcell.htc.memory.max.mb=${htcMaxMemoryMB} \
-Dvcell.htc.memory.pu.floor.mb=${htcPowerUserMemoryFloorMB} \
-Dvcell.htc.memory.pu.max.mb=${htcPowerUserMemoryMaxMB} \
-cp "./lib/*" cbit.vcell.message.server.batch.sim.HtcSimulationWorker