| FROM eclipse-temurin:17 as jre-build |
|
|
| |
| RUN $JAVA_HOME/bin/jlink \ |
| --add-modules ALL-MODULE-PATH \ |
| --strip-debug \ |
| --no-man-pages \ |
| --no-header-files \ |
| --compress=2 \ |
| --output /javaruntime |
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|
| |
| FROM debian:bullseye-slim |
| ENV JAVA_HOME=/opt/java/openjdk |
| ENV PATH "${JAVA_HOME}/bin:${PATH}" |
| COPY --from=jre-build /javaruntime $JAVA_HOME |
|
|
| RUN mkdir -p /usr/local/app && \ |
| apt -y update && \ |
| apt -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu |
|
|
| RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata |
| RUN unlink /etc/localtime || true |
| RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime |
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|
| |
| RUN groupadd -g 10000 vcellgroup && \ |
| useradd -rm -d /home/vcell -s /bin/bash -u 10001 -g vcellgroup vcell |
|
|
| USER vcell |
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|
| RUN mkdir -p ~vcell/.ssh && \ |
| chmod 700 ~vcell/.ssh |
|
|
| WORKDIR /usr/local/app |
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|
| COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \ |
| ./vcell-server/target/maven-jars/*.jar \ |
| ./lib/ |
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|
|
|
| COPY ./docker/build/vcell-submit.log4j.xml . |
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|
| 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" \ |
| |
| simdatadir_external=/path/to/external/simdata/ \ |
| simdatadir_secondary_external=/path/to/external/secondary/simdata/ \ |
| simdatadir_parallel_external=/path/to/external/parallel/simdata/ \ |
| |
| 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" \ |
| vcell_ssh_cmd_options_csv="cmdSrvcSshCmdRestoreOptionsCsv-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 |
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|
| EXPOSE 8000 |
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|
| ENTRYPOINT java \ |
| -Xdebug -agentlib:jdwp=transport=dt_socket,address=*:8000,server=y,suspend=n \ |
| -XX:MaxRAMPercentage=80 \ |
| |
| -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=${vcell_ssh_cmd_restoretimeout} \ |
| -Dvcell.ssh.cmd.options.csv=${vcell_ssh_cmd_options_csv} \ |
| -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 |
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