FROM eclipse-temurin:17 as jre-build # Create a custom Java runtime RUN $JAVA_HOME/bin/jlink \ --add-modules ALL-MODULE-PATH \ --strip-debug \ --no-man-pages \ --no-header-files \ --compress=2 \ --output /javaruntime # Define base image and copy in jlink created minimal Java 17 environment FROM debian:bullseye-slim ENV JAVA_HOME=/opt/java/openjdk ENV PATH "${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 # 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" \ 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 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=${vcell_ssh_cmd_restoretimeout} \ -Dvcell.ssh.cmd.options.csv=${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