Dockerfile-submit-dev

FROM openjdk:8u151-jdk-alpine3.7

RUN mkdir -p /usr/local/app && \
	apk update && \
    apk add openssh-client && \
    apk add screen

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_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" \
    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="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_local_singularity_dir="slurm_local_singularity_dir-not-set" \
    slurm_central_singularity_dir="slurm_central_singularity_dir-not-set" \
    jmsblob_minsize=100000 \
    vcell_ssh_cmd_cmdtimeout="cmdSrvcSshCmdTimeoutMS-not-set" \
    vcell_ssh_cmd_restoretimeout="cmdSrvcSshCmdRestoreTimeoutFactor-not-set" \
    simdatadir_archive_host="simdatadir_archive_host-not-set"

ENV jmspswdfile=/run/secrets/jmspswd \
	jmsrestpswdfile=/run/secrets/jmsrestpswd \
    batchuserkeyfile=/run/secrets/batchuserkeyfile

VOLUME /simdata
VOLUME /share/apps/vcell10/users
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="${softwareVersion}" \
	-Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager \
	-Dlog4j.configurationFile=/usr/local/app/vcell-submit.log4j.xml \
	-Dvcell.server.id="${serverid}" \
	-Dvcell.primarySimdatadir.internal=/simdata \
	-Dvcell.htc.simPerUserMemLimitFile=sim_mem_per_user_limits.txt \
	-Dvcell.primarySimdatadir.external="${simdatadir_external}" \
	-Dvcell.parallelDatadir.external="${simdatadir_parallel_external}" \
	-Dvcell.nativesolverdir.external="${nativesolverdir_external}" \
	-Dvcell.htc.user="${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="${slurm_partition}" \
	-Dvcell.slurm.reservation="${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="${slurm_tmpdir}" \
	-Dvcell.slurm.local.singularity.dir="${slurm_local_singularity_dir}" \
	-Dvcell.slurm.central.singularity.dir="${slurm_central_singularity_dir}" \
	-Dvcell.batch.singularity.image="${singularity_imagefile}" \
	-Dvcell.batch.docker.name="${docker_name}" \
	-Dvcell.simulation.postprocessor=JavaPostprocessor64 \
	-Dvcell.simulation.preprocessor=JavaPreprocessor64 \
	-Dvcell.javaSimulation.executable=JavaSimExe64 \
	-Dvcell.installDir=/usr/local/app \
	-Dvcell.jms.int.host.internal="${jmshost_int_internal}" \
	-Dvcell.jms.int.port.internal="${jmsport_int_internal}" \
	-Dvcell.jms.int.restport.internal="${jmsrestport_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.host=${simdatadir_archive_host} \
	-Dvcell.ssh.cmd.cmdtimeout=${vcell_ssh_cmd_cmdtimeout} \
	-Dvcell.ssh.cmd.restoretimeout=${vcell_ssh_cmd_restoretimeout} \
	-cp "./lib/*" cbit.vcell.message.server.batch.sim.HtcSimulationWorker \
	"${batchhost}" "${batchuser}" "${batchuserkeyfile}"