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https://github.com/ClusterCockpit/cc-docker.git
synced 2025-07-23 21:31:42 +02:00
Introduce slurm cluster
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47
slurm/controller/Dockerfile
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47
slurm/controller/Dockerfile
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FROM scidas/slurm.base:19.05.1
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MAINTAINER Michael J. Stealey <stealey@renci.org>
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# install openmpi 3.0.1
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RUN yum -y install \
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gcc-c++ \
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gcc-gfortran \
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&& yum -y localinstall \
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/packages/openmpi-*.rpm
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# install Lmod 7.7
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RUN yum -y install \
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lua-posix \
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lua \
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lua-filesystem \
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lua-devel \
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wget \
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bzip2 \
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expectk \
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make \
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&& wget https://sourceforge.net/projects/lmod/files/Lmod-7.7.tar.bz2 \
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&& tar -xjvf Lmod-7.7.tar.bz2
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WORKDIR /Lmod-7.7
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RUN ./configure --prefix=/opt/apps \
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&& make install \
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&& ln -s /opt/apps/lmod/lmod/init/profile /etc/profile.d/z00_lmod.sh \
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&& ln -s /opt/apps/lmod/lmod/init/cshrc /etc/profile.d/z00_lmod.csh
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WORKDIR /
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ENV USE_SLURMDBD=true \
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CLUSTER_NAME=snowflake \
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CONTROL_MACHINE=controller \
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SLURMCTLD_PORT=6817 \
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SLURMD_PORT=6818 \
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ACCOUNTING_STORAGE_HOST=database \
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ACCOUNTING_STORAGE_PORT=6819 \
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PARTITION_NAME=docker
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# clean up
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RUN rm -f /packages/slurm-*.rpm /packages/openmpi-*.rpm \
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&& yum clean all \
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&& rm -rf /var/cache/yum \
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&& rm -f /Lmod-7.7.tar.bz2
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COPY docker-entrypoint.sh /docker-entrypoint.sh
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ENTRYPOINT ["/usr/local/bin/tini", "--", "/docker-entrypoint.sh"]
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14
slurm/controller/Makefile
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14
slurm/controller/Makefile
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SLURM_VERSION = 19.05.1
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IMAGE = scidas/slurm.controller
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.PHONY: all build clean test
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all: build
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build:
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docker build -t $(IMAGE):$(SLURM_VERSION) .
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clean:
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@[ -z $(docker images -q $(IMAGE):$(SLURM_VERSION)) ] || docker rmi $(IMAGE):$(SLURM_VERSION)
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3
slurm/controller/README.md
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3
slurm/controller/README.md
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# Slurm Controller
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TODO
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200
slurm/controller/docker-entrypoint.sh
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200
slurm/controller/docker-entrypoint.sh
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#!/usr/bin/env bash
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set -e
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# start sshd server
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_sshd_host() {
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if [ ! -d /var/run/sshd ]; then
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mkdir /var/run/sshd
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ssh-keygen -t rsa -f /etc/ssh/ssh_host_rsa_key -N ''
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fi
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/usr/sbin/sshd
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}
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# setup worker ssh to be passwordless
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_ssh_worker() {
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if [[ ! -d /home/worker ]]; then
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mkdir -p /home/worker
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chown -R worker:worker /home/worker
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fi
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cat > /home/worker/setup-worker-ssh.sh <<'EOF2'
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mkdir -p ~/.ssh
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chmod 0700 ~/.ssh
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ssh-keygen -b 2048 -t rsa -f ~/.ssh/id_rsa -q -N "" -C "$(whoami)@$(hostname)-$(date -I)"
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cat ~/.ssh/id_rsa.pub > ~/.ssh/authorized_keys
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chmod 0640 ~/.ssh/authorized_keys
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cat >> ~/.ssh/config <<EOF
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Host *
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StrictHostKeyChecking no
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UserKnownHostsFile /dev/null
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LogLevel QUIET
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EOF
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chmod 0644 ~/.ssh/config
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cd ~/
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tar -czvf ~/worker-secret.tar.gz .ssh
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cd -
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EOF2
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chmod +x /home/worker/setup-worker-ssh.sh
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chown worker: /home/worker/setup-worker-ssh.sh
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sudo -u worker /home/worker/setup-worker-ssh.sh
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}
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# start munge and generate key
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_munge_start() {
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chown -R munge: /etc/munge /var/lib/munge /var/log/munge /var/run/munge
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chmod 0700 /etc/munge
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chmod 0711 /var/lib/munge
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chmod 0700 /var/log/munge
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chmod 0755 /var/run/munge
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/sbin/create-munge-key -f
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sudo -u munge /sbin/munged
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munge -n
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munge -n | unmunge
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remunge
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}
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# copy secrets to /.secret directory for other nodes
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_copy_secrets() {
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cp /home/worker/worker-secret.tar.gz /.secret/worker-secret.tar.gz
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cp /home/worker/setup-worker-ssh.sh /.secret/setup-worker-ssh.sh
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cp /etc/munge/munge.key /.secret/munge.key
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rm -f /home/worker/worker-secret.tar.gz
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rm -f /home/worker/setup-worker-ssh.sh
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}
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# generate slurm.conf
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_generate_slurm_conf() {
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cat > /etc/slurm/slurm.conf <<EOF
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#
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# Example slurm.conf file. Please run configurator.html
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# (in doc/html) to build a configuration file customized
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# for your environment.
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#
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#
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# slurm.conf file generated by configurator.html.
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#
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# See the slurm.conf man page for more information.
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#
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ClusterName=$CLUSTER_NAME
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SlurmctldHost=$CONTROL_MACHINE
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#SlurmctldHostr=
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#
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SlurmUser=slurm
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#SlurmdUser=root
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SlurmctldPort=$SLURMCTLD_PORT
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SlurmdPort=$SLURMD_PORT
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AuthType=auth/munge
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#JobCredentialPrivateKey=
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#JobCredentialPublicCertificate=
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StateSaveLocation=/var/spool/slurm/ctld
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SlurmdSpoolDir=/var/spool/slurm/d
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SwitchType=switch/none
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MpiDefault=none
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SlurmctldPidFile=/var/run/slurmctld.pid
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SlurmdPidFile=/var/run/slurmd.pid
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ProctrackType=proctrack/pgid
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#PluginDir=
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#FirstJobId=
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ReturnToService=0
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#MaxJobCount=
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#PlugStackConfig=
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#PropagatePrioProcess=
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#PropagateResourceLimits=
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#PropagateResourceLimitsExcept=
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#Prolog=
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#Epilog=
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#SrunProlog=
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#SrunEpilog=
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#TaskProlog=
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#TaskEpilog=
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#TaskPlugin=
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#TrackWCKey=no
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#TreeWidth=50
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#TmpFS=
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#UsePAM=
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#
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# TIMERS
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SlurmctldTimeout=300
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SlurmdTimeout=300
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InactiveLimit=0
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MinJobAge=300
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KillWait=30
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Waittime=0
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#
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# SCHEDULING
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SchedulerType=sched/backfill
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#SchedulerAuth=
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#SelectType=select/linear
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FastSchedule=1
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#PriorityType=priority/multifactor
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#PriorityDecayHalfLife=14-0
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#PriorityUsageResetPeriod=14-0
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#PriorityWeightFairshare=100000
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#PriorityWeightAge=1000
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#PriorityWeightPartition=10000
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#PriorityWeightJobSize=1000
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#PriorityMaxAge=1-0
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#
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# LOGGING
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SlurmctldDebug=3
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SlurmctldLogFile=/var/log/slurmctld.log
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SlurmdDebug=3
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SlurmdLogFile=/var/log/slurmd.log
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JobCompType=jobcomp/none
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#JobCompLoc=
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#
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# ACCOUNTING
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JobAcctGatherType=jobacct_gather/linux
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#JobAcctGatherFrequency=30
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#
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AccountingStorageType=accounting_storage/slurmdbd
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AccountingStorageHost=$ACCOUNTING_STORAGE_HOST
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AccountingStoragePort=$ACCOUNTING_STORAGE_PORT
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#AccountingStorageLoc=
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#AccountingStoragePass=
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#AccountingStorageUser=
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#
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# COMPUTE NODES
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NodeName=worker[01-02] RealMemory=1800 CPUs=1 State=UNKNOWN
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PartitionName=$PARTITION_NAME Nodes=ALL Default=YES MaxTime=INFINITE State=UP
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EOF
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}
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# run slurmctld
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_slurmctld() {
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if $USE_SLURMDBD; then
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echo -n "cheking for slurmdbd.conf"
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while [ ! -f /.secret/slurmdbd.conf ]; do
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echo -n "."
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sleep 1
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done
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echo ""
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fi
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mkdir -p /var/spool/slurm/ctld \
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/var/spool/slurm/d \
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/var/log/slurm
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chown -R slurm: /var/spool/slurm/ctld \
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/var/spool/slurm/d \
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/var/log/slurm
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touch /var/log/slurmctld.log
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chown slurm: /var/log/slurmctld.log
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if [[ ! -f /home/config/slurm.conf ]]; then
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echo "### generate slurm.conf ###"
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_generate_slurm_conf
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else
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echo "### use provided slurm.conf ###"
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cp /home/config/slurm.conf /etc/slurm/slurm.conf
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fi
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sacctmgr -i add cluster "${CLUSTER_NAME}"
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sleep 2s
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/usr/sbin/slurmctld
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cp -f /etc/slurm/slurm.conf /.secret/
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}
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### main ###
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_sshd_host
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_ssh_worker
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_munge_start
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_copy_secrets
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_slurmctld
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tail -f /dev/null
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