mirror of
https://github.com/ClusterCockpit/cc-docker.git
synced 2024-12-26 07:09:06 +01:00
Start converting to Rocky Linux base image
This commit is contained in:
parent
fa2287c661
commit
f0a6652fb0
@ -131,34 +131,34 @@ services:
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STORAGE_PASS: password
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STORAGE_USER: slurm
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slurm-worker01:
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container_name: slurm-worker01
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build:
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context: ./slurm/worker
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depends_on:
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- slurm-controller
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privileged: true
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volumes:
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- ./home:/home
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- ./secret:/.secret
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restart: always
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environment:
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CONTROL_MACHINE: controller
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ACCOUNTING_STORAGE_HOST: database
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COMPUTE_NODES: worker01 worker02
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# slurm-worker01:
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# container_name: slurm-worker01
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# build:
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# context: ./slurm/worker
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# depends_on:
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# - slurm-controller
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# privileged: true
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# volumes:
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# - ./home:/home
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# - ./secret:/.secret
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# restart: always
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# environment:
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# CONTROL_MACHINE: controller
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# ACCOUNTING_STORAGE_HOST: database
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# COMPUTE_NODES: worker01 worker02
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slurm-worker02:
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container_name: slurm-worker02
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build:
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context: ./slurm/worker
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depends_on:
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- slurm-controller
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privileged: true
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volumes:
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- ./home:/home
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- ./secret:/.secret
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restart: always
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environment:
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CONTROL_MACHINE: controller
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ACCOUNTING_STORAGE_HOST: database
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COMPUTE_NODES: worker01 worker02
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# slurm-worker02:
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# container_name: slurm-worker02
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# build:
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# context: ./slurm/worker
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# depends_on:
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# - slurm-controller
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# privileged: true
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# volumes:
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# - ./home:/home
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# - ./secret:/.secret
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# restart: always
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# environment:
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# CONTROL_MACHINE: controller
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# ACCOUNTING_STORAGE_HOST: database
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# COMPUTE_NODES: worker01 worker02
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@ -1,46 +0,0 @@
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FROM krallin/centos-tini:7
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MAINTAINER Michael J. Stealey <stealey@renci.org>
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ENV SLURM_VERSION=19.05.1 \
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MUNGE_UID=981 \
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SLURM_UID=982 \
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WORKER_UID=1000
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RUN groupadd -g $MUNGE_UID munge \
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&& useradd -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u $MUNGE_UID -g munge -s /sbin/nologin munge \
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&& groupadd -g $SLURM_UID slurm \
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&& useradd -m -c "Slurm workload manager" -d /var/lib/slurm -u $SLURM_UID -g slurm -s /bin/bash slurm \
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&& groupadd -g $WORKER_UID worker \
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&& useradd -m -c "Workflow user" -d /home/worker -u $WORKER_UID -g worker -s /bin/bash worker
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# install packages for general functionality
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RUN yum -y install \
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epel-release \
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&& yum -y install \
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sudo \
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wget \
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which \
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tree \
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mariadb-server \
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mariadb-devel \
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munge \
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munge-libs \
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munge-devel \
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openssh-server \
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openssh-clients
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# install slurm 19.05.1
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COPY rpms /packages
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# /usr/bin/mpiexec from slurm-torque conflicts with openmpi install
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WORKDIR /packages
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RUN yum -y localinstall $(ls | grep -v -e 'torque' -e 'openmpi')
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WORKDIR /
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VOLUME ["/home", "/.secret"]
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# 22: SSH
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# 3306: MariaDB
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# 6817: Slurm Ctl D
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# 6818: Slurm D
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# 6819: Slurm DBD
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EXPOSE 22 3306 6817 6818 6819
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@ -1,17 +0,0 @@
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SLURM_VERSION = 19.05.1
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IMAGE = scidas/slurm.base
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DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
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.PHONY: all build clean test
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all: build
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build:
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cp -r "$(DIR)/../packages/centos-7/rpms" .
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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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rm -rf rpms
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@ -1,3 +0,0 @@
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# Slurm Base Image
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TODO
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@ -1,31 +1,35 @@
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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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FROM rockylinux:8
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MAINTAINER Jan Eitzinger <jan.eitzinger@fau.de>
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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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ENV SLURM_VERSION=19.05.1 \
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MUNGE_UID=981 \
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SLURM_UID=982 \
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WORKER_UID=1000
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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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RUN yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm -y
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RUN groupadd -g $MUNGE_UID munge \
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&& useradd -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u $MUNGE_UID -g munge -s /sbin/nologin munge \
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&& groupadd -g $SLURM_UID slurm \
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&& useradd -m -c "Slurm workload manager" -d /var/lib/slurm -u $SLURM_UID -g slurm -s /bin/bash slurm \
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&& groupadd -g $WORKER_UID worker \
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&& useradd -m -c "Workflow user" -d /home/worker -u $WORKER_UID -g worker -s /bin/bash worker
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RUN yum install -y munge munge-libs
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RUN dnf --enablerepo=powertools install munge-devel -y
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RUN yum install rng-tools -y
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RUN yum install -y python3 gcc openssl openssl-devel \
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pam-devel numactl numactl-devel hwloc sudo \
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lua readline-devel ncurses-devel man2html \
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libibmad libibumad rpm-build perl-ExtUtils-MakeMaker.noarch rpm-build make wget
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RUN dnf --enablerepo=powertools install rrdtool-devel lua-devel hwloc-devel rpm-build -y
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RUN dnf install mariadb-server mariadb-devel -y
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RUN mkdir /usr/local/slurm-tmp
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RUN cd /usr/local/slurm-tmp
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RUN wget https://download.schedmd.com/slurm/slurm-22.05.6.tar.bz2
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RUN rpmbuild -ta slurm-22.05.6.tar.bz2
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ENV USE_SLURMDBD=true \
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CLUSTER_NAME=snowflake \
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@ -36,12 +40,12 @@ ENV USE_SLURMDBD=true \
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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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VOLUME ["/home", "/.secret"]
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# 22: SSH
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# 3306: MariaDB
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# 6817: SlurmCtlD
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# 6818: SlurmD
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# 6819: SlurmDBD
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EXPOSE 22 3306 6817 6818 6819
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ENTRYPOINT ["/docker-entrypoint.sh"]
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@ -16,23 +16,23 @@ _ssh_worker() {
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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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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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StrictHostKeyChecking no
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UserKnownHostsFile /dev/null
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LogLevel QUIET
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EOF2
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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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@ -46,6 +46,11 @@ _munge_start() {
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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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rngd -r /dev/urandom
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/usr/sbin/create-munge-key -r -f
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sh -c "dd if=/dev/urandom bs=1 count=1024 > /etc/munge/munge.key"
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chown munge: /etc/munge/munge.key
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chmod 400 /etc/munge/munge.key
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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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@ -76,15 +81,10 @@ _generate_slurm_conf() {
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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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@ -92,25 +92,7 @@ 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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@ -122,17 +104,7 @@ 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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@ -161,20 +133,18 @@ EOF
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# run slurmctld
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_slurmctld() {
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cd /root/rpmbuild/RPMS/aarch64
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yum -y --nogpgcheck localinstall slurm-22.05.6-1.el8.aarch64.rpm slurm-perlapi-22.05.6-1.el8.aarch64.rpm slurm-slurmctld-22.05.6-1.el8.aarch64.rpm
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if $USE_SLURMDBD; then
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echo -n "cheking for slurmdbd.conf"
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echo -n "checking 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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mkdir -p /var/spool/slurm/ctld /var/spool/slurmd /var/log/slurm /etc/slurm
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chown -R slurm: /var/spool/slurm/ctld /var/spool/slurmd /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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@ -1,5 +1,36 @@
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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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FROM rockylinux:8
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MAINTAINER Jan Eitzinger <jan.eitzinger@fau.de>
|
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|
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ENV SLURM_VERSION=19.05.1 \
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MUNGE_UID=981 \
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SLURM_UID=982 \
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WORKER_UID=1000
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RUN yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm -y
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RUN groupadd -g $MUNGE_UID munge \
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&& useradd -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u $MUNGE_UID -g munge -s /sbin/nologin munge \
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&& groupadd -g $SLURM_UID slurm \
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&& useradd -m -c "Slurm workload manager" -d /var/lib/slurm -u $SLURM_UID -g slurm -s /bin/bash slurm \
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&& groupadd -g $WORKER_UID worker \
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&& useradd -m -c "Workflow user" -d /home/worker -u $WORKER_UID -g worker -s /bin/bash worker
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RUN yum install -y munge munge-libs
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RUN dnf --enablerepo=powertools install munge-devel -y
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RUN yum install rng-tools -y
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|
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RUN yum install -y python3 gcc openssl openssl-devel \
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pam-devel numactl numactl-devel hwloc sudo \
|
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lua readline-devel ncurses-devel man2html \
|
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libibmad libibumad rpm-build perl-ExtUtils-MakeMaker.noarch rpm-build make wget
|
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|
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RUN dnf --enablerepo=powertools install rrdtool-devel lua-devel hwloc-devel rpm-build -y
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RUN dnf install mariadb-server mariadb-devel -y
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RUN mkdir /usr/local/slurm-tmp
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RUN cd /usr/local/slurm-tmp
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RUN wget https://download.schedmd.com/slurm/slurm-22.05.6.tar.bz2
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RUN rpmbuild -ta slurm-22.05.6.tar.bz2
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ENV DBD_ADDR=database \
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DBD_HOST=database \
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@ -9,11 +40,12 @@ ENV DBD_ADDR=database \
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STORAGE_PASS=password \
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STORAGE_USER=slurm
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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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COPY docker-entrypoint.sh /docker-entrypoint.sh
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ENTRYPOINT ["/usr/local/bin/tini", "--", "/docker-entrypoint.sh"]
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VOLUME ["/home", "/.secret"]
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# 22: SSH
|
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# 3306: MariaDB
|
||||
# 6817: Slurm Ctl D
|
||||
# 6818: Slurm D
|
||||
# 6819: Slurm DBD
|
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EXPOSE 22 3306 6817 6818 6819
|
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ENTRYPOINT ["/docker-entrypoint.sh"]
|
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|
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@ -41,7 +41,7 @@ _mariadb_start() {
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# start munge using existing key
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_munge_start_using_key() {
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if [ ! -f /.secret/munge.key ]; then
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echo -n "cheking for munge.key"
|
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echo -n "checking for munge.key"
|
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while [ ! -f /.secret/munge.key ]; do
|
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echo -n "."
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sleep 1
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@ -63,7 +63,7 @@ _munge_start_using_key() {
|
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# wait for worker user in shared /home volume
|
||||
_wait_for_worker() {
|
||||
if [ ! -f /home/worker/.ssh/id_rsa.pub ]; then
|
||||
echo -n "cheking for id_rsa.pub"
|
||||
echo -n "checking for id_rsa.pub"
|
||||
while [ ! -f /home/worker/.ssh/id_rsa.pub ]; do
|
||||
echo -n "."
|
||||
sleep 1
|
||||
|
||||
48
slurm/slurm.conf
Normal file
48
slurm/slurm.conf
Normal file
@ -0,0 +1,48 @@
|
||||
# slurm.conf file generated by configurator.html.
|
||||
# Put this file on all nodes of your cluster.
|
||||
# See the slurm.conf man page for more information.
|
||||
#
|
||||
ClusterName=snowflake
|
||||
SlurmctldHost=linux0
|
||||
SlurmUser=slurm
|
||||
SlurmctldPort=6817
|
||||
SlurmdPort=6818
|
||||
MpiDefault=none
|
||||
ProctrackType=proctrack/cgroup
|
||||
ReturnToService=1
|
||||
SlurmctldPidFile=/var/run/slurmctld.pid
|
||||
SlurmdPidFile=/var/run/slurmd.pid
|
||||
SlurmdSpoolDir=/var/spool/slurmd
|
||||
StateSaveLocation=/var/spool/slurmctld
|
||||
SwitchType=switch/none
|
||||
TaskPlugin=task/affinity,task/cgroup
|
||||
#
|
||||
# TIMERS
|
||||
InactiveLimit=0
|
||||
KillWait=30
|
||||
MinJobAge=300
|
||||
SlurmctldTimeout=120
|
||||
SlurmdTimeout=300
|
||||
Waittime=0
|
||||
#
|
||||
# SCHEDULING
|
||||
SchedulerType=sched/backfill
|
||||
SelectType=select/cons_tres
|
||||
#
|
||||
# LOGGING AND ACCOUNTING
|
||||
AccountingStorageHost=slurm-db
|
||||
AccountingStoragePort=6818
|
||||
AccountingStorageType=accounting_storage/slurmdbd
|
||||
AccountingStorageUser=slurm
|
||||
AccountingStoreFlags=job_script,job_comment,job_env,job_extra
|
||||
JobCompType=jobcomp/none
|
||||
JobAcctGatherFrequency=30
|
||||
JobAcctGatherType=jobacct_gather/cgroup
|
||||
SlurmctldDebug=info
|
||||
SlurmctldLogFile=/var/log/slurmctld.log
|
||||
SlurmdDebug=info
|
||||
SlurmdLogFile=/var/log/slurmd.log
|
||||
#
|
||||
# COMPUTE NODES
|
||||
NodeName=linux[1-32] CPUs=1 State=UNKNOWN
|
||||
PartitionName=debug Nodes=ALL Default=YES MaxTime=INFINITE State=UP
|
||||
@ -1,39 +1,43 @@
|
||||
FROM scidas/slurm.base:19.05.1
|
||||
MAINTAINER Michael J. Stealey <stealey@renci.org>
|
||||
FROM rockylinux:8
|
||||
MAINTAINER Jan Eitzinger <jan.eitzinger@fau.de>
|
||||
|
||||
# install openmpi 3.0.1
|
||||
RUN yum -y install \
|
||||
gcc-c++ \
|
||||
gcc-gfortran \
|
||||
&& yum -y localinstall \
|
||||
/packages/openmpi-*.rpm
|
||||
ENV SLURM_VERSION=19.05.1 \
|
||||
MUNGE_UID=981 \
|
||||
SLURM_UID=982 \
|
||||
WORKER_UID=1000
|
||||
|
||||
# install Lmod 7.7
|
||||
RUN yum -y install \
|
||||
lua-posix \
|
||||
lua \
|
||||
lua-filesystem \
|
||||
lua-devel \
|
||||
wget \
|
||||
bzip2 \
|
||||
expectk \
|
||||
make \
|
||||
&& wget https://sourceforge.net/projects/lmod/files/Lmod-7.7.tar.bz2 \
|
||||
&& tar -xjvf Lmod-7.7.tar.bz2
|
||||
WORKDIR /Lmod-7.7
|
||||
RUN ./configure --prefix=/opt/apps \
|
||||
&& make install \
|
||||
&& ln -s /opt/apps/lmod/lmod/init/profile /etc/profile.d/z00_lmod.sh \
|
||||
&& ln -s /opt/apps/lmod/lmod/init/cshrc /etc/profile.d/z00_lmod.csh
|
||||
RUN yum install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm -y
|
||||
|
||||
RUN groupadd -g $MUNGE_UID munge \
|
||||
&& useradd -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge -u $MUNGE_UID -g munge -s /sbin/nologin munge \
|
||||
&& groupadd -g $SLURM_UID slurm \
|
||||
&& useradd -m -c "Slurm workload manager" -d /var/lib/slurm -u $SLURM_UID -g slurm -s /bin/bash slurm \
|
||||
&& groupadd -g $WORKER_UID worker \
|
||||
&& useradd -m -c "Workflow user" -d /home/worker -u $WORKER_UID -g worker -s /bin/bash worker
|
||||
|
||||
RUN yum install -y munge munge-libs
|
||||
RUN dnf --enablerepo=powertools install munge-devel -y
|
||||
RUN yum install rng-tools -y
|
||||
|
||||
RUN yum install -y python3 gcc openssl openssl-devel \
|
||||
pam-devel numactl numactl-devel hwloc sudo \
|
||||
lua readline-devel ncurses-devel man2html \
|
||||
libibmad libibumad rpm-build perl-ExtUtils-MakeMaker.noarch rpm-build make wget
|
||||
|
||||
RUN dnf --enablerepo=powertools install rrdtool-devel lua-devel hwloc-devel rpm-build -y
|
||||
RUN dnf install mariadb-server mariadb-devel -y
|
||||
RUN mkdir /usr/local/slurm-tmp
|
||||
RUN cd /usr/local/slurm-tmp
|
||||
RUN wget https://download.schedmd.com/slurm/slurm-22.05.6.tar.bz2
|
||||
RUN rpmbuild -ta slurm-22.05.6.tar.bz2
|
||||
|
||||
VOLUME ["/home", "/.secret"]
|
||||
# 22: SSH
|
||||
# 3306: MariaDB
|
||||
# 6817: SlurmCtlD
|
||||
# 6818: SlurmD
|
||||
# 6819: SlurmDBD
|
||||
EXPOSE 22 3306 6817 6818 6819
|
||||
WORKDIR /home/worker
|
||||
|
||||
# clean up
|
||||
RUN rm -f /packages/slurm-*.rpm /packages/openmpi-*.rpm \
|
||||
&& yum clean all \
|
||||
&& rm -rf /var/cache/yum \
|
||||
&& rm -f /Lmod-7.7.tar.bz2
|
||||
|
||||
COPY docker-entrypoint.sh /docker-entrypoint.sh
|
||||
|
||||
ENTRYPOINT ["/usr/local/bin/tini", "--", "/docker-entrypoint.sh"]
|
||||
ENTRYPOINT ["/docker-entrypoint.sh"]
|
||||
|
||||
@ -45,7 +45,7 @@ _wait_for_worker() {
|
||||
# run slurmd
|
||||
_slurmd() {
|
||||
if [ ! -f /.secret/slurm.conf ]; then
|
||||
echo -n "cheking for slurm.conf"
|
||||
echo -n "checking for slurm.conf"
|
||||
while [ ! -f /.secret/slurm.conf ]; do
|
||||
echo -n "."
|
||||
sleep 1
|
||||
|
||||
Loading…
Reference in New Issue
Block a user