Introduce slurm cluster

slurm/worker/Dockerfile

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+FROM scidas/slurm.base:19.05.1
+MAINTAINER Michael J. Stealey <stealey@renci.org>
+
+# install openmpi 3.0.1
+RUN yum -y install \
+  gcc-c++ \
+  gcc-gfortran \
+  && yum -y localinstall \
+  /packages/openmpi-*.rpm
+
+# 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
+
+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"]

slurm/worker/Makefile

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+
+SLURM_VERSION = 19.05.1
+IMAGE = scidas/slurm.worker
+
+.PHONY: all build clean test
+
+all: build
+
+build:
+	docker build -t $(IMAGE):$(SLURM_VERSION) .
+
+clean:
+	@[ -z $(docker images -q $(IMAGE):$(SLURM_VERSION)) ] || docker rmi $(IMAGE):$(SLURM_VERSION)

slurm/worker/README.md

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+# Slurm Worker
+
+TODO

slurm/worker/docker-entrypoint.sh

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+#!/usr/bin/env bash
+set -e
+
+# start sshd server
+_sshd_host() {
+  if [ ! -d /var/run/sshd ]; then
+    mkdir /var/run/sshd
+    ssh-keygen -t rsa -f /etc/ssh/ssh_host_rsa_key -N ''
+  fi
+  /usr/sbin/sshd
+}
+
+# start munge using existing key
+_munge_start_using_key() {
+  echo -n "cheking for munge.key"
+  while [ ! -f /.secret/munge.key ]; do
+    echo -n "."
+    sleep 1
+  done
+  echo ""
+  cp /.secret/munge.key /etc/munge/munge.key
+  chown -R munge: /etc/munge /var/lib/munge /var/log/munge /var/run/munge
+  chmod 0700 /etc/munge
+  chmod 0711 /var/lib/munge
+  chmod 0700 /var/log/munge
+  chmod 0755 /var/run/munge
+  sudo -u munge /sbin/munged
+  munge -n
+  munge -n | unmunge
+  remunge
+}
+
+# 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"
+    while [ ! -f /home/worker/.ssh/id_rsa.pub ]; do
+      echo -n "."
+      sleep 1
+    done
+    echo ""
+  fi
+}
+
+# run slurmd
+_slurmd() {
+  if [ ! -f /.secret/slurm.conf ]; then
+    echo -n "cheking for slurm.conf"
+    while [ ! -f /.secret/slurm.conf ]; do
+      echo -n "."
+      sleep 1
+    done
+    echo ""
+  fi
+  mkdir -p /var/spool/slurm/d
+  chown slurm: /var/spool/slurm/d
+  cp /.secret/slurm.conf /etc/slurm/slurm.conf
+  touch /var/log/slurmd.log
+  chown slurm: /var/log/slurmd.log
+  /usr/sbin/slurmd
+}
+
+### main ###
+_sshd_host
+_munge_start_using_key
+_wait_for_worker
+_slurmd
+
+tail -f /dev/null