From 1922bd4255bdce46da5f08ada9bca33872adf86b Mon Sep 17 00:00:00 2001
From: Enis Afgan <afgane@gmail.com>
Date: Fri, 24 May 2019 12:37:33 -0400
Subject: [PATCH] Add Slurm to the CVMFS container
---
docker/cvmfs/Dockerfile | 20 ++++++++++++++------
docker/cvmfs/README.md | 5 +++++
docker/testing/configure_slurm.py | 13 ++++++++++---
3 files changed, 29 insertions(+), 9 deletions(-)
create mode 100644 docker/cvmfs/README.md
diff --git a/docker/cvmfs/Dockerfile b/docker/cvmfs/Dockerfile
index 03ae9475..deb7f213 100644
--- a/docker/cvmfs/Dockerfile
+++ b/docker/cvmfs/Dockerfile
@@ -15,14 +15,17 @@ RUN apt-get update \
# Install packages
&& apt-get update \
&& apt-get install -y --no-install-recommends gcc python-setuptools \
- python-dev python-pip cvmfs cvmfs-config-default \
+ python-dev python-pip \
+ cvmfs cvmfs-config-default \
+ slurm-llnl slurm-drmaa-dev \
# Install Pulsar Python requirements
- && pip install --no-cache-dir -r /pulsar/requirements.txt \
+ && pip install --no-cache-dir -r /pulsar/requirements.txt drmaa \
# Remove build deps and cleanup
&& apt-get -y remove python-dev gcc wget lsb-release \
&& apt-get -y autoremove \
&& apt-get autoclean \
- && rm -rf /var/lib/apt/lists/* /var/log/dpkg.log
+ && rm -rf /var/lib/apt/lists/* /var/log/dpkg.log \
+ && /usr/sbin/create-munge-key
# Create pulsar user environment
RUN adduser --disabled-password --gecos '' pulsar \
@@ -32,10 +35,13 @@ RUN adduser --disabled-password --gecos '' pulsar \
WORKDIR /pulsar/
# Add files to the image
-ADD . /pulsar
+ADD . /pulsar/
# Change ownership to pulsar & configure CVMFS
RUN python setup.py install \
&& pulsar-config --auto_conda --host 0.0.0.0 \
+ && echo "export DRMAA_LIBRARY_PATH=/usr/lib/slurm-drmaa/lib/libdrmaa.so" >> local_env.sh \
+ && cp docker/cvmfs/app.yml . \
+ && cp ./docker/testing/configure_slurm.py /usr/sbin/configure_slurm.py \
&& chown -R pulsar:pulsar /pulsar \
&& chmod +x /usr/local/bin/pulsar \
&& cp /pulsar/docker/cvmfs/default.local /etc/cvmfs/ \
@@ -47,5 +53,7 @@ RUN python setup.py install \
EXPOSE 8913
# Must run CVMFS setup otherwise autofs does not get configured nor automount
-# starts. Then switch to less-priviledged user for running Pulsar.
-CMD /usr/bin/cvmfs_config setup; su pulsar -c "/usr/local/bin/pulsar"
+# starts. Then start Slurm and switch to a less-priviledged user for Pulsar.
+CMD /usr/bin/cvmfs_config setup; service munge start; \
+ python /usr/sbin/configure_slurm.py; service slurmd start; \
+ service slurmctld start; su pulsar -c "/usr/local/bin/pulsar"
diff --git a/docker/cvmfs/README.md b/docker/cvmfs/README.md
new file mode 100644
index 00000000..fa0aaae2
--- /dev/null
+++ b/docker/cvmfs/README.md
@@ -0,0 +1,5 @@
+Build this image from the repo root folder using the following command:
+
+```
+docker build -f docker/cvmfs/Dockerfile -t galaxy/pulsar:dev .
+```
\ No newline at end of file
diff --git a/docker/testing/configure_slurm.py b/docker/testing/configure_slurm.py
index d1ca485b..f768e616 100644
--- a/docker/testing/configure_slurm.py
+++ b/docker/testing/configure_slurm.py
@@ -1,7 +1,12 @@
+"""
+This file is also being used by the GalaxyCloudRunner (gcr) Docker image.
+"""
+
+from getpass import getuser
+from multiprocessing import cpu_count
from socket import gethostname
from string import Template
from subprocess import call
-from getpass import getuser
SLURM_CONFIG_TEMPLATE = '''
# slurm.conf file generated by configurator.html.
@@ -75,13 +80,15 @@ SlurmctldDebug=3
#SlurmctldLogFile=
SlurmdDebug=3
#SlurmdLogFile=
-NodeName=$hostname CPUs=1 State=UNKNOWN
+NodeName=$hostname CPUs=$cpus State=UNKNOWN
PartitionName=debug Nodes=$hostname Default=YES MaxTime=INFINITE State=UP
'''
def main():
- template_params = {"hostname": gethostname(), "user": getuser()}
+ template_params = {"hostname": gethostname(),
+ "user": getuser(),
+ "cpus": cpu_count()}
config_contents = Template(SLURM_CONFIG_TEMPLATE).substitute(template_params)
open("/etc/slurm-llnl/slurm.conf", "w").write(config_contents)
--
GitLab