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[WIP] Instructions for using compose setup with minikube. #313

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[WIP] Instructions for using compose setup with minikube. #313

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254a0d5
Add instructions and script for converting compose to k8.
jmchilton Apr 25, 2017
93788a3
More progress toward k8 compat. for compose setup.
jmchilton Apr 28, 2017
b805504
Kompose does not respect "hostname" - so rewrite this to be service n…
jmchilton Apr 28, 2017
a7400b8
Switch docker-compose.yml to match up service and hostnames.
jmchilton Apr 28, 2017
fde887c
Baby steps toward a working Kubernetes setup.
jmchilton Apr 28, 2017
191c59f
Adapt configure_slurm.py to allow Kubernetes style naming.
jmchilton Apr 29, 2017
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3 changes: 2 additions & 1 deletion compose/galaxy-slurm/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,8 @@ ENV GALAXY_DIR=/export/galaxy-central \
SLURM_GID=1450 \
SLURM_PARTITION_NAME=work \
SLURM_CLUSTER_NAME=Cluster \
SLURM_CONTROL_MACHINE=galaxy-slurm \
SLURM_CONTROL_ADDR=galaxy-slurm \
SLURM_NODE_NAME=galaxy-slurm \
SLURMD_AUTOSTART=True \
SLURMCTLD_AUTOSTART=True \
SLURM_CONF_PATH=/export/slurm.conf \
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9 changes: 7 additions & 2 deletions compose/galaxy-slurm/configure_slurm.py
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Expand Up @@ -76,7 +76,7 @@
#SlurmctldLogFile=
SlurmdDebug=3
#SlurmdLogFile=
NodeName=$hostname CPUs=$cpus RealMemory=$memory State=UNKNOWN
NodeName=$node_name NodeAddr=$hostname CPUs=$cpus RealMemory=$memory State=UNKNOWN
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Ah, interesting!

PartitionName=$partition_name Nodes=$nodes Default=YES MaxTime=INFINITE State=UP Shared=YES
'''

Expand All @@ -91,9 +91,11 @@

def main():
hostname = gethostname()
node_name = environ.get('SLURM_NODE_NAME', hostname)
template_params = {
"hostname": hostname,
"nodes": ",".join(environ.get('SLURM_NODES', hostname).split(',')),
"node_name": node_name,
"nodes": ",".join(environ.get('SLURM_NODES', node_name).split(',')),
"cluster_name": environ.get('SLURM_CLUSTER_NAME', 'Cluster'),
"control_machine": environ.get('SLURM_CONTROL_MACHINE', hostname),
"user": environ.get('SLURM_USER_NAME', '{{ galaxy_user_name }}'),
Expand All @@ -102,6 +104,9 @@ def main():
"memory": environ.get("SLURM_MEMORY", int(mem / (1024 * 1024)))
}
config_contents = Template(SLURM_CONFIG_TEMPLATE).substitute(template_params)
control_addr = environ.get('SLURM_CONTROL_ADDR', None)
if control_addr:
config_contents = config_contents.replace("#ControlAddr=", "ControlAddr=%s" % control_addr)
open("/etc/slurm-llnl/slurm.conf", "w").write(config_contents)

if __name__ == "__main__":
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