From 28add1a7096a305447cbcae28df2910585e7ce7c Mon Sep 17 00:00:00 2001
From: Jan David Mol <mol@astron.nl>
Date: Wed, 6 Apr 2016 14:11:14 +0000
Subject: [PATCH] Task #8437: Remove bash from docker command line to make
signal propagation easier
---
.../lofarpipe/support/remotecommand.py | 30 ++++++++++++-------
.../recipes/sip/pipeline.cfg.CEP4.tmpl | 2 +-
2 files changed, 21 insertions(+), 11 deletions(-)
diff --git a/CEP/Pipeline/framework/lofarpipe/support/remotecommand.py b/CEP/Pipeline/framework/lofarpipe/support/remotecommand.py
index 7ac394c699e..4edf2d52a2c 100644
--- a/CEP/Pipeline/framework/lofarpipe/support/remotecommand.py
+++ b/CEP/Pipeline/framework/lofarpipe/support/remotecommand.py
@@ -196,7 +196,9 @@ def run_via_custom_cmdline(logger, host, command, environment, arguments, config
with the following strings replaced:
{host} := host to execute command on
- {command} := bash command line to be executed
+ {env} := "A=B C=D" string, the environment to set
+ {docker_env} := "-e A=B -e C=D" string, the environment to set
+ {command} := command to be executed
{uid} := uid of the calling user
{slurm_job_id} := the SLURM job id to allocate resources in
@@ -205,9 +207,17 @@ def run_via_custom_cmdline(logger, host, command, environment, arguments, config
{nr_cores} := number of cores to allocate for this job
"""
- commandArray = ["%s=%s" % (key, value) for key, value in environment.items()]
- commandArray.append(command)
- commandArray.extend(re.escape(str(arg)) for arg in arguments)
+
+ # construct {env}
+ envPairs = ["%s=%s" % (key, value) for key, value in environment.items()]
+ envStr = " ".join(envPairs)
+
+ # construct {docker-env}
+ dockerEnvPairs = ["-e %s=%s" % (key, value) for key, value in environment.items()]
+ dockerEnvStr = " ".join(dockerEnvPairs)
+
+ # construct {command}
+ commandArray = [command] + [re.escape(str(arg)) for arg in arguments]
commandStr = " ".join(commandArray)
# Determine job name
@@ -219,20 +229,20 @@ def run_via_custom_cmdline(logger, host, command, environment, arguments, config
return args[1] if args[0] == "python" else args[0]
- # Construct the full command line, except for {command}, as that itself
- # can contain spaces which we don't want to split on.
+ # Construct the full command line
full_command_line = config.get('remote', 'cmdline').format(
uid = os.geteuid(),
slurm_job_id = os.environ.get("SLURM_JOB_ID"),
host = host,
- command = "{command}",
+
+ env = envStr,
+ docker_env = dockerEnvStr,
+
+ command = commandStr,
job_name = jobname(command),
nr_cores = resources.get("cores", 1),
).split(' ')
- # Fill in {command} somewhere
- full_command_line = [x.format(command = commandStr) for x in full_command_line]
-
logger.debug("Dispatching command to %s with custom_cmdline: %s" % (host, full_command_line))
process = spawn_process(full_command_line, logger)
diff --git a/CEP/Pipeline/recipes/sip/pipeline.cfg.CEP4.tmpl b/CEP/Pipeline/recipes/sip/pipeline.cfg.CEP4.tmpl
index 6c1c35a244a..473eb91eeaf 100644
--- a/CEP/Pipeline/recipes/sip/pipeline.cfg.CEP4.tmpl
+++ b/CEP/Pipeline/recipes/sip/pipeline.cfg.CEP4.tmpl
@@ -67,4 +67,4 @@ globalfs = yes
# /bin/bash -c
#
# Required because the pipeline framework needs some bash functionality in the commands it starts.
-cmdline = ssh -n -tt -x localhost srun --exclusive --ntasks=1 --cpus-per-task={nr_cores} --jobid={slurm_job_id} --job-name={job_name} docker run --rm -e LUSER={uid} -v /data:/data --net=host lofar-pipeline:${LOFAR_TAG} /bin/bash -c "\"{command}\""
+cmdline = ssh -n -tt -x localhost srun --exclusive --ntasks=1 --cpus-per-task={nr_cores} --jobid={slurm_job_id} --job-name={job_name} docker run --rm -e LUSER={uid} -v /data:/data --net=host lofar-pipeline:${LOFAR_TAG} {docker-env} {command}
--
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