From 9c376ec8c2e29b33f3801e53485a6c3d80298463 Mon Sep 17 00:00:00 2001
From: Stefano Alberto Russo <stefano.russo@gmail.com>
Date: Thu, 4 Nov 2021 18:57:51 +0100
Subject: [PATCH] Fixed bugs in running tasks on standalone computing
resources.
---
.../rosetta/core_app/computing_managers.py | 32 +++++++------------
1 file changed, 12 insertions(+), 20 deletions(-)
diff --git a/services/webapp/code/rosetta/core_app/computing_managers.py b/services/webapp/code/rosetta/core_app/computing_managers.py
index 1e15f51..792e5a7 100644
--- a/services/webapp/code/rosetta/core_app/computing_managers.py
+++ b/services/webapp/code/rosetta/core_app/computing_managers.py
@@ -194,16 +194,17 @@ class SSHSingleNodeComputingManager(SingleNodeComputingManager, SSHComputingMana
from.utils import get_webapp_conn_string
webapp_conn_string = get_webapp_conn_string()
- # Run the container on the host (non blocking)
- if task.container.type == 'singularity':
+ # Handle container runtime
+ if task.computing.default_container_runtime == 'singularity':
+ #if not task.container.supports_custom_interface_port:
+ # raise Exception('This task does not support dynamic port allocation and is therefore not supported using singularity on Slurm')
# Set pass if any
- if task.auth_pass:
- authstring = ' export SINGULARITYENV_AUTH_PASS={} && '.format(task.auth_pass)
- else:
- authstring = ''
-
+ authstring = ''
+ if not task.requires_proxy_auth and task.password:
+ authstring = ' export SINGULARITYENV_AUTH_PASS={} && '.format(task.password)
+
# Set binds, only from sys config if the resource is not owned by the user
if self.computing.user != task.user:
binds = self.computing.sys_conf.get('binds')
@@ -227,19 +228,10 @@ class SSHSingleNodeComputingManager(SingleNodeComputingManager, SSHComputingMana
run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)
run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --no-home --home=/home/metauser --workdir /tmp/{}_data/tmp -B/tmp/{}_data/home:/home --containall --cleanenv '.format(binds, task.uuid, task.uuid)
- # Set registry
- if task.container.registry == 'docker_local':
- # Get local Docker registry conn string
- from.utils import get_local_docker_registry_conn_string
- local_docker_registry_conn_string = get_local_docker_registry_conn_string()
- registry = 'docker://{}/'.format(local_docker_registry_conn_string)
- elif task.container.registry == 'docker_hub':
- registry = 'docker://'
- else:
- raise NotImplementedError('Registry {} not supported'.format(task.container.registry))
-
- run_command+='{}{} &>> /tmp/{}_data/task.log & echo \$!"\''.format(registry, task.container.image, task.uuid)
+ # Container part
+ run_command+='docker://{}/{}:{} &>> /tmp/{}_data/task.log & echo \$!"\''.format(task.container.registry, task.container.image, task.container.tag, task.uuid)
+
else:
raise NotImplementedError('Container {} not supported'.format(task.container.type))
@@ -274,7 +266,7 @@ class SSHSingleNodeComputingManager(SingleNodeComputingManager, SSHComputingMana
user = self.computing.conf.get('user')
# Stop the task remotely
- stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "kill -9 {}"\''.format(user_keys.private_key_file, user, host, task.pid)
+ stop_command = 'ssh -o LogLevel=ERROR -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "kill -9 {}"\''.format(user_keys.private_key_file, user, host, task.id)
out = os_shell(stop_command, capture=True)
if out.exit_code != 0:
if not 'No such process' in out.stderr:
--
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