From 1fbf9cd8a35b3363688f74650a8c673726aedad5 Mon Sep 17 00:00:00 2001
From: Stefano Alberto Russo <stefano.russo@gmail.com>
Date: Wed, 13 May 2020 18:08:25 +0200
Subject: [PATCH] Added support for custom singularity bindings for user-owned
computing resources.
---
.../rosetta/core_app/computing_managers.py | 36 +++++++++++++++----
1 file changed, 30 insertions(+), 6 deletions(-)
diff --git a/services/webapp/code/rosetta/core_app/computing_managers.py b/services/webapp/code/rosetta/core_app/computing_managers.py
index 118ee95..b9a5936 100644
--- a/services/webapp/code/rosetta/core_app/computing_managers.py
+++ b/services/webapp/code/rosetta/core_app/computing_managers.py
@@ -185,10 +185,20 @@ class RemoteComputingManager(ComputingManager):
else:
authstring = ''
+ # Set bindings, only from sys config if the resource is not owned by the user
+ if task.computing.user != task.user:
+ bindings = task.computing.get_conf_param('bindings', from_sys_only=True )
+ else:
+ bindings = task.computing.get_conf_param('bindings')
+ if not bindings:
+ bindings = ''
+ else:
+ bindings = '-B {}'.format(bindings)
+
run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
run_command += '/bin/bash -c \'"wget {}/api/v1/base/agent/?task_uuid={} -O \$HOME/agent_{}.py &> /dev/null && export BASE_PORT=\$(python \$HOME/agent_{}.py 2> \$HOME/{}.log) && '.format(webapp_conn_string, task.uuid, task.uuid, task.uuid, task.uuid)
run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)
- run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '
+ run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --containall --cleanenv '.format(bindings)
# Set registry
if task.container.registry == 'docker_local':
@@ -325,7 +335,11 @@ class SlurmComputingManager(ComputingManager):
else:
authstring = ''
- bindings = task.computing.get_conf_param('bindings', from_sys_only=True )
+ # Set bindings, only from sys config if the resource is not owned by the user
+ if task.computing.user != task.user:
+ bindings = task.computing.get_conf_param('bindings', from_sys_only=True )
+ else:
+ bindings = task.computing.get_conf_param('bindings')
if not bindings:
bindings = ''
else:
@@ -443,7 +457,7 @@ class RemotehopComputingManager(ComputingManager):
second_user = task.computing.get_conf_param('second_user')
setup_command = task.computing.get_conf_param('setup_command')
- # De hard-code
+ # TODO: De hard-code
use_agent = False
# Get user keys
@@ -467,7 +481,17 @@ class RemotehopComputingManager(ComputingManager):
authstring = ' export SINGULARITYENV_AUTH_PASS={} && '.format(task.auth_pass)
else:
authstring = ''
-
+
+ # Set bindings, only from sys config if the resource is not owned by the user
+ if task.computing.user != task.user:
+ bindings = task.computing.get_conf_param('bindings', from_sys_only=True )
+ else:
+ bindings = task.computing.get_conf_param('bindings')
+ if not bindings:
+ bindings = ''
+ else:
+ bindings = '-B {}'.format(bindings)
+
run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, first_user, first_host)
run_command += '"ssh -4 -o StrictHostKeyChecking=no {}@{} /bin/bash -c \''.format(second_user, second_host)
@@ -476,13 +500,13 @@ class RemotehopComputingManager(ComputingManager):
if setup_command:
run_command += setup_command + ' && '
run_command += '\'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT=\$BASE_PORT && {} '.format(authstring)
- run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '
+ run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --containall --cleanenv '.format(bindings)
else:
run_command += ' : && ' # Trick to prevent some issues in exporting variables
if setup_command:
run_command += setup_command + ' && '
run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_BASE_PORT={} && {} '.format(task.port, authstring)
- run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '
+ run_command += 'exec nohup singularity run {} --pid --writable-tmpfs --containall --cleanenv '.format(bindings)
# Set registry
if task.container.registry == 'docker_local':
--
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