Added support for setting task extra volumes at runtime. (aefaca3d) · Commits · ExaCT / Rosetta

services/webapp/code/rosetta/core_app/computing_managers.py

+26 −3

Original line number	Diff line number	Diff line
		@@ -134,6 +134,9 @@ class LocalComputingManager(ComputingManager):

		out = os_shell(stop_command, capture=True)
		if out.exit_code != 0:
		if 'No such container' in out.stderr:
		pass
		else:
		raise Exception(out.stderr)

		# Set task as stopped
		@@ -195,6 +198,13 @@ class RemoteComputingManager(ComputingManager):
		else:
		bindings = '-B {}'.format(bindings)

		# Manage task extra volumes
		if task.extra_volumes:
		if not bindings:
		bindings = '-B {}'.format(task.extra_volumes)
		else:
		bindings += ',{}'.format(task.extra_volumes)

		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)
		@@ -345,8 +355,14 @@ class SlurmComputingManager(ComputingManager):
		else:
		bindings = '-B {}'.format(bindings)

		run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
		# Manage task extra volumes
		if task.extra_volumes:
		if not bindings:
		bindings = '-B {}'.format(task.extra_volumes)
		else:
		bindings += ',{}'.format(task.extra_volumes)

		run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
		run_command += '\'bash -c "echo \\"#!/bin/bash\nwget {}/api/v1/base/agent/?task_uuid={} -O \$HOME/agent_{}.py &> \$HOME/{}.log && export BASE_PORT=\\\\\\$(python \$HOME/agent_{}.py 2> \$HOME/{}.log) && '.format(webapp_conn_string, task.uuid, 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 '.format(bindings)
		@@ -492,6 +508,13 @@ class RemotehopComputingManager(ComputingManager):
		else:
		bindings = '-B {}'.format(bindings)

		# Manage task extra volumes
		if task.extra_volumes:
		if not bindings:
		bindings = '-B {}'.format(task.extra_volumes)
		else:
		bindings += ',{}'.format(task.extra_volumes)

		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)

services/webapp/code/rosetta/core_app/models.py

+1 −0

Original line number	Diff line number	Diff line
		@@ -272,6 +272,7 @@ class Task(models.Model):
		port = models.IntegerField('Task port', blank=True, null=True)
		ip = models.CharField('Task ip address', max_length=36, blank=True, null=True)
		tunnel_port = models.IntegerField('Task tunnel port', blank=True, null=True)
		extra_volumes = models.CharField('Extra volumes', max_length=4096, blank=True, null=True)

		# Links
		computing = models.ForeignKey(Computing, related_name='+', on_delete=models.CASCADE)

services/webapp/code/rosetta/core_app/templates/components/task.html

+7 −5

Original line number	Diff line number	Diff line
		@@ -46,10 +46,10 @@
		<td>{{ task.computing }}</td>
		</tr>

		<!-- <tr>
		<td><b>Task pid</b></td>
		<td>{{ task.pid}}</td>
		</tr> -->
		<tr>
		<td><b>Extra volumes</b></td>
		<td>{{ task.extra_volumes }}</td>
		</tr>

		<tr>
		<td><b>IP</b></td>
		@@ -74,6 +74,8 @@
		{% endif %}




		<tr>
		<td><b>Operations</b></td>

services/webapp/code/rosetta/core_app/templates/create_task.html

+13 −2

Original line number	Diff line number	Diff line
		@@ -135,7 +135,7 @@
		<td valign="top" style="width:180px"><b>Set custom port </b></td>
		<td>
		<input type="text" name="task_base_port" value="" placeholder="" size="23" style="margin-bottom:5px"/><br>
		<p style="line-height: 0.9"><font size=-1>This container supports dynamic ports and you can thus set a custom port (>5900) to avoid clashes with services already running on the computing resource.</font></p>
		<p style="line-height: 0.95"><font size=-1>This container supports dynamic ports and you can thus set a custom port (>5900) to avoid clashes with services already running on the computing resource.</font></p>
		</td>
		</tr>
		{% endif %}
		@@ -150,6 +150,17 @@
		</tr>
		{% endif %}


		{% if data.task_container.type == 'singularity' %}
		<tr>
		<td valign="top" style="width:180px"><b>Extra volumes</b></td>
		<td>
		<input type="text" name="extra_volumes" value="" placeholder="" size="23" /><br>
		<p style="line-height: 0.95"><font size=-1>Here you can set extra volume bindings on top of the ones already define by the administrator. Format is <i>host_directory:container_directory</i>, comma separated.</font></p>
		</td>
		</tr>
		{% endif %}

		<tr>
		<td><b>Access method</b></td><td>
		<select name="access_method" >
		@@ -184,7 +195,7 @@

		<tr><td colspan=2>
		<table><tr><td style="border: 1px solid lightgray;" >
		I understand that files saved or modified in this container, if not explicitly saved to a persistent storage, will be LOST when the task ends.
		I understand that files saved or modified in this container, if not explicitly saved to a persistent volume, will be LOST when the task ends.
		</td><td style="border: 1px solid lightgray;" >
		<input class="form-check-input" type="checkbox" value="" id="invalidCheck" required>
		</td></table>

services/webapp/code/rosetta/core_app/views.py

+6 −2

Original line number	Diff line number	Diff line
		@@ -553,14 +553,15 @@ def create_task(request):
		if task_base_port:
		task.port = task_base_port

		# Cheks
		# Checks
		if task.auth_pass and len(task.auth_pass) < 6:
		raise ErrorMessage('Task password must be at least 6 chars')

		# Computing options # TODO: This is hardcoded thinking about Slurm
		# Computing options # TODO: This is hardcoded thinking about Slurm and Singularity
		computing_cpus = request.POST.get('computing_cpus', None)
		computing_memory = request.POST.get('computing_memory', None)
		computing_partition = request.POST.get('computing_partition', None)
		extra_volumes = request.POST.get('extra_volumes', None)

		computing_options = {}
		if computing_cpus:
		@@ -587,6 +588,9 @@ def create_task(request):
		if task.container.ports:
		task.port = task.container.port

		# Set exttra volumes if any:
		task.extra_volumes = extra_volumes

		# Save the task before starting it, or the computing manager will not be able to work properly
		task.save()