From aefaca3d27bf61698a444a192355ece82847e617 Mon Sep 17 00:00:00 2001
From: Stefano Alberto Russo <stefano.russo@gmail.com>
Date: Thu, 14 May 2020 14:25:21 +0200
Subject: [PATCH] Added support for setting task extra volumes at runtime.
---
.../rosetta/core_app/computing_managers.py | 29 +++++++++++++++++--
.../webapp/code/rosetta/core_app/models.py | 1 +
.../core_app/templates/components/task.html | 12 ++++----
.../core_app/templates/create_task.html | 15 ++++++++--
.../webapp/code/rosetta/core_app/views.py | 8 +++--
5 files changed, 53 insertions(+), 12 deletions(-)
diff --git a/services/webapp/code/rosetta/core_app/computing_managers.py b/services/webapp/code/rosetta/core_app/computing_managers.py
index b9a5936..0aeee44 100644
--- a/services/webapp/code/rosetta/core_app/computing_managers.py
+++ b/services/webapp/code/rosetta/core_app/computing_managers.py
@@ -134,7 +134,10 @@ class LocalComputingManager(ComputingManager):
out = os_shell(stop_command, capture=True)
if out.exit_code != 0:
- raise Exception(out.stderr)
+ if 'No such container' in out.stderr:
+ pass
+ else:
+ raise Exception(out.stderr)
# Set task as stopped
task.status = TaskStatuses.stopped
@@ -194,7 +197,14 @@ class RemoteComputingManager(ComputingManager):
bindings = ''
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)
diff --git a/services/webapp/code/rosetta/core_app/models.py b/services/webapp/code/rosetta/core_app/models.py
index 05d9979..933ba01 100644
--- a/services/webapp/code/rosetta/core_app/models.py
+++ b/services/webapp/code/rosetta/core_app/models.py
@@ -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)
diff --git a/services/webapp/code/rosetta/core_app/templates/components/task.html b/services/webapp/code/rosetta/core_app/templates/components/task.html
index 90e6247..bc0f165 100644
--- a/services/webapp/code/rosetta/core_app/templates/components/task.html
+++ b/services/webapp/code/rosetta/core_app/templates/components/task.html
@@ -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>
@@ -72,7 +72,9 @@
<td>******</td>
</tr>
{% endif %}
-
+
+
+
<tr>
<td><b>Operations</b></td>
diff --git a/services/webapp/code/rosetta/core_app/templates/create_task.html b/services/webapp/code/rosetta/core_app/templates/create_task.html
index f7fb9bc..4c0b303 100644
--- a/services/webapp/code/rosetta/core_app/templates/create_task.html
+++ b/services/webapp/code/rosetta/core_app/templates/create_task.html
@@ -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>
diff --git a/services/webapp/code/rosetta/core_app/views.py b/services/webapp/code/rosetta/core_app/views.py
index 3e710b8..c3fb5ce 100644
--- a/services/webapp/code/rosetta/core_app/views.py
+++ b/services/webapp/code/rosetta/core_app/views.py
@@ -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:
@@ -586,6 +587,9 @@ def create_task(request):
if not task.container.supports_dynamic_ports:
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()
--
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