From 37f9580d2eba7c69b7959f106d639de1e9b69b5a Mon Sep 17 00:00:00 2001
From: Stefano Alberto Russo <stefano.russo@gmail.com>
Date: Thu, 30 Apr 2020 10:03:04 +0200
Subject: [PATCH] Added first sbatch support.
---
services/webapp/code/rosetta/base_app/tasks.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/services/webapp/code/rosetta/base_app/tasks.py b/services/webapp/code/rosetta/base_app/tasks.py
index 39f66fa..bd95299 100644
--- a/services/webapp/code/rosetta/base_app/tasks.py
+++ b/services/webapp/code/rosetta/base_app/tasks.py
@@ -240,10 +240,13 @@ def start_task(task):
run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {} '.format(user_keys.private_key_file, host)
- run_command += '"echo \\"wget {}:8080/api/v1/base/agent/?task_uuid={} -O /tmp/agent_{}.py &> /dev/null && export TASK_PORT=\\\\\\$(python /tmp/agent_{}.py 2> /tmp/{}.log) && '.format(webapp_ip, task.uuid, task.uuid, task.uuid, task.uuid)
+ run_command += '"echo \\"#!/bin/bash\nwget {}:8080/api/v1/base/agent/?task_uuid={} -O /tmp/agent_{}.py &> /dev/null && export TASK_PORT=\\\\\\$(python /tmp/agent_{}.py 2> /tmp/{}.log) && '.format(webapp_ip, task.uuid, task.uuid, task.uuid, task.uuid)
run_command += 'export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_TASK_PORT=\\\\\\$TASK_PORT && {} '.format(authstring)
run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '
+
+ # Double to escape for python six for shell (double times three as \\\ escapes a single slash in shell)
+
# ssh -i /rosetta/.ssh/id_rsa -4 -o StrictHostKeyChecking=no slurmclustermaster-main "echo \"wget 172.18.0.5:8080/api/v1/base/agent/?task_uuid=558c65c3-8b72-4d6b-8119-e1dcf6f81177 -O /tmp/agent_558c65c3-8b72-4d6b-8119-e1dcf6f81177.py &> /dev/null
# && export TASK_PORT=\\\$(python /tmp/agent_558c65c3-8b72-4d6b-8119-e1dcf6f81177.py 2> /tmp/558c65c3-8b72-4d6b-8119-e1dcf6f81177.log) && export SINGULARITY_NOHTTPS=true && export SINGULARITYENV_TASK_PORT=\\\$TASK_PORT && export SINGULARITYENV_AUTH_PASS=testpass
# && exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv docker://dregistry:5000/rosetta/metadesktop &> /tmp/558c65c3-8b72-4d6b-8119-e1dcf6f81177.log\" > /tmp/558c65c3-8b72-4d6b-8119-e1dcf6f81177.sh"
@@ -257,7 +260,7 @@ def start_task(task):
else:
raise NotImplementedError('Registry {} not supported'.format(task.container.registry))
- run_command+='{}{} &> /tmp/{}.log\\" > /tmp/{}.sh"'.format(registry, task.container.image, task.uuid, task.uuid)
+ run_command+='{}{} &> /tmp/{}.log\\" > /tmp/{}.sh && sbatch -p partition1 /tmp/{}.sh"'.format(registry, task.container.image, task.uuid, task.uuid, task.uuid)
else:
--
GitLab