diff --git a/services/slurmbase/Dockerfile b/services/slurmbase/Dockerfile
index 7abc48159561fd7276d63db67fc088e2fe7a8956..18e4791cbed5b337ae99bcbc045684145b626e9c 100755
--- a/services/slurmbase/Dockerfile
+++ b/services/slurmbase/Dockerfile
@@ -25,5 +25,6 @@ RUN ln -s /var/log/slurm-llnl /var/log/slurm-wlm
# Add slurmtestuser user
RUN useradd slurmtestuser
-RUN cp -a /rosetta/.ssh /home/slurmtestuser
+RUN mkdir -p /home/slurmtestuser/.ssh
+RUN cat /rosetta/.ssh/id_rsa.pub >> /home/slurmtestuser/.ssh/authorized_keys
RUN chown -R slurmtestuser:slurmtestuser /home/slurmtestuser
diff --git a/services/webapp/code/rosetta/base_app/computing_managers.py b/services/webapp/code/rosetta/base_app/computing_managers.py
index 3ad3aaa6d5a957b20560b4cc878e1c719700976f..0083a85ad40c4e7007234aebc7a6c83d5619b1c5 100644
--- a/services/webapp/code/rosetta/base_app/computing_managers.py
+++ b/services/webapp/code/rosetta/base_app/computing_managers.py
@@ -154,6 +154,7 @@ class RemoteComputingManager(ComputingManager):
# Get computing host
host = task.computing.get_conf_param('host')
+ user = task.computing.get_conf_param('user')
# Get user keys
if task.computing.require_user_keys:
@@ -178,8 +179,8 @@ class RemoteComputingManager(ComputingManager):
hostname = socket.gethostname()
webapp_ip = socket.gethostbyname(hostname)
- run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {} '.format(user_keys.private_key_file, host)
- run_command+= '"wget {}:8080/api/v1/base/agent/?task_uuid={} -O /tmp/agent_{}.py &> /dev/null && export BASE_PORT=\$(python /tmp/agent_{}.py 2> /tmp/{}.log) && '.format(webapp_ip, task.uuid, task.uuid, task.uuid, task.uuid)
+ run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
+ run_command += '/bin/bash -c \'"wget {}:8080/api/v1/base/agent/?task_uuid={} -O /tmp/agent_{}.py &> /dev/null && export BASE_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_BASE_PORT=\$BASE_PORT && {} '.format(authstring)
run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '
@@ -198,7 +199,7 @@ class RemoteComputingManager(ComputingManager):
else:
raise NotImplementedError('Registry {} not supported'.format(task.container.registry))
- run_command+='{}{} &>> /tmp/{}.log & echo \$!"'.format(registry, task.container.image, task.uuid)
+ run_command+='{}{} &>> /tmp/{}.log & echo \$!"\''.format(registry, task.container.image, task.uuid)
else:
raise NotImplementedError('Container {} not supported'.format(task.container.type))
@@ -236,9 +237,10 @@ class RemoteComputingManager(ComputingManager):
# Get computing host
host = task.computing.get_conf_param('host')
+ user = task.computing.get_conf_param('user')
# Stop the task remotely
- stop_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {} "kill -9 {}"'.format(user_keys.private_key_file, host, task.pid)
+ stop_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} \'/bin/bash -c "kill -9 {}"\''.format(user_keys.private_key_file, user, host, task.pid)
logger.debug(stop_command)
out = os_shell(stop_command, capture=True)
if out.exit_code != 0:
@@ -255,10 +257,10 @@ class RemoteComputingManager(ComputingManager):
user_keys = Keys.objects.get(user=task.user, default=True)
id_rsa_file = user_keys.private_key_file
else:
- raise NotImplementedError('temote with no keys not yet')
+ raise NotImplementedError('Remote with no keys not yet')
# View the Singularity container log
- view_log_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {} "cat /tmp/{}.log"'.format(id_rsa_file, host, task.uuid)
+ view_log_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {} \'/bin/bash -c "cat /tmp/{}.log"\''.format(id_rsa_file, host, task.uuid)
logger.debug(view_log_command)
out = os_shell(view_log_command, capture=True)
if out.exit_code != 0:
@@ -275,7 +277,8 @@ class SlurmComputingManager(ComputingManager):
# Get computing host #Key Error ATM
host = 'slurmclustermaster-main' #task.computing.get_conf_param('host')
-
+ user = task.computing.get_conf_param('user')
+
# Get user keys
if task.computing.require_user_keys:
user_keys = Keys.objects.get(user=task.user, default=True)
@@ -286,7 +289,7 @@ class SlurmComputingManager(ComputingManager):
if task.container.type == 'singularity':
- if not task.dynamic_ports:
+ if not task.container.dynamic_ports:
raise Exception('This task does not support dynamic port allocation and is therefore not supported using singularity on Slurm')
# Set pass if any
@@ -299,9 +302,9 @@ class SlurmComputingManager(ComputingManager):
hostname = socket.gethostname()
webapp_ip = socket.gethostbyname(hostname)
- run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {} '.format(user_keys.private_key_file, host)
+ run_command = 'ssh -i {} -4 -o StrictHostKeyChecking=no {}@{} '.format(user_keys.private_key_file, user, host)
- run_command += '"echo \\"#!/bin/bash\nwget {}:8080/api/v1/base/agent/?task_uuid={} -O /tmp/agent_{}.py &> /dev/null && export BASE_PORT=\\\\\\$(python /tmp/agent_{}.py 2> /tmp/{}.log) && '.format(webapp_ip, task.uuid, task.uuid, task.uuid, task.uuid)
+ run_command += '\'bash -c "echo \\"#!/bin/bash\nwget {}:8080/api/v1/base/agent/?task_uuid={} -O /tmp/agent_{}.py &> /dev/null && export BASE_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_BASE_PORT=\\\\\\$BASE_PORT && {} '.format(authstring)
run_command += 'exec nohup singularity run --pid --writable-tmpfs --containall --cleanenv '
@@ -321,7 +324,7 @@ class SlurmComputingManager(ComputingManager):
else:
raise NotImplementedError('Registry {} not supported'.format(task.container.registry))
- run_command+='{}{} &> /tmp/{}.log\\" > /tmp/{}.sh && sbatch -p partition1 /tmp/{}.sh"'.format(registry, task.container.image, task.uuid, 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: