def _bootstrap_bcbio(args, ansible_base):
"""Install bcbio_vm and docker container with tools. Set core and memory usage.
"""
cluster = common.ecluster_config(args.econfig).load_cluster(args.cluster)
inventory_path = os.path.join(
cluster.repository.storage_path,
'ansible-inventory.{}'.format(args.cluster))
playbook_path = os.path.join(
ansible_base, "roles", "bcbio_bootstrap", "tasks", "main.yml")
def _extra_vars(args, cluster_config):
# Calculate cores and memory
compute_nodes = int(
tz.get_in(["nodes", "frontend", "compute_nodes"], cluster_config, 0))
if compute_nodes > 0:
machine = tz.get_in(["nodes", "compute", "flavor"], cluster_config)
else:
machine = tz.get_in(["nodes", "frontend", "flavor"], cluster_config)
cores, mem = AWS_INFO[machine]
# For small number of compute nodes, leave space for runner and controller
if compute_nodes < 5 and compute_nodes > 0:
cores = cores - 2
return {"target_cores": cores, "target_memory": mem,
"upgrade_host_os_and_reboot": not args.no_reboot}
common.run_ansible_pb(
inventory_path, playbook_path, args, _extra_vars)
def _bootstrap_bcbio(args, ansible_base):
"""Install bcbio_vm and docker container with tools. Set core and memory usage.
"""
cluster = common.ecluster_config(args.econfig).load_cluster(args.cluster)
inventory_path = os.path.join(cluster.repository.storage_path,
'ansible-inventory.{}'.format(args.cluster))
playbook_path = os.path.join(ansible_base, "roles", "bcbio_bootstrap",
"tasks", "main.yml")
def _extra_vars(args, cluster_config):
# Calculate cores and memory
compute_nodes = int(
tz.get_in(["nodes", "frontend", "compute_nodes"], cluster_config,
0))
if compute_nodes > 0:
machine = tz.get_in(["nodes", "compute", "flavor"], cluster_config)
else:
machine = tz.get_in(["nodes", "frontend", "flavor"],
cluster_config)
cores, mem = AWS_INFO[machine]
cores = ipython.per_machine_target_cores(cores, compute_nodes)
return {
"target_cores": cores,
"target_memory": mem,
"upgrade_host_os_and_reboot": not args.no_reboot
}
common.run_ansible_pb(inventory_path, playbook_path, args, _extra_vars)
def _bootstrap_nfs(args, ansible_base):
"""Mount encrypted NFS volume on master node and expose across worker nodes.
"""
cluster = common.ecluster_config(args.econfig).load_cluster(args.cluster)
inventory_path = os.path.join(cluster.repository.storage_path,
'ansible-inventory.{}'.format(args.cluster))
nfs_clients = []
with open(inventory_path) as in_handle:
for line in in_handle:
if line.startswith("frontend"):
nfs_server = line.split()[0]
elif line.startswith("compute"):
nfs_clients.append(line.split()[0])
playbook_path = os.path.join(ansible_base, "roles", "encrypted_nfs",
"tasks", "main.yml")
def _extra_vars(args, cluster_config):
return {
"encrypted_mount":
"/encrypted",
"nfs_server":
nfs_server,
"nfs_clients":
",".join(nfs_clients),
"login_user":
tz.get_in(["nodes", "frontend", "login"], cluster_config),
"encrypted_device":
tz.get_in(["nodes", "frontend", "encrypted_volume_device"],
cluster_config, "/dev/xvdf")
}
common.run_ansible_pb(inventory_path, playbook_path, args, _extra_vars)
def _run_docker_build(args):
playbook = os.path.join(common.ANSIBLE_BASE, "bcbio_vm_docker_local.yml")
inventory_path = os.path.join(common.ANSIBLE_BASE, "standard_hosts.txt")
def _setup_args(args, cluster_config):
return {"bcbio_bucket": args.bucket, "docker_buildtype": args.buildtype,
"bcbio_dir": args.rundir}
common.run_ansible_pb(inventory_path, playbook, args, _setup_args)
def _run_docker_build(args):
playbook = os.path.join(common.ANSIBLE_BASE, "bcbio_vm_docker_local.yml")
inventory_path = os.path.join(common.ANSIBLE_BASE, "standard_hosts.txt")
def _setup_args(args, cluster_config):
return {"bcbio_bucket": args.bucket, "docker_buildtype": args.buildtype,
"bcbio_dir": args.rundir}
common.run_ansible_pb(inventory_path, playbook, args, _setup_args)
def create(args):
if args.network:
cidr_regex = r'^\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}/\d{1,2}$'
if not re.search(cidr_regex, args.network):
sys.stderr.write(
'Network {} is not in CIDR (a.b.c.d/e) format.\n'.format(
args.network))
sys.exit(1)
config = common.ecluster_config(args.econfig)
cluster_config = config.cluster_conf[args.cluster]
try:
cluster = config.load_cluster(args.cluster)
cluster_storage_path = cluster.repository.storage_path
except elasticluster.exceptions.ClusterNotFound:
# Assume the default storage path if the cluster doesn't exist,
# so we can start an ICEL stack in parallel with cluster startup.
cluster_storage_path = common.get_storage_dir(args.econfig)
if not os.path.exists(cluster_storage_path):
os.makedirs(cluster_storage_path)
if not args.setup:
icel_param = {
'oss_count': args.oss_count,
'ost_vol_size': args.size / args.oss_count / args.lun_count,
'ost_vol_count': args.lun_count,
}
template_url = _upload_icel_cf_template(icel_param, args.bucket,
cluster_config['cloud'])
_create_stack(args.stack_name, template_url, args.network,
args.cluster, cluster_config, args.recreate)
try:
sys.stdout.write('Waiting for stack to launch (this will take '
'a few minutes)')
sys.stdout.flush()
_wait_for_stack(args.stack_name, 'CREATE_COMPLETE', 15 * 60,
cluster_config['cloud'])
except Exception as e:
sys.stderr.write('{}\n'.format(str(e)))
sys.exit(1)
ssh_config_path = os.path.join(
cluster_storage_path, 'icel-{}.ssh_config'.format(args.stack_name))
_write_ssh_config(ssh_config_path, args.stack_name, cluster_config)
ansible_config_path = os.path.join(
cluster_storage_path, 'icel-{}.ansible_config'.format(args.stack_name))
_write_ansible_config(ansible_config_path, args.stack_name,
cluster_storage_path)
inventory_path = os.path.join(cluster_storage_path,
'icel-{}.inventory'.format(args.stack_name))
_write_inventory(inventory_path, args.stack_name, cluster_config['cloud'])
playbook_path = os.path.join(common.ANSIBLE_BASE, "roles", "icel", "tasks",
"main.yml")
common.run_ansible_pb(inventory_path,
playbook_path,
args,
ansible_cfg=ansible_config_path)
def create(args):
if args.network:
cidr_regex = r'^\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}/\d{1,2}$'
if not re.search(cidr_regex, args.network):
sys.stderr.write(
'Network {} is not in CIDR (a.b.c.d/e) format.\n'.format(
args.network))
sys.exit(1)
config = common.ecluster_config(args.econfig)
cluster_config = config.cluster_conf[args.cluster]
try:
cluster = config.load_cluster(args.cluster)
cluster_storage_path = cluster.repository.storage_path
except elasticluster.exceptions.ClusterNotFound:
# Assume the default storage path if the cluster doesn't exist,
# so we can start an ICEL stack in parallel with cluster startup.
cluster_storage_path = elasticluster.conf.Configurator.default_storage_dir
icel_param = {
'oss_count': args.oss_count,
'ost_vol_size': args.size / args.oss_count / args.lun_count,
'ost_vol_count': args.lun_count,
}
template_url = _upload_icel_cf_template(
icel_param, args.bucket, cluster_config['cloud'])
_create_stack(
args.stack_name, template_url, args.network,
args.cluster, cluster_config, args.recreate)
try:
sys.stdout.write('Waiting for stack to launch (this will take '
'a few minutes)')
sys.stdout.flush()
_wait_for_stack(args.stack_name, 'CREATE_COMPLETE',
15 * 60, cluster_config['cloud'])
except Exception as e:
sys.stderr.write('{}\n'.format(str(e)))
sys.exit(1)
ssh_config_path = os.path.join(
cluster_storage_path, 'icel-{}.ssh_config'.format(args.stack_name))
_write_ssh_config(ssh_config_path, args.stack_name, cluster_config)
ansible_config_path = os.path.join(
cluster_storage_path,
'icel-{}.ansible_config'.format(args.stack_name))
_write_ansible_config(
ansible_config_path, args.stack_name, cluster_storage_path)
inventory_path = os.path.join(
cluster_storage_path,
'icel-{}.inventory'.format(args.stack_name))
_write_inventory(inventory_path, args.stack_name, cluster_config['cloud'])
playbook_path = os.path.join(
common.ANSIBLE_BASE, "roles", "icel", "tasks", "main.yml")
common.run_ansible_pb(
inventory_path, playbook_path, args, ansible_cfg=ansible_config_path)
def _bootstrap_baseline(args, ansible_base):
"""Install required tools -- docker and gof3r on system.
"""
cluster = common.ecluster_config(args.econfig).load_cluster(args.cluster)
inventory_path = os.path.join(cluster.repository.storage_path,
'ansible-inventory.{}'.format(args.cluster))
docker_pb = os.path.join(ansible_base, "roles", "docker", "tasks",
"main.yml")
common.run_ansible_pb(inventory_path, docker_pb, args)
gof3r_pb = os.path.join(ansible_base, "roles", "gof3r", "tasks",
"main.yml")
common.run_ansible_pb(inventory_path, gof3r_pb, args)
def _bootstrap_baseline(args, ansible_base):
"""Install required tools -- docker and gof3r on system.
"""
cluster = common.ecluster_config(args.econfig).load_cluster(args.cluster)
inventory_path = os.path.join(
cluster.repository.storage_path,
'ansible-inventory.{}'.format(args.cluster))
docker_pb = os.path.join(
ansible_base, "roles", "docker", "tasks", "main.yml")
common.run_ansible_pb(inventory_path, docker_pb, args)
gof3r_pb = os.path.join(
ansible_base, "roles", "gof3r", "tasks", "main.yml")
common.run_ansible_pb(inventory_path, gof3r_pb, args)
def mount_or_unmount(args, mount=True):
cluster = common.ecluster_config(args.econfig).load_cluster(args.cluster)
inventory_path = os.path.join(cluster.repository.storage_path,
'ansible-inventory.{}'.format(args.cluster))
if mount:
playbook_file = "mount.yml"
else:
playbook_file = "unmount.yml"
playbook_path = os.path.join(common.ANSIBLE_BASE, "roles", "lustre_client",
"tasks", playbook_file)
def get_lustre_vars(args, cluster_config):
return {
'lustre_fs_spec':
_get_fs_spec(args.stack_name, cluster_config['cloud'])
}
common.run_ansible_pb(inventory_path, playbook_path, args, get_lustre_vars)
def mount_or_unmount(args, mount=True):
cluster = common.ecluster_config(args.econfig).load_cluster(args.cluster)
inventory_path = os.path.join(
cluster.repository.storage_path,
'ansible-inventory.{}'.format(args.cluster))
if mount:
playbook_file = "mount.yml"
else:
playbook_file = "unmount.yml"
playbook_path = os.path.join(
common.ANSIBLE_BASE, "roles", "lustre_client", "tasks", playbook_file)
def get_lustre_vars(args, cluster_config):
return {'lustre_fs_spec': _get_fs_spec(
args.stack_name, cluster_config['cloud'])}
common.run_ansible_pb(
inventory_path, playbook_path, args, get_lustre_vars)
def _bootstrap_nfs(args, ansible_base):
"""Mount encrypted NFS volume on master node and expose across worker nodes.
"""
cluster = common.ecluster_config(args.econfig).load_cluster(args.cluster)
inventory_path = os.path.join(cluster.repository.storage_path,
'ansible-inventory.{}'.format(args.cluster))
nfs_clients = []
with open(inventory_path) as in_handle:
for line in in_handle:
if line.startswith("frontend"):
nfs_server = line.split()[0]
elif line.startswith("compute"):
nfs_clients.append(line.split()[0])
playbook_path = os.path.join(ansible_base, "roles", "encrypted_nfs", "tasks", "main.yml")
def _extra_vars(args, cluster_config):
return {"encrypted_mount": "/encrypted",
"nfs_server": nfs_server,
"nfs_clients": ",".join(nfs_clients),
"login_user": tz.get_in(["nodes", "frontend", "login"], cluster_config),
"encrypted_device": tz.get_in(["nodes", "frontend", "encrypted_volume_device"],
cluster_config, "/dev/xvdf")}
common.run_ansible_pb(inventory_path, playbook_path, args, _extra_vars)