diff --git a/.DS_Store b/.DS_Store
new file mode 100644
index 0000000..f496074
Binary files /dev/null and b/.DS_Store differ
diff --git a/.gitignore b/.gitignogre
similarity index 99%
rename from .gitignore
rename to .gitignogre
index 7604ea9..c3f3bbf 100644
--- a/.gitignore
+++ b/.gitignogre
@@ -1,3 +1,4 @@
+.idea/
aws_config/
# Byte-compiled / optimized / DLL files
diff --git a/LICENSE b/LICENSE
index 9cecc1d..6ec89f7 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,674 +1,21 @@
- GNU GENERAL PUBLIC LICENSE
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-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
-
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
- {one line to give the program's name and a brief idea of what it does.}
- Copyright (C) {year} {name of author}
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
-
-Also add information on how to contact you by electronic and paper mail.
-
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
- {project} Copyright (C) {year} {fullname}
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-.
+MIT License
+
+Copyright (c) 2018 Justin Fu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
index eb33a0d..bb90c1e 100644
--- a/README.md
+++ b/README.md
@@ -25,6 +25,11 @@ python scripts/ec2_setup.py
- (Optional) Set up [Docker](https://docs.docker.com/engine/installation/). This is required on the target machine if running in a Docker-enabled mode.
+- (Optional) Set up GCP
+ - https://cloud.google.com/sdk/docs/quickstart-debian-ubuntu
+ - https://cloud.google.com/compute/docs/tutorials/python-guide
+ - https://cloud.google.com/storage/docs/reference/libraries#client-libraries-install-python
+
## Example
diff --git a/doodad/arg_parse.py b/doodad/arg_parse.py
index c194814..e0a4c24 100644
--- a/doodad/arg_parse.py
+++ b/doodad/arg_parse.py
@@ -9,7 +9,7 @@
__ARGS = None
-def __get_arg_config():
+def __get_unpickled_arg_config():
"""
global __ARGS
if __ARGS is not None:
@@ -34,7 +34,7 @@ def __get_arg_config():
def get_args(key=None, default=None):
- args = __get_arg_config()
+ args = __get_unpickled_arg_config()
if args.args_data:
if args.use_cloudpickle:
diff --git a/doodad/gcp/gcp_util.py b/doodad/gcp/gcp_util.py
new file mode 100644
index 0000000..940a049
--- /dev/null
+++ b/doodad/gcp/gcp_util.py
@@ -0,0 +1,55 @@
+import os
+
+from doodad.utils import hash_file, call_and_wait, CommandBuilder, REPO_DIR
+
+GCP_STARTUP_SCRIPT_PATH = os.path.join(REPO_DIR, "scripts/gcp/gcp_startup_script.sh")
+GCP_SHUTDOWN_SCRIPT_PATH = os.path.join(REPO_DIR, "scripts/gcp/gcp_shutdown_script.sh")
+
+def upload_file_to_gcp_storage(
+ bucket_name,
+ file_name,
+ remote_filename=None,
+ dry=False,
+ check_exists=True
+):
+ from google.cloud import storage
+ storage_client = storage.Client()
+ bucket = storage_client.get_bucket(bucket_name)
+
+ if remote_filename is None:
+ remote_filename = os.path.basename(file_name)
+ remote_path = 'doodad/mount/' + remote_filename
+ blob = bucket.blob(remote_path)
+ if check_exists and blob.exists(storage_client):
+ print("{remote_path} already exists".format(remote_path=remote_path))
+ return remote_path
+ blob.upload_from_filename(file_name)
+ return remote_path
+
+def get_machine_type(zone, instance_type):
+ return "zones/{zone}/machineTypes/{instance_type}".format(
+ zone=zone,
+ instance_type=instance_type,
+ )
+
+def get_gpu_type(project, zone, gpu_model):
+ """
+ Check the available gpu models for each zone
+ https://cloud.google.com/compute/docs/gpus/
+ """
+ assert gpu_model in [
+ 'nvidia-tesla-p4',
+ 'nvidia-tesla-k80',
+ 'nvidia-tesla-v100',
+ 'nvidia-tesla-p100'
+ ]
+
+ return (
+ "https://www.googleapis.com/compute/v1/"
+ "projects/{project}/zones/{zone}/acceleratorTypes/{gpu_model}".format(
+ project=project,
+ zone=zone,
+ gpu_model=gpu_model
+ )
+ )
+
diff --git a/doodad/launch_tools.py b/doodad/launch_tools.py
index c5e1e07..292f630 100644
--- a/doodad/launch_tools.py
+++ b/doodad/launch_tools.py
@@ -22,13 +22,12 @@ def launch_python(
mode=LOCAL,
mount_points=None,
args=None,
- env=None,
- dry=False,
fake_display=False,
target_mount_dir='target',
- verbose=False,
use_cloudpickle=False,
target_mount=None,
+ launch_locally=None,
+ **launch_command_kwargs
):
"""
@@ -37,7 +36,6 @@ def launch_python(
:param mode:
:param mount_points:
:param args:
- :param env:
:param dry:
:param fake_display:
:param target_mount_dir:
@@ -50,6 +48,8 @@ def launch_python(
args = {}
if mount_points is None:
mount_points = []
+ if launch_locally is None:
+ launch_locally = isinstance(mode, Local)
if target_mount is None:
# mount
@@ -57,12 +57,12 @@ def launch_python(
if not target_mount_dir:
target_mount_dir = target_dir
target_mount_dir = os.path.join(target_mount_dir, os.path.basename(target_dir))
- if isinstance(mode, Local):
+ if launch_locally:
target_mount = MountLocal(local_dir=target_dir)
else:
target_mount = MountLocal(local_dir=target_dir, mount_point=target_mount_dir)
mount_points = mount_points + [target_mount]
- target_full_path = os.path.join(target_mount.docker_mount_dir(), os.path.basename(target))
+ target_full_path = os.path.join(target_mount.mount_dir(), os.path.basename(target))
command = make_python_command(
target_full_path,
@@ -71,7 +71,8 @@ def launch_python(
fake_display=fake_display,
use_cloudpickle=use_cloudpickle,
)
- mode.launch_command(command, mount_points=mount_points, dry=dry, verbose=verbose)
+ mode.launch_command(command, mount_points=mount_points,
+ **launch_command_kwargs)
return target_mount
HEADLESS = 'xvfb-run -a -s "-ac -screen 0 1400x900x24 +extension RANDR"'
@@ -90,8 +91,8 @@ def make_python_command(
args_encoded, cp_version = encode_args(args, cloudpickle=use_cloudpickle)
if args:
- cmd = '%s=%s %s=%s %s=%s %s' % (ARGS_DATA, args_encoded,
- USE_CLOUDPICKLE, str(int(use_cloudpickle)),
+ cmd = '%s=%s %s=%s %s=%s %s' % (ARGS_DATA, args_encoded,
+ USE_CLOUDPICKLE, str(int(use_cloudpickle)),
CLOUDPICKLE_VERSION, cp_version,
cmd)
diff --git a/doodad/mode.py b/doodad/mode.py
index e729da5..a5a5571 100644
--- a/doodad/mode.py
+++ b/doodad/mode.py
@@ -1,31 +1,33 @@
import os
+import stat
import subprocess
import tempfile
import uuid
import time
import base64
-
-from doodad.ec2.autoconfig import AUTOCONFIG
+import json
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
-from .mount import *
-from .utils import hash_file, call_and_wait, CommandBuilder
+from .mount import MountLocal, MountS3, MountGCP
+from .utils import hash_file, call_and_wait, CommandBuilder, REPO_DIR
from .ec2.aws_util import s3_upload, s3_exists
+from .gcp.gcp_util import GCP_STARTUP_SCRIPT_PATH, GCP_SHUTDOWN_SCRIPT_PATH, \
+ upload_file_to_gcp_storage, get_machine_type, get_gpu_type
class LaunchMode(object):
def launch_command(self, cmd, mount_points=None, dry=False, verbose=False):
raise NotImplementedError()
-
class Local(LaunchMode):
- def __init__(self):
+ def __init__(self, skip_wait=False):
super(Local, self).__init__()
self.env = {}
+ self.skip_wait = skip_wait
def launch_command(self, cmd, mount_points=None, dry=False, verbose=False):
if dry:
@@ -63,7 +65,8 @@ def launch_command(self, cmd, mount_points=None, dry=False, verbose=False):
commands.extend(cleanup_commands)
# Call everything
- commands.call_and_wait()
+ commands.call_and_wait(verbose=verbose, dry=dry,
+ skip_wait=self.skip_wait)
LOCAL = Local()
@@ -76,7 +79,7 @@ def __init__(self, image='ubuntu:16.04', gpu=False):
self.gpu = gpu
def get_docker_cmd(self, main_cmd, extra_args='', use_tty=True, verbose=True, pythonpath=None, pre_cmd=None, post_cmd=None,
- checkpoint=False, no_root=False):
+ checkpoint=False, no_root=False, use_docker_generated_name=False):
cmd_list= CommandBuilder()
if pre_cmd:
cmd_list.extend(pre_cmd)
@@ -101,7 +104,7 @@ def get_docker_cmd(self, main_cmd, extra_args='', use_tty=True, verbose=True, py
cmd_list.extend(post_cmd)
docker_name = self.docker_name
- if docker_name:
+ if docker_name and not use_docker_generated_name:
extra_args += ' --name %s '%docker_name
if checkpoint:
@@ -121,9 +124,10 @@ def get_docker_cmd(self, main_cmd, extra_args='', use_tty=True, verbose=True, py
class LocalDocker(DockerMode):
- def __init__(self, checkpoints=None, **kwargs):
+ def __init__(self, checkpoints=None, skip_wait=False, **kwargs):
super(LocalDocker, self).__init__(**kwargs)
self.checkpoints = checkpoints
+ self.skip_wait = skip_wait
def launch_command(self, cmd, mount_points=None, dry=False, verbose=False):
mnt_args = ''
@@ -131,7 +135,7 @@ def launch_command(self, cmd, mount_points=None, dry=False, verbose=False):
for mount in mount_points:
if isinstance(mount, MountLocal):
#mount_pnt = os.path.expanduser(mount.mount_point)
- mount_pnt = mount.docker_mount_dir()
+ mount_pnt = mount.mount_dir()
mnt_args += ' -v %s:%s' % (mount.local_dir, mount_pnt)
call_and_wait('mkdir -p %s' % mount.local_dir)
if mount.pythonpath:
@@ -141,9 +145,8 @@ def launch_command(self, cmd, mount_points=None, dry=False, verbose=False):
full_cmd = self.get_docker_cmd(cmd, extra_args=mnt_args, pythonpath=py_path,
checkpoint=self.checkpoints)
- if verbose:
- print(full_cmd)
- call_and_wait(full_cmd, dry=dry)
+ call_and_wait(full_cmd, verbose=verbose, dry=dry,
+ skip_wait=self.skip_wait)
class SSHDocker(DockerMode):
@@ -181,7 +184,7 @@ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
remote_cmds.append('mkdir -p %s' % remote_mnt_dir)
unzip_cmd = 'tar -xf %s -C %s' % (remote_tar, remote_mnt_dir)
remote_cmds.append(unzip_cmd)
- mount_point = mount.docker_mount_dir()
+ mount_point = mount.mount_dir()
mnt_args += ' -v %s:%s' % (os.path.join(remote_mnt_dir, os.path.basename(mount.mount_point)) ,mount_point)
else:
#remote_cmds.append('mkdir -p %s' % mount.mount_point)
@@ -235,8 +238,10 @@ def __init__(self,
security_groups=None,
aws_s3_path=None,
extra_ec2_instance_kwargs=None,
+ num_exps=1,
+ swap_size=4096,
**kwargs
- ):
+ ):
super(EC2SpotDocker, self).__init__(**kwargs)
if security_group_ids is None:
security_group_ids = []
@@ -257,6 +262,8 @@ def __init__(self,
self.security_groups = security_groups
self.iam_instance_profile_name = iam_instance_profile_name
self.extra_ec2_instance_kwargs = extra_ec2_instance_kwargs
+ self.num_exps = num_exps
+ self.swap_size = swap_size
self.checkpoint = None
self.s3_mount_path = 's3://%s/doodad/mount' % self.s3_bucket
@@ -304,9 +311,11 @@ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
exp_name = self.s3_log_name
exp_prefix = self.s3_log_prefix
s3_base_dir = os.path.join(self.aws_s3_path, exp_prefix.replace("_", "-"), exp_name)
+ stdout_log_s3_path = os.path.join(s3_base_dir, 'stdout_$EC2_INSTANCE_ID.log')
sio = StringIO()
sio.write("#!/bin/bash\n")
+ sio.write("set -v")
sio.write("truncate -s 0 /home/ubuntu/user_data.log\n")
sio.write("{\n")
sio.write('die() { status=$1; shift; echo "FATAL: $*"; exit $status; }\n')
@@ -317,6 +326,20 @@ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
sio.write("""
aws ec2 create-tags --resources $EC2_INSTANCE_ID --tags Key=exp_prefix,Value={exp_prefix} --region {aws_region}
""".format(exp_prefix=exp_prefix, aws_region=self.region))
+
+ # Add swap file
+ if self.gpu:
+ swap_location = '/mnt/swapfile'
+ else:
+ swap_location = '/var/swap.1'
+ sio.write(
+ 'sudo dd if=/dev/zero of={swap_location} bs=1M count={swap_size}\n'
+ .format(swap_location=swap_location, swap_size=self.swap_size))
+ sio.write('sudo mkswap {swap_location}\n'.format(swap_location=swap_location))
+ sio.write('sudo chmod 600 {swap_location}\n'.format(swap_location=swap_location))
+ sio.write('sudo swapon {swap_location}\n'.format(swap_location=swap_location))
+
+
sio.write("service docker start\n")
sio.write("docker --config /home/ubuntu/.docker pull {docker_image}\n".format(docker_image=self.docker_image))
sio.write("export AWS_DEFAULT_REGION={aws_region}\n".format(aws_region=self.s3_bucket_region))
@@ -367,6 +390,8 @@ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
# spot instance
ec2_local_dir = mount.mount_point
s3_path = os.path.join(s3_base_dir, mount.s3_path)
+ if self.num_exps == 1:
+ stdout_log_s3_path = os.path.join(s3_path, 'stdout_$EC2_INSTANCE_ID.log')
if not mount.output:
raise NotImplementedError()
local_output_dir_and_s3_path.append(
@@ -403,6 +428,7 @@ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
then
logger "Running shutdown hook."
aws s3 cp --recursive {log_dir} {s3_path}
+ aws s3 cp /home/ubuntu/user_data.log {stdout_log_s3_path}
break
else
# Spot instance not yet marked for termination.
@@ -415,13 +441,20 @@ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
""".format(
log_dir=ec2_local_dir,
s3_path=s3_path,
+ stdout_log_s3_path=stdout_log_s3_path,
))
else:
raise NotImplementedError()
-
- sio.write("aws ec2 create-tags --resources $EC2_INSTANCE_ID --tags Key=Name,Value={exp_name} --region {aws_region}\n".format(
- exp_name=exp_name, aws_region=self.region))
+ sio.write("""
+ while /bin/true; do
+ aws s3 cp /home/ubuntu/user_data.log {stdout_log_s3_path}
+ sleep {periodic_sync_interval}
+ done & echo sync initiated
+ """.format(
+ stdout_log_s3_path=stdout_log_s3_path,
+ periodic_sync_interval=max_sync_interval
+ ))
if self.gpu:
#sio.write('echo "LSMOD NVIDIA:"\n')
@@ -448,7 +481,10 @@ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
if self.checkpoint and self.checkpoint.restore:
raise NotImplementedError()
else:
- docker_cmd = self.get_docker_cmd(main_cmd, use_tty=False, extra_args=mnt_args, pythonpath=py_path)
+ docker_cmd = self.get_docker_cmd(main_cmd, use_tty=False, extra_args=mnt_args, pythonpath=py_path, use_docker_generated_name=True)
+ assert self.num_exps > 0
+ for _ in range(self.num_exps - 1):
+ sio.write(docker_cmd+' &\n')
sio.write(docker_cmd+'\n')
# Sync all output mounts to s3 after running the user script
@@ -460,7 +496,10 @@ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
local_dir=local_output_dir,
s3_dir=s3_dir_path
))
- sio.write("aws s3 cp /home/ubuntu/user_data.log {s3_dir_path}/stdout.log\n".format(s3_dir_path=s3_base_dir))
+
+ sio.write("aws s3 cp /home/ubuntu/user_data.log {}\n".format(
+ stdout_log_s3_path,
+ ))
# Wait for last sync
if max_sync_interval > 0:
@@ -588,8 +627,335 @@ def __init__(self,
)
+class GCPDocker(DockerMode):
+ def __init__(
+ self,
+ zone="us-east4-a",
+ gcp_bucket_name=None,
+ instance_type='n1-standard-4',
+ image_name=None,
+ image_project=None,
+ disk_size:"Gb"=64,
+ terminate=True,
+ preemptible=True,
+ gcp_log_prefix='experiment',
+ gcp_log_name=None,
+ gcp_log_path=None,
+ gpu_kwargs=None,
+ **kwargs
+ ):
+ super(GCPDocker, self).__init__(**kwargs)
+ assert 'CLOUDSDK_CORE_PROJECT' in os.environ.keys()
+ self.project = os.environ['CLOUDSDK_CORE_PROJECT']
+ self.zone = zone
+ self.gcp_bucket_name = gcp_bucket_name
+ self.instance_type = instance_type
+ self.terminate = terminate
+ self.disk_size = disk_size
+ self.image_project = image_project
+ self.image_name = image_name
+ self.preemptible = preemptible
+
+ self.gcp_log_prefix = gcp_log_prefix
+ self.gcp_log_name = gcp_log_name
+ self.gcp_log_path = gcp_log_path or 'doodad/logs'
+ if self.gpu:
+ self.num_gpu = gpu_kwargs['num_gpu']
+ self.gpu_model = gpu_kwargs['gpu_model']
+ self.gpu_type = get_gpu_type(self.project, self.zone, self.gpu_model)
+
+ import googleapiclient.discovery
+ self.compute = googleapiclient.discovery.build('compute', 'v1')
+
+ def launch_command(self, main_cmd, mount_points=None, dry=False, verbose=False):
+ if self.gcp_log_name is None:
+ exp_name = "{}-{}".format(self.gcp_log_prefix, EC2SpotDocker.make_timekey(self))
+ else:
+ exp_name = self.gcp_log_name
+ exp_prefix = self.gcp_log_prefix
+ gcp_base_dir = os.path.join(self.gcp_log_path, exp_prefix.replace("_", "-"), exp_name)
+
+ mnt_args = ''
+ py_path = []
+ gcp_mount_info = []
+ max_sync_interval = 0
+ local_mounts = []
+ for mount in mount_points:
+ print('Handling mount: ', mount)
+ if isinstance(mount, MountLocal): # TODO: these should be mount_s3 objects
+ if mount.read_only:
+ if mount.path_on_remote is None:
+ with mount.gzip() as gzip_file:
+ gzip_path = os.path.realpath(gzip_file)
+ file_hash = hash_file(gzip_path)
+ gcp_path = upload_file_to_gcp_storage(
+ bucket_name=self.gcp_bucket_name,
+ file_name=gzip_path,
+ remote_filename=file_hash+'.tar'
+ )
+ mount.path_on_remote = gcp_path
+ mount.local_file_hash = file_hash
+ else:
+ file_hash = mount.local_file_hash
+ gcp_path = mount.path_on_remote
+ remote_unpack_name = '/tmp/'+file_hash
+ mount_point = os.path.join('/mounts', mount.mount_point.replace('~/',''))
+ mnt_args += ' -v %s:%s' % (os.path.join(remote_unpack_name, os.path.basename(mount.local_dir)), mount_point)
+ if mount.pythonpath:
+ py_path.append(mount_point)
+ local_mounts.append(file_hash)
+ else:
+ raise ValueError()
+ elif isinstance(mount, MountGCP):
+ gcp_local_dir = mount.mount_point
+ gcp_path = os.path.join(gcp_base_dir, mount.gcp_path)
+ if not mount.output:
+ raise NotImplementedError()
+ gcp_mount_info.append(
+ (gcp_local_dir, gcp_path, mount.include_string, mount.sync_interval)
+ )
+ mnt_args += ' -v %s:%s' % (gcp_local_dir, mount.mount_point)
+ else:
+ raise NotImplementedError()
+
+ docker_cmd = self.get_docker_cmd(main_cmd, use_tty=False, extra_args=mnt_args, pythonpath=py_path)
+
+ metadata = {
+ 'bucket_name': self.gcp_bucket_name,
+ 'docker_cmd': docker_cmd,
+ 'docker_image': self.docker_image,
+ 'local_mounts': json.dumps(local_mounts),
+ 'gcp_mounts': json.dumps(gcp_mount_info),
+ 'use_gpu': json.dumps(self.gpu),
+ 'terminate': json.dumps(self.terminate),
+ 'startup-script': open(GCP_STARTUP_SCRIPT_PATH, "r").read(),
+ 'shutdown-script': open(GCP_SHUTDOWN_SCRIPT_PATH, "r").read(),
+ }
+ # instance name must match regex '(?:[a-z](?:[-a-z0-9]{0,61}[a-z0-9])?)'">
+ unique_name= "doodad" + str(uuid.uuid4()).replace("-", "")
+ self.create_instance(metadata, unique_name, exp_name, exp_prefix)
+ if verbose:
+ print(unique_name)
+ print(metadata)
+
+ def create_instance(self, metadata, name, exp_name="", exp_prefix=""):
+ image_response = self.compute.images().get(
+ project=self.image_project,
+ image=self.image_name,
+ ).execute()
+ source_disk_image = image_response['selfLink']
+ config = {
+ 'name': name,
+ 'machineType': get_machine_type(self.zone, self.instance_type),
+ 'disks': [{
+ 'boot': True,
+ 'autoDelete': True,
+ 'initializeParams': {
+ 'sourceImage': source_disk_image,
+ 'diskSizeGb': self.disk_size,
+ }
+ }],
+ 'networkInterfaces': [{
+ 'network': 'global/networks/default',
+ 'accessConfigs': [
+ {'type': 'ONE_TO_ONE_NAT', 'name': 'External NAT'}
+ ]
+ }],
+ 'serviceAccounts': [{
+ 'email': 'default',
+ 'scopes': ['https://www.googleapis.com/auth/cloud-platform']
+ }],
+ 'metadata': {
+ 'items': [
+ {'key': key, 'value': value}
+ for key, value in metadata.items()
+ ]
+ },
+ 'scheduling': {
+ "onHostMaintenance": "terminate",
+ "automaticRestart": False,
+ "preemptible": self.preemptible,
+ },
+ "labels": {
+ "exp_name": exp_name,
+ "exp_prefix": exp_prefix,
+ }
+ }
+ if self.gpu:
+ config["guestAccelerators"] = [{
+ "acceleratorType": self.gpu_type,
+ "acceleratorCount": self.num_gpu,
+ }]
+ return self.compute.instances().insert(
+ project=self.project,
+ zone=self.zone,
+ body=config
+ ).execute()
+
class CodalabDocker(DockerMode):
def __init__(self):
super(CodalabDocker, self).__init__()
raise NotImplementedError()
+
+class SingularityMode(LaunchMode):
+ def __init__(self, image, gpu=False, pre_cmd=None,
+ post_cmd=None, skip_wait=False):
+ super(SingularityMode, self).__init__()
+ self.singularity_image = image
+ self.gpu = gpu
+ self.pre_cmd = pre_cmd
+ self.post_cmd = post_cmd
+ self.skip_wait = skip_wait
+
+ def get_singularity_cmd(
+ self,
+ main_cmd,
+ extra_args='',
+ verbose=True,
+ pythonpath=None,
+ ):
+ cmd_list= CommandBuilder()
+ if self.pre_cmd:
+ cmd_list.extend(self.pre_cmd)
+
+ if verbose:
+ if self.gpu:
+ cmd_list.append('echo \"Running in singularity (gpu)\"')
+ else:
+ cmd_list.append('echo \"Running in singularity\"')
+ if pythonpath:
+ cmd_list.append('export PYTHONPATH=$PYTHONPATH:%s' % (':'.join(pythonpath)))
+
+ cmd_list.append(main_cmd)
+ if self.post_cmd:
+ cmd_list.extend(self.post_cmd)
+
+ if self.gpu:
+ extra_args += ' --nv '
+ singularity_prefix = 'singularity exec %s %s /bin/bash -c ' % (
+ extra_args,
+ self.singularity_image,
+ )
+ main_cmd = cmd_list.to_string()
+ full_cmd = singularity_prefix + ("\'%s\'" % main_cmd)
+ return full_cmd
+
+
+class LocalSingularity(SingularityMode):
+ def launch_command(self, cmd, mount_points=None, dry=False, verbose=False):
+ py_path = []
+ for mount in mount_points:
+ if isinstance(mount, MountLocal):
+ if mount.pythonpath:
+ py_path.append(mount.local_dir)
+ else:
+ raise NotImplementedError(type(mount))
+
+ full_cmd = self.get_singularity_cmd(
+ cmd,
+ pythonpath=py_path,
+ verbose=verbose,
+ )
+ call_and_wait(full_cmd, verbose=verbose, dry=dry,
+ skip_wait=self.skip_wait)
+
+
+class SlurmSingularity(LocalSingularity):
+ # TODO: set up an auto-config
+ def __init__(
+ self, image, account_name, partition, time_in_mins,
+ qos=None,
+ nodes=1,
+ n_tasks=1,
+ n_gpus=1,
+ **kwargs
+ ):
+ super(SlurmSingularity, self).__init__(image, **kwargs)
+ self.account_name = account_name
+ self.partition = partition
+ self.time_in_mins = time_in_mins
+ self.nodes = nodes
+ self.n_tasks = n_tasks
+ self.n_gpus = n_gpus
+
+ def create_slurm_command(self, cmd, mount_points=None, verbose=False):
+ py_path = []
+ for mount in mount_points:
+ if isinstance(mount, MountLocal):
+ if mount.pythonpath:
+ py_path.append(mount.local_dir)
+ else:
+ raise NotImplementedError(type(mount))
+
+ singularity_cmd = self.get_singularity_cmd(
+ cmd,
+ pythonpath=py_path,
+ verbose=verbose,
+ )
+ if self.gpu:
+ full_cmd = (
+ "sbatch -A {account_name} -p {partition} -t {time}"
+ " -N {nodes} -n {n_tasks} --cpus-per-task={cpus_per_task}"
+ " --gres=gpu:{n_gpus} {cmd}".format(
+ account_name=self.account_name,
+ partition=self.partition,
+ time=self.time_in_mins,
+ nodes=self.nodes,
+ n_tasks=self.n_tasks,
+ cpus_per_task=2*self.n_gpus,
+ n_gpus=self.n_gpus,
+ cmd=singularity_cmd,
+ )
+ )
+ else:
+ full_cmd = "sbatch -A {account_name} -p {partition} -t {time} {cmd}".format(
+ account_name=self.account_name,
+ partition=self.partition,
+ time=self.time_in_mins,
+ cmd=singularity_cmd,
+ )
+ if verbose:
+ print(full_cmd)
+
+ def launch_command(self, cmd, mount_points=None, dry=False, verbose=False):
+ full_cmd = self.create_slurm_command(
+ cmd, mount_points=mount_points, verbose=verbose,
+ )
+ call_and_wait(full_cmd, dry=dry, skip_wait=self.skip_wait)
+
+
+class ScriptSlurmSingularity(SlurmSingularity):
+ """
+ Create or add to a script to run a bunch of slurm jobs.
+ """
+ TMP_FILE = '/tmp/script_to_scp_over.sh'
+
+ def __init__(self, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.is_first_time = False
+
+ def set_first_time(self, is_first_time):
+ self.is_first_time = is_first_time
+
+ def launch_command(
+ self,
+ cmd,
+ dry=False,
+ mount_points=None,
+ verbose=False,
+ ):
+ full_cmd = self.create_slurm_command(
+ cmd, mount_points=mount_points, verbose=verbose,
+ )
+ if self.is_first_time:
+ with open(self.TMP_FILE, "w") as myfile:
+ myfile.write(full_cmd + '\n')
+ # make file executable
+ st = os.stat(self.TMP_FILE)
+ os.chmod(self.TMP_FILE, st.st_mode | stat.S_IEXEC)
+ print("Script generated! scp this script over:", self.TMP_FILE)
+ else:
+ with open(self.TMP_FILE, "a") as myfile:
+ myfile.write(full_cmd + '\n')
+ print("Script updated. scp this script over:", self.TMP_FILE)
diff --git a/doodad/mount.py b/doodad/mount.py
index c1eab15..1b72591 100644
--- a/doodad/mount.py
+++ b/doodad/mount.py
@@ -77,7 +77,7 @@ def filter_func(tar_info):
def __str__(self):
return 'MountLocal@%s'%self.local_dir
- def docker_mount_dir(self):
+ def mount_dir(self):
return os.path.join('/mounts', self.mount_point.replace('~/',''))
@@ -89,6 +89,24 @@ def __init__(self, git_url, git_credentials=None, **kwargs):
raise NotImplementedError()
+class MountGCP(Mount):
+ def __init__(self, gcp_path, gcp_bucket_name, sync_interval=15, output=False,
+ include_types=('*.txt', '*.csv', '*.json', '*.gz', '*.tar', '*.log', '*.pkl'), **kwargs):
+ super(MountGCP, self).__init__(**kwargs)
+ self.gcp_bucket_name = gcp_bucket_name
+ self.gcp_path = gcp_path
+ self.output = output
+ self.sync_interval = sync_interval
+ self.sync_on_terminate = True
+ self.include_types = include_types
+
+ def __str__(self):
+ return 'MountGCP@gcp://%s/%s'% (self.gcp_bucket_name, self.gcp_path)
+
+ @property
+ def include_string(self):
+ return ' '.join(['--include \'%s\''%type_ for type_ in self.include_types])
+
class MountS3(Mount):
def __init__(self, s3_path, s3_bucket=None, sync_interval=15, output=False,
include_types=('*.txt', '*.csv', '*.json', '*.gz', '*.tar', '*.log', '*.pkl'), **kwargs):
diff --git a/doodad/utils.py b/doodad/utils.py
index 5bafeb3..1989239 100644
--- a/doodad/utils.py
+++ b/doodad/utils.py
@@ -8,7 +8,7 @@
REPO_DIR = os.path.dirname(THIS_FILE_DIR)
EXAMPLES_DIR = os.path.join(REPO_DIR, 'examples')
-HASH_BUF_SIZE = 65536
+HASH_BUF_SIZE = 65536
def hash_file(filename):
hasher = hashlib.md5()
@@ -21,11 +21,13 @@ def hash_file(filename):
return hasher.hexdigest()
-def call_and_wait(cmd, verbose=False, dry=False):
+def call_and_wait(cmd, verbose=False, dry=False, skip_wait=False):
if dry or verbose:
print(cmd)
if not dry:
p = subprocess.Popen(cmd, shell=True)
+ if skip_wait:
+ return
try:
p.wait()
except KeyboardInterrupt:
@@ -64,8 +66,13 @@ def __iter__(self):
for cmd in self.cmds:
yield cmd
- def call_and_wait(self, verbose=False, dry=False):
- return call_and_wait(self.to_string())
+ def call_and_wait(self, verbose=False, dry=False, skip_wait=False):
+ return call_and_wait(
+ self.to_string(),
+ verbose=verbose,
+ dry=dry,
+ skip_wait=skip_wait,
+ )
@contextlib.contextmanager
def as_script(self, suffix='.sh'):
diff --git a/scripts/gcp/gcp_shutdown_script.sh b/scripts/gcp/gcp_shutdown_script.sh
new file mode 100644
index 0000000..99cf3ff
--- /dev/null
+++ b/scripts/gcp/gcp_shutdown_script.sh
@@ -0,0 +1,20 @@
+#!/bin/bash
+query_metadata() {
+ attribute_name=$1
+ curl http://metadata/computeMetadata/v1/instance/attributes/$attribute_name -H "Metadata-Flavor: Google"
+}
+
+bucket_name=$(query_metadata bucket_name)
+gcp_mounts=$(query_metadata gcp_mounts)
+instance_name=$(curl http://metadata/computeMetadata/v1/instance/name -H "Metadata-Flavor: Google")
+
+num_gcp_mounts=$(jq length <<< $gcp_mounts)
+for ((i=0;i<$num_gcp_mounts;i++)); do
+ gcp_mount_info=$(jq .[$i] <<< $gcp_mounts)
+ # assume gcp_mount_info is a (local_path, bucket_path, include_string, periodic_sync_interval) tuple
+ local_path=$(jq .[0] <<< $gcp_mount_info | tr -d '"')
+ gcp_bucket_path=$(jq .[1] <<< $gcp_mount_info | tr -d '"')
+ gsutil -m rsync -r $local_path gs://$bucket_name/$gcp_bucket_path
+done
+
+gsutil cp /home/ubuntu/user_data.log gs://$bucket_name/$gcp_bucket_path/${instance_name}_stdout.log
diff --git a/scripts/gcp/gcp_startup_script.sh b/scripts/gcp/gcp_startup_script.sh
new file mode 100644
index 0000000..9338d87
--- /dev/null
+++ b/scripts/gcp/gcp_startup_script.sh
@@ -0,0 +1,95 @@
+#!/bin/bash
+install_docker() {
+ sudo apt-get install -y --no-install-recommends \
+ apt-transport-https \
+ curl \
+ software-properties-common
+ curl -fsSL 'https://sks-keyservers.net/pks/lookup?op=get&search=0xee6d536cf7dc86e2d7d56f59a178ac6c6238f52e' | sudo apt-key add -
+ sudo add-apt-repository \
+ "deb https://packages.docker.com/1.12/apt/repo/ \
+ ubuntu-$(lsb_release -cs) \
+ main"
+ sudo apt-get update
+ sudo apt-get -y install docker-engine
+ sudo usermod -a -G docker ubuntu
+}
+
+query_metadata() {
+ attribute_name=$1
+ curl http://metadata/computeMetadata/v1/instance/attributes/$attribute_name -H "Metadata-Flavor: Google"
+}
+
+{
+ bucket_name=$(query_metadata bucket_name)
+ docker_cmd=$(query_metadata docker_cmd)
+ docker_image=$(query_metadata docker_image)
+ local_mounts=$(query_metadata local_mounts)
+ gcp_mounts=$(query_metadata gcp_mounts)
+ use_gpu=$(query_metadata use_gpu)
+ terminate=$(query_metadata terminate)
+ instance_name=$(curl http://metadata/computeMetadata/v1/instance/name -H "Metadata-Flavor: Google")
+ echo "bucket_name:" $bucket_name
+ echo "docker_cmd:" $docker_cmd
+ echo "docker_image:" $docker_image
+ echo "local_mounts:" $local_mounts
+ echo "gcp_mounts:" $gcp_mounts
+ echo "use_gpu:" $use_gpu
+ echo "terminate:" $terminate
+ echo "instance_name:" $instance_name
+
+ sudo apt-get update
+ #install_docker
+ while sudo fuser /var/{lib/{dpkg,apt/lists},cache/apt/archives}/lock >/dev/null 2>&1; do
+ sleep 1
+ done
+ sudo apt-get install -y jq git unzip
+ die() { status=$1; shift; echo "FATAL: $*"; exit $status; }
+ service docker start
+ docker --config /home/ubuntu/.docker pull $docker_image
+
+ num_local_mounts=$(jq length <<< $local_mounts)
+ for ((i=0;i<$num_local_mounts;i++)); do
+ local_mount=$(jq .[$i] <<< $local_mounts | tr -d '"')
+ echo "Mounting " $local_mount
+ gsutil cp gs://$bucket_name/doodad/mount/$local_mount.tar /tmp/$local_mount.tar
+ mkdir -p /tmp/$local_mount
+ tar -xvf /tmp/$local_mount.tar -C /tmp/$local_mount
+ done
+
+ num_gcp_mounts=$(jq length <<< $gcp_mounts)
+ for ((i=0;i<$num_gcp_mounts;i++)); do
+ gcp_mount_info=$(jq .[$i] <<< $gcp_mounts)
+ # assume _mount_info is a (local_path, bucket_path, include_string, periodic_sync_interval) tuple
+ local_path=$(jq .[0] <<< $gcp_mount_info | tr -d '"')
+ gcp_bucket_path=$(jq .[1] <<< $gcp_mount_info | tr -d '"')
+ include_string=$(jq .[2] <<< $gcp_mount_info | tr -d '"')
+ periodic_sync_interval=$(jq .[3] <<< $gcp_mount_info | tr -d '"')
+ while /bin/true; do
+ gsutil -m rsync -r $local_path gs://$bucket_name/$gcp_bucket_path
+ sleep $periodic_sync_interval
+ done & echo sync from $local_path to gs://$bucket_name/$gcp_bucket_path initiated
+ done
+ while /bin/true; do
+ gsutil cp /home/ubuntu/user_data.log gs://$bucket_name/$gcp_bucket_path/${instance_name}_stdout.log
+ sleep 300
+ done &
+
+ if [ "$use_gpu" = "true" ]; then
+ for i in {1..800}; do su -c "nvidia-modprobe -u -c=0" ubuntu && break || sleep 3; done
+ systemctl start nvidia-docker
+ echo 'Testing nvidia-smi'
+ nvidia-smi
+ echo 'Testing nvidia-smi inside docker'
+ nvidia-docker run --rm $docker_image nvidia-smi
+ fi
+
+ echo $docker_cmd >> run_docker_command.sh
+ bash run_docker_command.sh
+
+ if [ "$terminate" = "true" ]; then
+ echo "Finished experiment. Terminating"
+ zone=$(curl http://metadata/computeMetadata/v1/instance/zone -H "Metadata-Flavor: Google")
+ zone="${zone##*/}"
+ gcloud compute instances delete $instance_name --zone $zone --quiet
+ fi
+} >> /home/ubuntu/user_data.log 2>&1
diff --git a/scripts/setup_ec2.py b/scripts/setup_ec2.py
index 6b4ece3..45ed52e 100644
--- a/scripts/setup_ec2.py
+++ b/scripts/setup_ec2.py
@@ -24,7 +24,7 @@
raise ValueError('Please set the $AWS_ACCESS_KEY environment variable')
ACCESS_SECRET = os.environ.get("AWS_ACCESS_SECRET", None)
if ACCESS_SECRET is None:
- raise ValueError('Please set the $AWS_ACCESS_KEY environment variable')
+ raise ValueError('Please set the $AWS_ACCESS_SECRET environment variable')
S3_BUCKET_NAME = os.environ.get("DOODAD_S3_BUCKET", None)
if S3_BUCKET_NAME is None:
raise ValueError('Please set the $DOODAD_S3_BUCKET environment variable')
diff --git a/setup.py b/setup.py
index e69de29..6914311 100644
--- a/setup.py
+++ b/setup.py
@@ -0,0 +1,7 @@
+from setuptools import setup
+
+setup(name='doodad',
+ version='0.0.1',
+ description="Doodad: easy setup of AWS EC2/S3",
+ install_requires=[],
+)
\ No newline at end of file