raid

command module
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Published: Apr 4, 2019 License: NCSA Imports: 2 Imported by: 0

README

raid Build Status

Features

  • Submissions of projects to a remote server
  • Work on CUDA code without the need of hardware or software installed on local System
  • Use CUDA hardware architectures which are not available on commodity systems

Terminology

We will use the following terms throughout this document. For the publically available services, this document assume reader is familiar with them, their limitations, and semantics:

  • Client/rai: the client which users use to interact with the RAI system. This includes the RAI client as well as the docker builder website. The client is usually installed on user’s machine and is used primarily to submit tasks to the system. At any point in time, there can be more thanone client running and submitting jobs to the system. The client should work on any OS and does not require any special hardware to be installed on the system.
  • Job Queue: User’s jobs are submitted onto a queue (using sharding, for example). The queue currently uses Amazon’s SQS queue system. There can be more than one queue, but we currently use only one.
  • Pub/Sub Queue: Output for jobs are published onto a pub/sub server. RAI currently uses Redis for pub/sub. Multiple Redis servers can be used, but we currently use only one.
  • Server/raid: All work/execution is run on the server. The server listens to the queue and executes jobs if capable. Depending on the load, more than one server can be run at any point in time. The number of jobs that a server can handle is configurable. Linux is required to use the server with GPU capabilities.
  • Docker: User code execution occurs only within a docker container. Docker is also used to build docker images as well as publishing images to the docker registry. * CUDA Volume: A docker plugin that mounts nvidia driver and cuda libraries within the launched docker container.
  • STS: Amazon’s STS allows one to place a time constraints on the amazon access tokens (also known as roles) being issued. The current constraint is 15 minutes.
  • Store/File Server: The location where user’s data files are stored. The rai system currently uses Amazon’s S3 for storage.
  • Auth: Only users with credentials can submit tasks to rai. Authentication keys can be generated using the rai-keygen tool. In the backend, we use Auth0 as the database.
  • App secret: all keys, such as credentials to login to the pub/sub server, are encrypted using AES32 based encryption. For prebuilt binaries, the app secret is embedded in the executable. A user can specify the secret from the command line as well.

Components

components

Execution Flow

flow

  1. A client submits a task to RAI
    1. Credentials are validated
    2. The directory is archived and uploaded to the file server
    3. The task is submitted to the queue
    4. The user subscribes to the pub/sub server and prints all messages being received
  2. A server accepts a task from the queue
    1. Check if the task is valid
    2. Either build or downloads the docker images required to run the task
    3. Download the user directory
    4. Start a publish channel to the pub/sub server
    5. Start a docker container and run the user commands (if gpu is requested, then the cuda volume is mounted)
    6. All stdout/stderr messages from the docker container are forwarded to the publish channel
    7. Wait for either tasks to complete or a timeout h. The output directory is uploaded to the file server and a link is published
    8. Close the publish channel / docker container

Installation and Service Prerequisites

STS Permissions

Set up STS permissions so that users can upload to an S3 bucket and publish to an SQS queue. This can be done via the IAM AWS console. The STS currently being used only allows one to attach to a rai role which has very limited permissions:

Simple Queue Service

Create an SQS queue using the AWS console.

  • Navigate to the SQS service page
  • "Create New Queue"
  • Enter the queue name
  • Choose standard for the type.
  • Optionally, configure various queue parameters under "configure queue"

Create a IAM Policy that allows reading and writing to the new queue. Use the Policy Generator.

  • Select Amazon SQS for AWS Service.
  • Choose the following actions:
    • GetQueueUrl
    • ReceiveMessage
    • DeleteMessage
    • DeleteMessageBatch
    • SendMessage
    • SendMessageBatch
  • Create an ARN. The account ID may be found on the AWS account page. For example arn:aws:sqs:*:account-id:rai2 for the rai2 sqs queue.

The ARN controls which queues the policy applies to. For example, arn:aws:sqs:*:account-id:rai* will apply to all queues that match rai*.

S3 Bucket

Create an S3 bucket using the AWS console

MongoDB

Create a mongodb to store submissions from the client.

  • Create a security group that allows ssh (port 22) and mongodb (port 27017)
  • Create an AWS EC2 instance to run the database and add it to that security group

Install docker

curl -fsSL get.docker.com -o get-docker.sh | sudo sh
sudo usermod -aG docker $USER

Log out and log back in. Start mongo 3.0

docker run -p 27017:27017 --restart always -d --name rai-mongo -v /data/db:/data/db mongo:3.0 --auth

Takes a while to preallocate some files. You can monitor with docker logs -f rai-mongo. Then connect to the admin database as admin

docker exec -it rai-mongo mongo --authenticationDatabase admin admin

Add a rai-root user that can administer any database

db.createUser({ user: 'rai-root', pwd: 'some-password', roles: [ { role: "root", db: "admin" } ] });

Exit and connect to the admin database as that user

docker exec -it rai-mongo mongo --authenticationDatabase admin -u rai-root -p some-password admin

Switch to the rai database This doesn't actually create a database until you put something into the database

use rai

Create a collection for the submissions.

db.createCollection("rankings")

Now that the rankings database exists, add a user for the rai-client

db.createUser({ user: 'rai-client', pwd: 'some-password', roles: [ { role: "readWrite", db: "rai" } ] });

To nuke the database and start from scratch if you goof up:

docker rm -f rai-mongo && docker volume prune

To backup the database, instructions from [here]:(https://docs.mongodb.com/manual/tutorial/install-mongodb-on-ubuntu/#packages)

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv 0C49F3730359A14518585931BC711F9BA15703C6
echo "deb [ arch=amd64,arm64 ] http://repo.mongodb.org/apt/ubuntu xenial/mongodb-org/3.4 multiverse" | sudo tee /etc/apt/sources.list.d/mongodb-org-3.4.list
sudo apt update
sudo apt install mongodb-org-tools
mongodump -h localhost:27017 -u rai-root -p rai-root-password --authenticationDatabase admin
Redis Server

Install a redis server. A docker container can also be used.

CUDA Docker Integration

Rai offers two ways of using GPUs within the system. Either the nvidia-docker approach (recommended) or the rai-cuda approach should work.

NVIDIA-Docker

Install the nvidia-docker package. Installation instructions can be found here

Rai CUDA Volume Plugin

Follow the instructions at rai-project/rai-docker-volume.

Prebuilt binaries exist on S3 at /files.rai-project.com/dist/rai-docker-volume/stable/latest.

These binaries are not publicly readable, you need an AWS_KEY / SECRET to access them.

RAI Client Installation

See rai-project/rai

RAID server installation

Provisioning Ubuntu machine on AWS

Increase the open file limit:

add the following to /etc/security/limits.conf

root soft nofile 500000
root hard nofile 500000
* soft nofile 500000
* hard nofile 500000

add the following to /etc/pam.d/common-session and /etc/pam.d/common-session-noninteractive

session required pam_limits.so

Reboot. Check the open file limit with

ulimit -n

RAID Server Installation from Binary

Prebuilt raid binaries exist on s3 in /files.rai-project.com/dist/raid/stable/latest

These binaries are not publicly readable, you need an AWS_KEY / SECRET to access them.

RAID Server Installation from Source

RAI is developed using golang which needs to be installed for code to be compiled from source. You can install Golang either through Go Version Manager(recommended) or from the instructions on the golang site. We recommend the Go Version Manager.

The following are instruction on how to install Go 1.8 through Go version manager. Go version 1.8+ is required to compile RAI.

Download the GVM using

bash < <(curl -s -S -L https://raw.githubusercontent.com/moovweb/gvm/master/binscripts/gvm-installer)

Add the following line to your .bashrc(or .zshrc if using zsh) to set up the GVM environment. This is sometimes done for you by default.

[[ -s "$HOME/.gvm/scripts/gvm" ]] && source "$HOME/.gvm/scripts/gvm"

You can then install the Go 1.8 binary and set it as the default

gvm install go1.11 -B
gvm use go1.11 --default

gvm will setup both your $GOPATH and $GOROOT and you can validate that the installation completed by invoking

$ go env
GOARCH="amd64"
GOBIN=""
GOEXE=""
GOHOSTARCH="amd64"
GOHOSTOS="linux"
GOOS="linux"
GOPATH="/home/abduld/.gvm/pkgsets/go1.11/global"
GORACE=""
GOROOT="/home/abduld/.gvm/gos/go1.11"
GOTOOLDIR="/home/abduld/.gvm/gos/go1.11/pkg/tool/linux_amd64"
GCCGO="gccgo"
CC="gcc"
GOGCCFLAGS="-fPIC -m64 -pthread -fmessage-length=0 -fdebug-prefix-map=/tmp/go-build917072201=/tmp/go-build -gno-record-gcc-switches"
CXX="g++"
CGO_ENABLED="1"
PKG_CONFIG="pkg-config"
CGO_CFLAGS="-g -O2"
CGO_CPPFLAGS=""
CGO_CXXFLAGS="-g -O2"
CGO_FFLAGS="-g -O2"
CGO_LDFLAGS="-g -O2"
Installing using rai-srcmanager

First, install the rai-srcmanager by

go get -u -v github.com/rai-project/rai-srcmanager

Download the required public repositories by

rai-srcmanager update --public

Now all the relevant repositories should now be in $GOPATH/src/github.com/rai-project.

Installing using glide
  1. Install glide by running go get github.com/Masterminds/glide
  2. Clone the raid repository
go get -d -u -v github.com/rai-project/raid
  1. Install the software dependencies using glide.
cd $GOPATH/src/github.com/rai-project/raid
glide install
Build Binary

Create an executable (optionally, embed the secret. You won't have to use the -s flag later)

go build

or

go build -ldflags="-s -w -X main.AppSecret=${APP_SECRET}"

you can then validate if raid has been compiled correctly by invoking

./raid help

Configuration

Much of rai/raid is controlled by configuration files. Services that are shared between the client and server must match. In this section we will explain the minimal configurations needed for both the client and server

Note: One can create secret keys recognizable by rai/raid using rai-crypto tool. If you want to encrypt a string using “PASS” as your app secret, then you’d want to invoke

    rai-crypto encrypt –s PASS MY_PLAIN_TEXT_STRING

Configurations are specified in YAML format and exist either in $HOME/.rai_config.yml or are embedded within the executable. There are many more configurations that can be set, but if omitted then sensible defaults are used.

Client Configuration

The client configuration configures the client for usage with a cluster of rai servers.

    app:
        name: rai # name of the application
        verbose: false # whether to enable verbosity by default
        debug: false # whether to enable debug output by default
    aws:
        access_key_id: AWS_ACCESS_KEY # the aws access key (encrypted)
        secret_access_key: AWS_SECRET_KEY # the aws secret key
        region: us-east-1 # the aws region to use
        sts_account: STS_ACCOUNT # the sts account number
        sts_role: rai # the sts role
        sts_role_duration_seconds: 15m # the maximum time period the sts role can be assumed
    store:
        provider: s3 # the store provider
        base_url: http://s3.amazonaws.com # the base url of the file store
        acl: public-read # the default permissions for the files uploaded to the file store
    client:
        name: rai # name of the client
        upload_bucket: files.rai-project.com # base url or the store buceket
        bucket: userdata # location to store the uploaded user data (user input)
        build_file: rai_build # location to store the result build data (user output)
        rai_queue_name: << Amazon AWS Simple Queue Service Name >>
    auth:
        provider: auth0 # the authentication provider
        domain: raiproject.auth0.com # the domain of the authentication provider
        client_id: AUTH0_CLIENT_ID # the client id from the authentication. The auth0 client id for example
        client_secret: AUTH0_CLIENT_SECRET # the client secret from the authentication. The auth0 client secret for example
    pubsub:
        endpoints: # list of endpoints for the pub sub service
            - pubsub.rai-project.com:6379 # the pubsub server location + port
        password: PUBSUB_PASSWORD # password to the pub/sub service

Note: During the travis build process the client configurations are embedded into the client binary. Therefore the $HOME/.rai_config.yml is never read.

Server Configuration

All servers within a cluster share the same configuration. Here is the configuration currently being used:

    app:
        name: rai # name of the application
        verbose: false # whether to enable verbosity by default
        debug: false # whether to enable debug output by default
    logger:
        hooks: # log hooks to enable
            - syslog # enable the syslog hook
    aws:
        access_key_id: AWS_ACCESS_KEY # the aws access key (encrypted)
        secret_access_key: AWS_SECRET_KEY # the aws secret key
        region: us-east-1 # the aws region to use
    store:
        provider: s3 # the store provider
        base_url: http://s3.amazonaws.com # the base url of the file store
        acl: public-read # the default permissions for the files uploaded to the file store
    broker: # broker/queue configuration section
        provider: sqs # the queue provider
        serializer: json # the serialization method to use for messages. Json is the default
        autoack: true # enable auto acknowledgement of messages
    client:
        name: rai # name of the client
        upload_bucket: files.rai-project.com # base url or the store buceket
        bucket: userdata # location to store the uploaded user data (user input)
        build_file: rai_build # location to store the result build data (user output)
        rai_queue_name: << Amazon AWS Simple Queue Service Name >>
    auth:
        provider: auth0 # the authentication provider
        domain: raiproject.auth0.com # the domain of the authentication provider
        client_id: AUTH0_CLIENT_ID # the client id from the authentication. The auth0 client id for example
        client_secret: AUTH0_CLIENT_SECRET # the client secret from the authentication. The auth0 client secret for example
    pubsub:
        endpoints: # list of endpoints for the pub sub service
            - pubsub.rai-project.com:6379 # the pubsub server location + port
        password: PUBSUB_PASSWORD # password to the pub/sub service

Other useful configuration options are docker.time_limit (default 1 hour), docker.memory_limit (default 16gb)

Changing the Listening Queue Name

Changing the queue name is used for testing the server without interfering with the currently deployed servers, or to have different clients utilizing different server clusters.

You can change the queue used by a server by changing the rai_queue_name option in the client section of the rai configuration configuration. The default value of the queue is the application name rai followed by an underscore, followed by the host machine architecture (amd64, ppc64le, ...). When running on a Power8 machine for example, the default server queue is rai_ppc64le.

Instructions on how to create an Amazon AWS Simple Queue Service is described at the top of the README.

Start/Stop Server

With the absence of integration of raid with system service management (such as SystemD, UpStart, ...) one needs to start and stop the raid server manually. \
Assuming you’ve already compiled the raid executable, you can run the server using the following command:

    ./raid –s ${MY_SECRET}

There are a few options that are available to control settings:

Table 1 : Command line options for raid server

Description Option
Debug Mode -d
Verbose Mode -v
Application Secret -s MY_SECRET

The above command will exit when a user exits the terminal session. Use the nohup command to avoid that

    nohup ./raid –d -v –s ${MY_SECRET} &
Starting raid and associated services on reboot

Copy the systemd service in '../raid/build/systemd/raid.service' to '/etc/systemd/system'. Enable auto start on reboot.

sudo cp ../raid/build/systemd/raid.service /etc/systemd/system/
sudo systemctl daemon-reload
sudo systemctl start raid.service
sudo systemctl enable raid

Make sure the raid.service service has been started.

sudo systemctl status raid

Example output below:

● raid.service - RAID
   Loaded: loaded (/lib/systemd/system/raid.service; enabled; vendor preset: enabled)
   Active: active (running) since Tue 2017-11-14 06:32:59 UTC; 2min 0s ago
     Docs: https://github.com/rai-project/raid
 Main PID: 5515 (raid)
    Tasks: 9
   Memory: 7.3M
      CPU: 78ms
   CGroup: /system.slice/raid.service
           └─5515 /usr/lib/raid/raid --config=/usr/lib/raid/rai_config.yml --queue=rai_amd64

In particular make sure raid is loaded, active, and enabled.

Setting up NVIDIA Persistence Mode

If using CUDA, make sure to enable persistence mode.

Copy the systemd service in build/systemd/nvidia-persistenced.service and modify the line

ExecStart=/usr/bin/nvidia-persistenced --user ubuntu

to launch using the user you want (here it's launching under the ubuntu user). Once modified, copy the file to /etc/systemd/system/ and start the systemd service

sudo mv nvidia-persistenced.service /etc/systemd/system/
sudo systemctl daemon-reload
sudo systemctl start nvidia-persistenced
sudo systemctl enable nvidia-persistenced

Make sure that the nvidia-persistenced.service service has been started and enabled. The command

sudo systemctl status nvidia-persistenced.service

should give an output similar to

● nvidia-persistenced.service - NVIDIA Persistence Daemon
   Loaded: loaded (/etc/systemd/system/nvidia-persistenced.service; disabled; vendor preset: enabled)
   Active: active (running) since Fri 2017-11-03 18:33:42 CDT; 5min ago
  Process: 71100 ExecStopPost=/bin/rm -rf /var/run/nvidia-persistenced (code=exited, status=0/SUCCESS)
  Process: 71103 ExecStart=/usr/bin/nvidia-persistenced --user abduld (code=exited, status=0/SUCCESS)
 Main PID: 71107 (nvidia-persiste)
    Tasks: 1
   Memory: 492.0K
      CPU: 3ms
   CGroup: /system.slice/nvidia-persistenced.service
           └─71107 /usr/bin/nvidia-persistenced --user abduld

Nov 03 18:33:42 whatever systemd[1]: Starting NVIDIA Persistence Daemon...
Nov 03 18:33:42 whatever nvidia-persistenced[71107]: Started (71107)
Nov 03 18:33:42 whatever systemd[1]: Started NVIDIA Persistence Daemon.

Finally, check that the driver is run in persistence mode

$ nvidia-smi -a | grep Pe
    Persistence Mode                : Enabled
        Pending                     : N/A
        Pending                     : N/A
    Performance State               : P5
        Pending                     : N/A
        Pending                     : N/A
Creating RAI Accounts

Either build the rai-keygen or download the prebuilt binaries which exist on s3 in /files.rai-project.com/dist/rai-keygen/stable/latest

Note: These binaries are not publically readable and you need an AWS_KEY / SECRET to access them.

One can use the rai-keygen to generate RAI and email account information to the people enrolled in the class. The mailing process uses mailgun. A prebuilt rai-keygen includes a builtin configuration file, but if compiling from source, then you need to add the email configuration options

    email:
        provider: mailgun # the email provider
        domain: email.webgpu.com # the domain of the
        source: postmaster@webgpu.com # the source email
        mailgun_active_api_key: API_KEY
        mailgun_email_validation_key: VALIDATION_KEY

You will not need the above if you do not need to email the generated keys.

Note: Docker builder does not require account generation, since account information is embedded into the webserver.

Administration Tips

The following tips are based on past experience administering clusters and managing arbitrary user execution:

  • If using CUDA, make sure to enable persistence mode. A systemd service exists within the raid repository
  • A system can become unstable when executing arbitrary code. Consult the logs (ideally a distributed logging) when trying to identify why certain tasks succeed while other fail.
  • Install Cadvistor (github.com/google/cadvisor) to examine the health of the docker container and monitor them.
  • Make sure that you have enough disk space. For example, last year the redis server ran out of disk space 2-3 days before the deadline.
AWS Admin Notes
Reboot all AWS Instances
instances=$(aws ec2 describe-instances --filters "Name=tag:name,Values=ece408.project" "Name=instance-state-code,Values=16" | jq -j '[.Reservations[].Instances[].InstanceId] | @sh')
echo ${instances}
for instance in ${instances}
do
  echo ${instance}
  #aws ec2 reboot-instances --dry-run --instance-ids ${instance}
done

or

instances=$(aws ec2 describe-instances --filters "Name=tag:name,Values=ece408.project" "Name=instance-state-code,Values=16" | jq -j '[.Reservations[].Instances[].InstanceId] | join(" --instance-ids ")')
aws ec2 reboot-instances --no-dry-run --instance-ids ${instances}

Logs

If journald is enabled, then you can view the server logs using journalctl -f -u raid.service

Reporting Issues

If emailing with a problem, then please include the output of

rai version

as well as the output of

rai buildtime

In your bug report. You can also invoke the rai command with verbose and debug outputs using

rai --verbose --debug

Please use the [Github issue manager] to report any issues or suggestions about the server.

License

NCSA/UIUC © Abdul Dakkak

Documentation

The Go Gopher

There is no documentation for this package.

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