RADCamp-NYC2019 redux & detailed configuration of google cloud HPC backend

Recently we ran RADCamp-NYC2019 and decided to use google cloud as the backend to provide massive computational resources to the workshop participants. Each participant from Part I of the workshop had generated 3RAD libraries, which we received grants from the SSE & SSB to have sequenced. In Part II, our goal was to have the participants assemble and analyse their real data during the course of the two day workshop.

At the end of the second day, we had a round-up, where each of the groups showed a results slide with a tree and a PCA from the real data! Awesome!

Take a look at the results of RADCamp-NYC2019.

Long story short, using google cloud for computational resources was critical for the success of the workshop, but the setup is quite complicated, so I document it here, in the event it should be useful.

Set up and configure vm instance to use as the master

Shared read-only drive for hosting data

  • Create a new disk, 250GB persistent and call it radcamp-data Unless you initialize the disk with an image they are uninitialized, so you have to format and mount. Attach the new disk to a running vm instance and follow these directions for formatting a new disk.

DL the raw data

The lftp app will do multi-threaded downloads (admera ftp server is dog-slow):

  • sudo apt-get install lftp
  • lftp ftp.admerahealth.com
  • mget -P 10 *.gz

Create the vm image as you like it

  • Create a new VM instance and choose n1-standard-16
  • Change the boot disk to Ubuntu 19.04 and set size to 100GB (standard persistent disk is default)
  • Choose advanced->additional disks->existing disk and choose radcamp-data
  • Select Firewalls and Allow HTTP and HTTPS traffic
  • Click create
  • Choose SSH open in a new window and perform the installs

SW install and configuration

## Install and configure conda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda* -b
miniconda3/bin/conda init
source ~/.bashrc
conda create -n ipyrad -y
conda activate ipyrad

## All the conda installs
conda install anaconda-client -y
conda install -c conda-forge vim nano -y
conda install -c bioconda -c ipyrad ipyrad jupyter fastqc mpi4py -y
conda install -c ipyrad structure clumpp bucky bpp mpi4py -y
conda install -c bioconda scikit-learn sra-tools raxml treemix -y
conda install -c eaton-lab toytree toyplot tetrad -y

## Set the default password for the jupyter notebook serer
mkdir .jupyter
jupyter notebook password

Advanced system configuration

We want the notebook server to bind to port 80, so here we set the system to allow users to run on privileged ports. Also, format and mount the ro data drive.

## This all has to be done by root
sudo su -
echo 'net.ipv4.ip_unprivileged_port_start=0' > /etc/sysctl.d/50-unprivileged-ports.conf
sysctl --system

mkdir /media/RADCamp
mount -o discard,defaults /dev/sdb /media/RADCamp/
blkid /dev/sdb
# /dev/sdb: UUID="8be0b7c5-3aa6-4cdc-bc04-d056a8bb60c8" TYPE="ext4"

echo "UUID=8be0b7c5-3aa6-4cdc-bc04-d056a8bb60c8 /media/RADCamp ext4 discard,defaults,nofail 0 2" >> /etc/fstab
mount -a
## Exit root
exit

Test that the notebook can talk on port 80

jupyter notebook --no-browser --ip=$(hostname -i) --port=80 &

Open a new tab, find the external ip of the master vm image, and browse to it. If it’s working it should prompt you for the password.

Configure the repo to be in dev mode to allow hot-updating

Run this as the default user:

git clone https://github.com/dereneaton/ipyrad.git
cd ipyrad
pip install -e .

Magic to start the notebook server on boot

Create a new file, which I called /etc/init.d/RADCamp-jupyter.sh:

## Pull from the github repository and Get notebook to run on startup.
## Write this command to a file called RADCamp-jupyter.sh
#!/bin/bash
echo "Starting jupyter" > /tmp/RADCamp.log
echo "Pulling ipyrad repository" >> /tmp/RADCamp.log
sudo su isaac_overcast - -c "cd ~/ipyrad; git pull >> /tmp/RADCamp.log"
start-stop-daemon --start --chuid 1001 --chdir /home/isaac_overcast --exec /home/isaac_overcast/miniconda3/envs/ipyrad/bin/jupyter -- notebook --no-browser --port=80 --ip=$(hostname -i) &

Add the file we just created to run at boot time in the crontab. This is a lame and hackish way of doing it, but it works.

sudo echo "@reboot     root        /etc/init.d/RADCamp-jupyter.sh" >> /etc/crontab

Configure the VM Image and Instance Templates

Pull an image from the master instance

  • Stop the master instance (you can’t pull an image when it’s running)
  • Go to Compute Engine->Images and choose Create Image
  • Name the image radcamp-image
  • Choose Source -> Disk
  • Choose Source disk -> instance 1
  • Click create

Create a new instance from this image by hand

Test your image by creating a new vm instance and verifying the setup.

  • Images->radcamp-image->Create new instance
  • Name: radcamp-vm1
  • Machine type: n1-standard-16
  • Allow HTTP/HTTPS
  • Create

Here’s the command to run in the cloud shell to create a new intance called instance-2using the radcamp-image as the base. Automating this could be cool, but dangerous!

gcloud beta compute --project=radcamp-255318 instances create instance-2 --zone=us-central1-a --machine-type=n1-standard-1 --subnet=default --network-tier=PREMIUM --maintenance-policy=MIGRATE --service-account=446371761382-compute@developer.gserviceaccount.com --scopes=https://www.googleapis.com/auth/devstorage.read_only,https://www.googleapis.com/auth/logging.write,https://www.googleapis.com/auth/monitoring.write,https://www.googleapis.com/auth/servicecontrol,https://www.googleapis.com/auth/service.management.readonly,https://www.googleapis.com/auth/trace.append --tags=http-server,https-server --image=radcamp-template --image-project=radcamp-255318 --boot-disk-size=100GB --boot-disk-type=pd-standard --boot-disk-device-name=instance-2 --reservation-affinity=any

Create instance from image with RADCamp disk attached ro

gcloud beta compute --project=radcamp-255318 instances create radcamp-a --zone=us-central1-a --machine-type=n1-standard-16 --subnet=default --network-tier=PREMIUM --maintenance-policy=MIGRATE --service-account=446371761382-compute@developer.gserviceaccount.com --scopes=https://www.googleapis.com/auth/devstorage.read_only,https://www.googleapis.com/auth/logging.write,https://www.googleapis.com/auth/monitoring.write,https://www.googleapis.com/auth/servicecontrol,https://www.googleapis.com/auth/service.management.readonly,https://www.googleapis.com/auth/trace.append --tags=http-server,https-server --image=radcamp-image --image-project=radcamp-255318 --boot-disk-size=100GB --boot-disk-type=pd-standard --boot-disk-device-name=radcamp-a --disk=name=radcamp-data,device-name=radcamp-data,mode=ro,boot=no --reservation-affinity=any

Create the instance template

Instance templates can be used to automate instance creation via the managed instance groups thing. Makes it easier to spin up a whole bunch of instances without monkeying around with scripting the creation, but you can’t start and stop instance groups, they are either running or they are deleted.

  • Name: radcamp-ig
  • set boot disk -> change -> custom -> radcamp-image
  • Set to allow http and https

Create instance group from instance template

Instance groups need to be created from with instance templates. There’s a bunch of stuff to manage how many instances you have running, which we don’t care about, but if you set min and max # of instances to the the same value it’s a handy way of spinning up an exact number of instances.

Managing instances through the cloud shell interface

CLI interface for controlling instances in cloud shell.

List running instances

## Dump lots of info about instances including the external IPs
gcloud compute instances list

## Just get the names (useful for bulk starting/stopping)
gcloud compute instances list | tr -s " " | cut -f 1 -d " "

Starting and stopping

Starting and stopping batches of isntances can be pretty simple, you just pass in a list of the instance names you want to operate on.

gcloud compute instances start <INSTANCE_NAMES>

attach disk

Can probably use the attach-disk command to bulk attach the radcamp-data disk ro to all the instances

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