Quick Start

Introduction

This quick start guide will demonstrate how to create a basic source detection pipeline operating on CFHT Megacam images within the CANFAR Virtual Machine (VM), with fast access to the CADC archive and storage. It will go over the following steps:

  • create, configure, and interact with Compute Canada OpenStack cloud, and CANFAR VMs
  • access CADC VOSpace storage
  • launch jobs running the pipeline installed on the VM with the CANFAR batch system

This guide is mostly geared to do data processing. If you just want to access the regular Compute Canada cloud to build non-batch VMs, we suggest this guide, which also applies to CANFAR.

Registration and Resource Allocation

Before starting this tutorial, you will need to have a CADC account (register).

Once registered, send an email to CANFAR support and include:

  • a CADC account name
  • a rough amount of required resources (storage capacity and processing capabilities), and if you need batch processing
  • a few sentences describing what you want to do.

Your request will be reviewed and you will be contacted by the CANFAR team which will also take care of your registration to Compute Canada infrastructure.

Once registered, make note of your:

  • [username] is your CADC username
  • [VOSpace] is the short name of the VOSpace you requested access to
  • [project] is the OpenStack project name you requested access to

Create a Virtual Machine

To access and manage your VM with OpenStack, we suggest using the web dashboard at Compute Canada.

Each CANFAR resource allocation corresponds to an OpenStack [project]. A user may be a member of multiple projects, and a project usually has multiple users. A pull-down menu near the top-left allows you to select between the different projects that you are a member of.

To create a VM, you can go over these instructions which we summarize in the 4 next sections.

Import an ssh public key

Access to VMs is facilitated by SSH key pairs rather than less secure user name / password. A private key resides on your own computer, and the public key is copied to all machines that you wish to connect to.

  • If you have not yet created a key pair on your system, run the ssh-keygen command from a terminal on your local machine to generate one, or follow this documentation for example.
  • On the dashboard, click on Compute, switch to the Key Pairs tab and click on the Import Key Pair button (top-right).
  • Choose a meaningful name for the key, and then copy and paste the contents of the public key. If you have not renamed your key, it will be on its default location at $HOME/.ssh/id_rsa.pub from the machine you plan to ssh from into the Public Key window.

Allocate a public IP address

You will need to connect to your VM via a public IP.

  • Click on the Floating IPs tab part of Network. If there are no IPs listed, click on the Allocate IP to Project button at the top-right.

Each project will typically be given one public IP. If you have already allocated all of your IPs, this button will read “Quota Exceeded”.

Launch a VM

We will now launch a VM. A VM comes with an operating system, and we support two Linux distributions: Ubuntu LTS and RedHat Enterprise Linux clone (before: CentOS, now: Rocky Linux). For this tutorial, we will select Ubuntu 20.04 based VM, with some CANFAR specific pre-installed packages.

Follow these steps to access and launch those pre-built VMs:

  • Switch to the Compute tab, then on Instances, click on the Launch Instance button on the right.
  • Fill up the form of your VM:
    • Details: choose a meaningful Instance Name
    • Source: select Boot Source as an Instance Snapshot and choose canfar-ubuntu-20.04. This is especially important to choose an Image or Instance Snaphot for batch processing. We
    • Flavor: the resources of the VM. c2-7.5gb-31 provides 2 CPU (equivalent), 7.5GB RAM, and a 31 GB ephemeral disk that will be used as scratch space. The flavours starting with p are persistent VMs, and do not have scratch space.
    • Key Pair: ensure that your SSH public key is selected
  • Finally, click the Launch button.

Connect to the VM

After launching the VM you are returned to the Instances window. You can check the VM status once booted by clicking on its name, wait for the power state to say Running. Before being able to ssh to your instance, you will need to attach the public IP address to it.

  • Select Associate Floating IP from the pull-down menu on the right of Create Snapshot button.
  • Select an allocated IP address

Your ssh public key will be injected into the VM under a generic account. The default username depends on the VM image you selected: an Ubuntu-based VM will have a default ubuntu user. A Rocky-Linux (open-srouce RedHat) based VM will have rocky as the default username. This user is not related to your CADC user.

You should be able to access your VM:

ssh ubuntu@[floating ip]

Once you are connected, we recommend to create a user on the VM with your CADC [username]. It will likely be easier to manage if you have software that you will install in the home directory. Create a user, using your CADC [username], with the following command:

sudo canfar_create_user [username]

You can now logout from the VM and ssh back in with ssh [username]@[floating ip], and have the same privileges as the default ubuntu user.

Install software on the VM

The VM operating system has only a minimal set of packages. For this example, we will use:

  • the SExtractor package to detect astronomical sources in FITS images, resulting in catalogues of stars and galaxies.
  • funpack a file decompressor. We also need to read FITS images. Most FITS images from CADC come Rice-compressed with an fz extension. SExtractor only reads uncompressed images, so we also need the funpack utility to uncompress the incoming data. In Debian/Ubuntu, the funpack executable is included in the package libcfitsio-bin.

Let’s install them both system wide since they are available in Ubuntu, after a fresh update of the Ubuntu repositories:

sudo apt update -y
sudo apt install -y source-extractor libcfitsio-bin

Test the Software on the VM

We are now ready to do our basic pipeline. Let’s download a FITS image to our scratch space. When we instantiated the VM we selected a flavour with an ephemeral disk. The disk was automatically mounted on /mnt. You want to access the ephemeral disk with a non-root user. You can use this simple command that will create a scratch directory on /mnt/scratch, and give the proper permissions.

sudo canfar_setup_scratch

Important notes concerning the scratch space:

  • You will need to run the canfar_setup_scratch command every time you launch a new VM from OpenStack.
  • When the VM runs in batch mode, the scratch directory is setup automatically in a different directory for each batch job, which is NOT /mnt/scratch (see below).

Next, enter the scratch directory, download an astronomical image from CADC of the CFHT Megaprime there, and detect the sources with SExtractor. Here we take the default configuration of SExtractor and decide to only output the positions and magnitudes of the detected sources.

cd /mnt/scratch
cp /usr/share/source-extractor/default* .
echo 'NUMBER
MAG_AUTO
X_IMAGE
Y_IMAGE' > default.param
cadc-data get CFHT 1056213p 
funpack -D 1056213p.fits.fz
source-extractor 1056213p.fits -CATALOG_NAME 1056213p.cat

The image 1056213p.fits is a Multi-Extension FITS file with 36 extensions, each containing data from one CCD from the CFHT Megacam camera. The cadc-data command downloads the FITS image from CADC and stores it on the current directory and is already installed on the VM (cadcdata python module) The resulting catalogue of detected sources is stored under 1056213p.cat.

Store results on the CANFAR VOSpace

All data stored on ephemeral disk are wiped out when the VM terminates. We only want to store the output catalogue 1056213p.cat at a persistent, externally-accessible location. We will use the CADC VOSpace for this purpose. To store files on the VOSpace from a command line, you will use the CADC python VOSpace client (vos python module) which is already installed on your VM.

For an automated procedure to access the VOSpace on your behalf, your proxy authorization must be present on the VM. You can accomplish this using a .netrc file that contains your CANFAR user name and password, and the command cadc-get-cert can obtain an X509 Proxy Certificate using that username/password combination without any further user interaction. The commands below will create the file and get a proxy certificate. A proxy certificate is by default valid 10 days.

cadc_dotnetrc # you only need this command once to create the file
cadc-get-cert -n

If you use batch, a new proxy certificate will automatically be created and injected into all the VM clones which will be processing at submission time.

Let’s check that the VOSpace client works by uploading the output source catalogue:

vcp 1056213p.cat vos:[VOSpace]

Verify that the file is properly uploaded by pointing your browser to the VOSpace browser interface.

Snapshot (save) the VM Instance

Now you want to save the VM with your software installed. Return to your browser on the OpenStack dashboard.

  • Save the state of your VM by navigating to the Instances window of the dashboard. and click on the Create Snapshot button to the right of your VM instance’s name. After selecting a meaningful name for the snapshot of the VM instance, e.g., image-reduction-2021-06-26, click the Create Snapshot button. The VM instance will eventually be saved and listed in the VM Images window, and will be available next time you launch an instance of that VM image in a few minutes.

While the system is taking a snapshot of your VM, avoid doing anything on your VM.

IMPORTANT : if you do not create a snapshot of the VM, you will loase all of your work when the VM is deleted. Volume-based VMs do not need snapshots and will persist the files directly on a persistent disk, but Volume-based VM can not be used for batch processing.

If you do not need batch processing, you are done. If you want to use batch, carry on.

Make a script to automate your pipeline

Batch jobs in CANFAR are scheduled and launched with the HTCondor software. The cloud scheduler which launch the VMs necessary to process the jobs on demand, and HTCondor will launch the jobs on the launched VMs (workers).

Now we want to automate the whole procedure as a batch script. ssh into the CANFAR batch cluster:

ssh [username]@batch.canfar.net

We need to recreate and automate the same procedure done interactively. We can simply put all the necessary command into a pipeline script. Paste the following commands into one BASH script named ~/do_catalogue.bash:

#!/bin/bash
id=$1
cadc-data get CFHT ${id}
funpack -D ${id}.fits.fz
cp /usr/share/source-extractor/default* .
echo 'NUMBER
MAG_AUTO
X_IMAGE
Y_IMAGE' > default.param
source-extractor ${id}.fits -CATALOG_NAME ${id}.cat
vcp ${id}.cat vos:[VOSpace]/

The script will repeat the same commands as before with one image observation ID as an argument:

  1. download the compressed FITS file corresponding to the ID from CADC
  2. uncompress the file
  3. detect the sources
  4. save the resulting catalogue of detected sources to the VOSpace.

Remember to substitute [VOSpace] with the VOSPace name that you requested (often this is your [username]).

Write your batch processing job submission

We now want to apply this pipeline to a few images. We need to write a submission file to tell the job scheduler to launch all necessary jobs, in this case one per image. We need to transfer the do_catalogue.bash script to a worker VM. The worker VM will be an instance of your snapshot VM image. For each given CADC CFHT observation ID, a job will run on the worker. Let’s take the following image IDs: 1056215p, 1056216p, 1056217p, and 1056218p. Fire up your favorite editor and paste the following text into a submission file:

executable = do_catalogue.bash

output = do_catalogue-$(arguments).out
error  = do_catalogue-$(arguments).err
log    = do_catalogue-$(arguments).log

queue arguments from (
  1056215p
  1056216p
  1056217p
  1056218p
)

Save the submission file as do_catalogue.sub. Each job will execute with an output and an error file, which will be uploaded to where you submitted the jobs from, only at the end of each job.

Submit the batch jobs

You will need two authorizations to run the batch jobs:

  • to give the scheduler access to the VM snapshot on the [project]
  • to write files to [VOSpace]

In your home directory on the batch submission, you will find one or more *-openrc.sh file(s), corresponding to the OpenStack projects you belong to.

Source the OpenStack RC project file, and enter your CADC password. This sets environment variables used by OpenStack (only required once per login session):

. [project]-openrc.sh

You can then submit your jobs to the condor job pool with our wrapper command:

canfar_submit do_catalogue.sub catalogue-software-2021-06-26 c2-7.5gb-36

where:

  • do_catalogue.sub: is the path of your submission file
  • image-reduction-2021-06-26: is the name of the snapshot VM used to install all the software
  • c2-7.5gb-36: is the flavor for the VM(s) that will execute the jobs. If you wish to use a different flavor, they are visible through the dashboard when launching an instance, or using the command line openstack flavor list.

In the background, your VM is shared with the batch processing system, and it will be replicated on all the free nodes.

After submitting, wait a couple of minutes. Check where your jobs stand in the queue:

condor_q

Monitoring the queue, you should see your jobs going from idle (I) to running (R). Once you have no more jobs in the queue, check the logs and output files 105621.* on the batch host, and check on your VOSpace browser that you have all 4 of the generated catalogues properly uploaded.

You can also check the status of the VMs and jobs running on the cloud summarizing all users:

condor_q -all

If you do need your VM anymore, you can terminate it from the OpenStack dashboard. You are done!

Extra: helpful CANFAR commands and VM maintenance

Once your VM is built, the responsibility is yours to maintain and update software. You may want to run sudo yum update or sudo apt dist-upgrade to make sure you get the latest security updates from the Linux distributions.

On the CANFAR pre-built VMs (canfar-ubuntu-20.04 and canfar-rocky-8), there are a few scripts to help out with CANFAR related activities, all of them come with a --help`:

  • cadc_cert -u [username]: get a CADC proxy certificate by various methods to access CADC VOSpace (legacy script)
  • cadc_dotnetrc: update / create a ${HOME}/.netrc file to ease out with CADC VOSpace access
  • canfar_setup_scratch: simple script to authorize a scratch space when in interactive mode on /mnt/scratch
  • canfar_create_user [user]: create a user with a name [user] on the VM and propagate ssh public key, and give sudo access
  • canfar_update: update all the CANFAR scripts and CADC clients on the VM with the latest versions.

You can find all these commands on /usr/local/bin, or at the GitHub source.