Just saw a post about the upcoming NASA hackday and starting thinking what would be some useful stuff to have ready to run in Bluemix? I find that playing around with Python is a good way to start and you can look at projects liks Astropy.org for examples, but a really fun way to get started is using iPython notebooks, they allow you to essentially document, run, and save your code snippets in a web based version of the interpreter.
So I wanted to show what it takes to get that running in Bluemix, here there was an existing tutorial by Peter Parante on DW from last August this is helpful but using the Heroku buildpack since a Python buildpack did not exist on Bluemix then. So we’ll use that example but use the IBM buildpack and add some Astropy.org goodies to get started :)
- Setup our Bluemix Application
- Setup our Git Repository
- Update our Application’s Python environment
- Admire our work and learn more
Setup our Bluemix Application
So fire up your browser and cf command line to get this party started. First go to Bluemix in your browser, for my example I created a new space to play around in, but you just need to get somewhere you have access to create applications. And create a new application, Web, and select Python.
Give your application a name, and once that completes you will get a chance to download you starter code.or if you want to use DevOps Services and Git skip the download for now and go to the next section.
You can also checkout the application running live http://python-hacking-for-science.mybluemix.net/ and you should see the default boilerplate welcome page that we look at later.
Setup our Git Repository
If you want to use DevOps Service you can switch tabs and push git and use your git commands to clone locally. Or if you want to setup git elsewhere.
In my case I just waited until the application was running and created a git repository from the Application page for clarity.
At the prompt you want to accept the defaults, as this will add the started application code we could have downloaded above to seed the repository and enable the Continuous Delivery Pipeline so we can have autodeploy on commit as we make changes later.
At this point I we can navigate to the git url listed on our newly created DevOps Services project swilbur/python-hacking-for-science. Once there you can either grab your git url and clone a local copy of your repo, or just hit the Edit Code button and start working in the web.
If you use the Edit Code feature all work is done inside the browser and you can directly sync your changes to a Bluemix application to redeploy any changes you make, good for content updates, not good while we make changes to the underlying configuration of the CloudFoundry Droplet so let’s hold off on that for this time.
The last thing to note, as part of our new project the integration setup an initial Continuous Delivery Pipeline that will auto-build on commit, and auto-deploy successful builds. We can turn this off or make changes but what this means is that we will automatically deploy any changes that we commit, since our build process is trivial it will never fail.
Update our Application’s Python environment
Now we should have a working starting point( either zip or git clone of repo), a running application, and we can open our favorite editor to start making changes push them back to cf and confirm they are working.
So unzip or clone your starter content.
sgwilbur@gura:~/workspaces$ mkdir python-hacking-for-science_fromzip sgwilbur@gura:~/workspaces$ cd python-hacking-for-science_fromzip sgwilbur@gura:~/workspaces/python-hacking-for-science_fromzip$ unzip ~/Downloads/python-hacking-for-science.zip Archive: /Users/sgwilbur/Downloads/python-hacking-for-science.zip inflating: Procfile inflating: static/images/newapp-icon.png inflating: static/index.html inflating: static/stylesheets/style.css inflating: server.py inflating: requirements.txt inflating: manifest.yml inflating: README.txt sgwilbur@gura:~/workspaces/python-hacking-for-science_fromzip$ ls Procfile README.txt manifest.yml requirements.txt server.py static
sgwilbur@gura:~/workspaces$ git clone https://hub.jazz.net/git/swilbur/python-hacking-for-science Cloning into 'python-hacking-for-science'... remote: Counting objects: 17, done remote: Finding sources: 100% (17/17) remote: Total 17 (delta 0), reused 17 (delta 0) Unpacking objects: 100% (17/17), done. Checking connectivity... done. sgwilbur@gura:~/workspaces$ cd python-hacking-for-science/ sgwilbur@gura:~/workspaces/python-hacking-for-science$ ls License.txt Procfile README.md README.txt manifest.yml requirements.txt server.py static
The only different is that IBM DevOps Services has added License.txt and README.md files, nothing functionaly different.
sgwilbur@gura:~/workspaces$ diff -d python-hacking-for-science_fromzip/ python-hacking-for-science Only in python-hacking-for-science: .git Only in python-hacking-for-science: License.txt Only in python-hacking-for-science: README.md Common subdirectories: python-hacking-for-science_fromzip/static and python-hacking-for-science/static
Of the files that are in the boiler plate project we are immediately concerned with 3 of them right now:
manifest.ymlOur definition of the application resources, routes, and dependencies from the Cloud Foundry Side.
applications: - disk_quota: 1024M buildpack: python_buildpack host: python-hacking-for-science name: python-hacking-for-science path: . domain: mybluemix.net instances: 1 memory: 256M
requirements.txtOur Python specific requirements, what modules we are going to use.
ProcfileThe start command to run our process (Update the Profile with a slight variation on the mouthful below as Peter added to his article).
web: ipython profile create; echo "c.NotebookApp.password = '$( python -c 'from IPython.lib import passwd; import os; print passwd(os.environ.get("PASSWORD", ""))' )'" >> ~/.ipython/profile_default/ipython_notebook_config.py; cd content; ipython notebook --port=$VCAP_APP_PORT --ip=$VCAP_APP_HOST --no-mathjax
You can take a look at the boiler plate options and see it is pretty simple, now we are ready to push these to Bluemix, the first time this will build a lot of stuff since the numeric libraries for
matplotlib are heavily reliant on C code under the covers, so run the push command and go grab a cup of coffee or snack:
sgwilbur@gura:~/workspaces/python-hacking-for-science$ cf push Using manifest file /Users/sgwilbur/workspaces/python-hacking-for-science/manifest.yml Updating app python-hacking-for-science in org email@example.com / space ipython as firstname.lastname@example.org... OK Using route python-hacking-for-science.mybluemix.net Uploading python-hacking-for-science... Uploading app files from: /Users/sgwilbur/workspaces/python-hacking-for-science Uploading 19.6K, 12 files Done uploading OK Stopping app python-hacking-for-science in org email@example.com / space ipython as firstname.lastname@example.org... OK Starting app python-hacking-for-science in org email@example.com / space ipython as firstname.lastname@example.org... -----> Downloaded app package (20K) -----> Downloaded app buildpack cache (31M) -------> Buildpack version 1.1.1 -----> Installing dependencies with pip Downloading/unpacking ipython[notebook] (from -r requirements.txt (line 1)) Downloading/unpacking matplotlib (from -r requirements.txt (line 2)) Running setup.py (path:/tmp/pip_build_vcap/matplotlib/setup.py) egg_info for package ... CUT OUT LOTS OF LINES OF SCROLLING ... Successfully installed ipython matplotlib terminado mistune pygments tornado jinja2 pyzmq jsonschema numpy six python-dateutil pytz pyparsing nose mock ptyprocess certifi backports.ssl-match-hostname markupsafe Cleaning up... -----> Uploading droplet (95M) 0 of 1 instances running, 1 starting 0 of 1 instances running, 1 starting 0 of 1 instances running, 1 starting 0 of 1 instances running, 1 starting 1 of 1 instances running App started OK App python-hacking-for-science was started using this command `ipython profile create; echo "c.NotebookApp.password = '$( python -c 'from IPython.lib import passwd; import os; print passwd(os.environ.get("PASSWORD", ""))' )'" >> ~/.ipython/profile_default/ipython_notebook_config.py; ipython notebook --port=$VCAP_APP_PORT --ip=$VCAP_APP_HOST --no-mathjax` Showing health and status for app python-hacking-for-science in org email@example.com / space ipython as firstname.lastname@example.org... OK requested state: started instances: 1/1 usage: 512M x 1 instances urls: python-hacking-for-science.mybluemix.net last uploaded: Tue Mar 31 21:11:59 +0000 2015 state since cpu memory disk details #0 running 2015-03-31 04:26:22 PM 0.0% 113.4M of 512M 266.6M of 1G
Then 10 or 15 minutes later you will hopefully get this nice message taht your app is done building and is running! Thankfully this stuff gets cached so if you want to make a change or add another module it is only the time required to add the new modules not to rebuild them all again.
Lets take a minute to cleanup our boilerplate and commit our changes, then we can head over to the IDS project and checkout the CD pipeline kicking in.
sgwilbur@gura:~/workspaces/python-hacking-for-science$ git status On branch master Your branch is up-to-date with 'origin/master'. Changes not staged for commit: (use "git add <file>..." to update what will be committed) (use "git checkout -- <file>..." to discard changes in working directory) modified: Procfile modified: manifest.yml modified: requirements.txt no changes added to commit (use "git add" and/or "git commit -a") sgwilbur@gura:~/workspaces/python-hacking-for-science$ ls -als total 48 0 drwxr-xr-x+ 11 sgwilbur staff 374 31 Mar 17:12 . 0 drwxr-xr-x+ 70 sgwilbur staff 2380 31 Mar 15:24 .. 0 drwxr-xr-x+ 13 sgwilbur staff 442 31 Mar 17:12 .git 8 -rw-r--r--+ 1 sgwilbur staff 69 31 Mar 15:23 License.txt 8 -rw-r--r--+ 1 sgwilbur staff 310 31 Mar 16:59 Procfile 8 -rw-r--r--+ 1 sgwilbur staff 914 31 Mar 15:23 README.md 0 drwxr-xr-x+ 2 sgwilbur staff 68 31 Mar 16:59 content 8 -rw-r--r--+ 1 sgwilbur staff 198 31 Mar 16:11 manifest.yml 8 -rw-r--r--+ 1 sgwilbur staff 28 31 Mar 16:11 requirements.txt 8 -rw-r--r--+ 1 sgwilbur staff 603 31 Mar 15:23 server.py 0 drwxr-xr-x+ 5 sgwilbur staff 170 31 Mar 15:23 static sgwilbur@gura:~/workspaces/python-hacking-for-science$ git add Procfile sgwilbur@gura:~/workspaces/python-hacking-for-science$ git add manifest.yml sgwilbur@gura:~/workspaces/python-hacking-for-science$ git add requirements.txt sgwilbur@gura:~/workspaces/python-hacking-for-science$ git rm README.txt rm 'README.txt' sgwilbur@gura:~/workspaces/python-hacking-for-science$ git rm server.py rm 'server.py' sgwilbur@gura:~/workspaces/python-hacking-for-science$ git rm -rf static/ rm 'static/images/newapp-icon.png' rm 'static/index.html' rm 'static/stylesheets/style.css' sgwilbur@gura:~/workspaces/python-hacking-for-science$ git status On branch master Your branch is up-to-date with 'origin/master'. Changes to be committed: (use "git reset HEAD <file>..." to unstage) modified: Procfile deleted: README.txt modified: manifest.yml modified: requirements.txt deleted: server.py deleted: static/images/newapp-icon.png deleted: static/index.html deleted: static/stylesheets/style.css sgwilbur@gura:~/workspaces/python-hacking-for-science$ git commit -m "Initial changes to get iPython and matplotlib running on Bluemix." [master ad5b567] Initial changes to get iPython and matplotlib running on Bluemix. 8 files changed, 4 insertions(+), 158 deletions(-) delete mode 100644 README.txt delete mode 100644 server.py delete mode 100644 static/images/newapp-icon.png delete mode 100644 static/index.html delete mode 100644 static/stylesheets/style.css sgwilbur@gura:~/workspaces/python-hacking-for-science$ git push origin master Counting objects: 10, done. Delta compression using up to 4 threads. Compressing objects: 100% (4/4), done. Writing objects: 100% (5/5), 724 bytes | 0 bytes/s, done. Total 5 (delta 1), reused 0 (delta 0) remote: Resolving deltas: 100% (1/1) remote: remote: Processing changes: refs: 1, done To https://hub.jazz.net/git/swilbur/python-hacking-for-science 270280a..ad5b567 master -> master
Now if you are quick enough or just have the browser open already you will see the pipeline kick in.
Take a look at the iPython tutorial which can be run from this web notebook without having to install it all locally.
PyCon 2014 In Depth iPython with creator Fernando Perez * Full 3 h session * session material ipython/ipython-in-depth
Take a look at the astropy.org/astropy-tutorials/ on how to get started, you will see that there tuturials are actually iPython notebooks :)
Nothing is persisted here, we are only ever writing to the runtime droplet and never committing those files back to git, so keep this in mind that the work is throw away and will not survive re-deployments.
Running this on a public server that you are paying for computer and memory usage on, it is not wise to leave it un protected like this so it is recommended that you setup a password or change the default password from blank as shown here when it is running on your Credit Card :)
This is not an ideal location for large data set calculation due to the potential memory requirements, but it is an easy way to get started with iPython and a few modules you are interested in within the hour.