Adventures in Signal Processing and Open Science

Category: Software tools

Collaborative live-coding with GPU

So, I wanted to combine teaching GPU computing in Python with collaborative notebooks. I got the idea of combining Numba, that I started exploring here, with a notebook that I could use in class with collaborative editing. As I mentioned earlier, I wanted to try out Google Colaboratory with its Jupyter-like notebooks. Google Colaboratory actually offers GPU support in their runtime, so this looked like the perfect match.

Well, so far I have not been able to make it work. It seems that the CUDA toolkit is not installed in the runtime environment from the beginning, so I had to find a way to do that. I have tried two approaches so far:

  1. Use pip to install Numba and then install the CUDA toolkit from NVIDIA’s repository using apt.
  2. Install Anaconda’s Miniconda installer and then use that to install Numba and the CUDA toolkit.

The good news: both approaches seem to work for installing the library/package. However, so far I cannot get any of it to run…

1. pip and apt

So this is what I have tried so far in a Google Colaboratory notebook.

First, installing Numba is straight-forward:

!pip install numba

Then I install CUDA from NVIDIA’s instructions. This works almost out of the box:

!wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/cuda-repo-ubuntu1604_9.1.85-1_amd64.deb
!dpkg -i cuda-repo-ubuntu1604_9.1.85-1_amd64.deb

Then I had to install the dependency dirmngr as well:

!apt install dirmngr

…and then continuing from NVIDIA’s instructions:

!apt-key adv --fetch-keys http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/7fa2af80.pub
!apt-get update
!apt-get install cuda

All of this went fine so far, but then I tried to run a Numba example:

import numpy as np
from numba import vectorize

@vectorize(['float32(float32, float32)'], target='cuda')
def Add(a, b):
    return a + b

# Initialize arrays
N = 100000
A = np.ones(N, dtype=np.float32)
B = np.ones(A.shape, dtype=A.dtype)
C = np.empty_like(A, dtype=A.dtype)

# Add arrays on GPU
C = Add(A, B)

Unfortunately Numba throws an error and complains:

---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/numba/cuda/cudadrv/nvvm.py in __new__(cls)
    110                 try:
--> 111                     inst.driver = open_cudalib('nvvm', ccc=True)
    112                 except OSError as e:

/usr/local/lib/python3.6/dist-packages/numba/cuda/cudadrv/libs.py in open_cudalib(lib, ccc)
     47     if path is None:
---> 48         raise OSError('library %s not found' % lib)
     49     if ccc:

OSError: library nvvm not found

It seems nvvm was supposed to be part of the CUDA toolkit, but it is nowhere to be found…

2. Anaconda

Then I decided to try using Anaconda instead since I know the CUDA toolkit is available here and straight-forward to install using the conda package manager. I started by downloading and installing Miniconda:

!wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
!bash Miniconda3-latest-Linux-x86_64.sh -b

This installed fine. Next, I decided to try installing the necessary packages in a conda environment:

!/content/miniconda3/bin/conda create -y -n cudaenv numba cudatoolkit

This worked as well – hooray! But: I cannot activate the cudaenv environment. Anaconda environments must be activated using the command source activate. But the bash command source is not available in collaboratory, so I am stuck here.

I have also tried to install Numba and CUDA directly in the default environment:

!/content/miniconda3/bin/conda install -y numba cudatoolkit

The installation works in this case as well, but I cannot seem to modify the path in the Colaboratory notebook to use Miniconda’s installed Python instead of the default system Python, so again I am stuck. I have tried prepending the path to Miniconda’s Python binary to both the system PATH variable as well as the PYTHONPATH variable via !export PATH…, but that does not seem to have any effect – I guess because we are already inside a notebook with a running Python interpreter.

Solution ideas are very welcome. I would love to get the Colaboratory notebook running with working Numba CUDA support, so I can use this to demonstrate GPU computing from Python in my course.

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Collaborative live-coding in class

I am in the process of revising a course I teach on scientific computing. This is also where my experiments with GPU computing introduced in my previous post come into play fairly soon.

The course progresses at a slow pace this spring, because I need some time to revise the lectures and experiment with the new content. In addition to replacing and updating some of the content of the course, I am also experimenting with ways to hopefully spice up my teaching a bit. Admitted, I am guilty of usually just “reciting slides” in this course and I think this is far too boring for the students and our time can be spent more efficiently and in a more engaging way.

I am going to introduce elements of flipped learning in the course. As a starting point, I have experimented with the two introductory lectures on Python that are some of the first the students see in the course. Some students have already been introduced to Python before in a previous course of mine. Some other students have never used Python before, but most of the students have prior programming experience. To cater to the latter students, I introduce the students quite briefly to Python and mainly by examples. I assume they understand typical programming concepts already and then it is more or less a question of learning which features exist in Python and how the syntax looks.

Now, as for the flipped learning aspects, my interpretation of this is that instead of just reciting slides to the students as usual, I have just given the slides to the students before the lecture and with the usual, more dense reading material as background literature so they can study this themselves. Then I instead spent the lectures on live-coding examples of the features I thought were important to demonstrate (they do exercises on their own as well). I want to improve on this later in the course or next spring to take feedback from the students beforehand on which areas seemed particularly difficult to them, and then focus on demonstrating those parts.

By live-coding examples, I mean that instead of just showing the students ready-made examples, I type and execute the examples (complete with typos, accidental runtime errors etc.) from scratch in front of the students. I believe this has several didactic benefits: it introduces the students to the example one line at a time without too much code to comprehend all at once. It keeps the pace down, hopefully making it easier to follow as I explain while typing. They get to experience hiccups along the way such as trouble caused by typos and maybe even me forgetting certain details. I hope this makes the development process more comfortable for them, seeing that “even I” can make mistakes, that they are no big deal, and how to constructively fix them along the way.

Now, I did not just want to keep it to live-coding for the students. I wanted to engage the students themselves in the process in a collaborative manner. My vision was this: I want a code-editing window on the projector screen where we can all type in code and execute it on the fly. My first idea for a solution was to use the Jupyter notebook. I like this interface because it allows me to “compartmentalise” code into separate cells containing the individual examples I want to make. The problem is that Jupyter does not really support real-time collaborative editing. Well, it seems it does through jupyterlab-google-drive, but unfortunately that is not going to last: Deprecation of the Google Realtime API. Because of this, I decided it did not want to bother trying to set it up for my course. There are probably other alternatives and I would really appreciate your tips, but for my first try I stumbled on CodeBunk.

CodeBunk is a simple real-time collaborative code editor with an interpreter terminal and a chat window. It supports Python 2.7 and 3.4 (which I need for my course), but also a wide range of other programming languages. When you create a new “bunk”, you can share the link to it with your collaborators who can then enter and you can all edit and execute the code at the same time. It seems it is meant as a tool for interviewing job candidates for programming jobs, and it is probably not meant for more than around five simultaneous collaborators, but I decided to just give it a try for my course (with about 30 students) anyway. It is a commercial product and you will have to pay for using it. Each time you enable a bunk for collaborative editing, you have to spend a session (which allows using the bunk for one or two hours as far as I recall). A new account comes with 5 trial sessions, but after that you will have to pay for more.

I started my live coding experiment from an empty code bunk. I showed the editor on the projector screen and also invited my students to join in from their own computers. I had prepared a “script” of different features that I wanted to demonstrate to the students and started creating examples of those. I invited the students to type in the solution if they knew how to it.

Screenshot-2018-3-6 CodeBunk Numerical Scientific Computing(1)

It worked quite well, but with some drawbacks:

  • First of all, I could only use it for my basic Python lecture as CodeBunk does not offer all of the scientific computing packages that I need for my course (it does have NumPy, SciPy, some sci-kits  – I do not know which, and Pandas, but you cannot use Matplotlib).
  • Handling about 30 students trying to contribute at the same time can be quite a mouthful. I am not sure the service was actually able to let them all interact with it at the same time (I could not keep track of the number of cursors). Most of the students played along nicely most of the time and were good at not all trying to type the same thing at the same time, but at times some of them also got a bit too busy typing silly comments.
  • Running the entire set of examples in just one big script is a bit too unstructured and I had to comment out previous parts as I went along in order not to have to re-run everything for each tiny new bit. This is where a Jupyter notebook with its separate cells would have been nice.

In their feedback, the students gave me the impression that they were overall satisfied with the experience. The complaints were about parts of the material being too basic, the whole session taking a bit too long, and the occasional chaos with bit too much of silly commenting going on. I of course need to adjust my teaching to their feedback, but in the big picture I like the concept and I would like to continue experimenting with it.

Since this experiment a couple of weeks ago, I have discovered Colaboratory from Google. This is based on the Jupyter notebook and also offers real-time collaborative editing. Moreover, it also offers more of the scientific computing packages I usually use, and you can even install additional packages available on PIP, so this will probably be the next experimental tool I introduce in the course.

I would love to hear from you on similar, or different, experiences with teaching scientific computing and coding.

Revisiting GPU Computing

A few years ago (ah well, I guess back in 2011…) I started experimenting with scientific computing on GPUs. The research project I was working in had equipped a couple of quite powerful servers with as many NVIDIA Tesla C1060s as we could cram in there.

Back then it was a lot of work getting algorithms to run on GPUs. First I would have to install the drivers for the GPUs manually which required some detective work to find the right configuration files to edit. Then I would have to install the CUDA toolkit manually. Once that worked, I could start writing code for it. As some may know, I like doing my computing in Python (for example this). Before that, I was an enthusiastic Matlab user, and ArrayFire (back then they were called Accelereyes) offered a very nice solution – Jacket – making it very easy to perform computations on GPU in Matlab. Unfortunately that solution was discontinued.

This was around the time I was starting to use Python instead. As far as I recall, PyCUDA was more or less the only option at the time to access the GPU from Python. This was a bit challenging as you would have to write your own kernels in CUDA C to be plugged into Python. Developing software for the GPU in CUDA C was way less efficient than Python coding. On top of that, things had to be optimised quite specifically for a particular GPU architecture. With each new generation of GPU, details changed quite drastically and your existing code would run inefficiently or not at all on newer GPUs. This made it too challenging to keep up and I decided to focus on more efficient code development in Python (when I say more efficient – I don’t mean in terms of execution time, I mean in terms of development time) and quietly mothballed my GPU computing.

Fast forward to today. A lot has happened since and the newest generations of NVIDIAs GPUs make the good old ones I was experimenting with almost ridiculous. Not least the explosion of research in and applications of deep neural networks has resulted in several high-quality software libraries for computing on GPUs. Most of these software libraries seem to be quite high-level, meaning that you can interface to the GPU and execute various operations on it at a high abstraction level. This includes simply calling functions directly in Python.

The emergence of new, high-level tools for GPU computing in Python (among other) has convinced me that the time is ripe for giving GPU computing another go. So I went and bought a GeForce GTX 1080 Ti for my office workstation to get back in the game with some newer hardware. The Tesla C1060s from back in the day were GPUs aimed for scientific computing and especially later generations of the Tesla line focused on getting good double precision floating point performance. The GeForce card here is a gaming card and relatively less powerful in double precision than single precision, but the newer Tesla cards are much too expensive, so I chose a GeForce card to keep the cost down.

Over the next few weeks I am going to be experimenting with various possibilities for interfacing to the GPU from Python. Luckily, this has become a walk in the park compared my earlier attempts:

  1. First I installed the NVIDIA GPU driver from this PPA (I am running Ubuntu). This seems a quite stable archive that does not resort to installing all sorts of unstable, bleeding-edge packages on your system. For me, it just worked out of the box without any manual configuration file editing. Wonderful!
  2. Since I use Continuum Analytics’ Anaconda distribution for all my Python needs, it is very convenient that it can also install the CUDA toolkit:
    conda install cudatoolkit
    And this also worked out of the box for me.

So, the first library I will be trying out is Numba: https://devblogs.nvidia.com/seven-things-numba/. Stay tuned for experiments and don’t hesitate to let me know of any great packages/toolboxes/libraries you think I should try.

Seriously, where is the source code?

Update: I sent this comment to the program committee of a conference as response to a recent review. It does not matter which conference; it goes for most of the conferences I am familiar with…

Dear program committee of conference X,

How is it that in this day and age you are still letting authors submit papers without disclosing their computational scripts? Most modern papers in our field rely heavily on computational methods and without being able to see the actual implementation it is impossible to assess whether the results are worth anything at all. Without seeing the actual code, “we used CVX” could mean just about anything; for example that the authors might not be solving the optimisation problem they think they are solving. I think it is downright frivolous to think that we can still get away with letting scientific research papers be superficial advertisement for the real scholarship that is tested in the computational code, but hidden away so that no-one has any chance of assessing the actual substance of the results being advertised. Further, asking reviewers to spend our time on it seemingly without considering this borders on being rude.

Magni 1.7.0 Released

A new version of the Magni software package was just released on the 1st of March. The previous release (1.6.0) introduced approximate message passing (AMP) and generalised approximate message passing (GAMP) reconstruction algorithms. This time we are extending the functionality of the GAMP algorithm to include weighted sparse priors. This effectively means that you can model sparse signals with non-identically distributed entries.

As far as I know, this way of modelling sparse signals in GAMP reconstruction are not part of any existing algorithms and will be described in further detail in an upcoming paper.

This new feature in GAMP can be found in the magni.cs.reconstruction.gamp module, more specifically magni.cs.reconstruction.gamp.input_channel.GWSdocumentation.

If you are not familiar with the Magni package and are interested in compressed sensing and/or atomic force microscopy, we invite you to explore the functionality the package offers. It also contains various iterative thresholding reconstruction algorithms, dictionary and measurement matrices for 1D and 2D compressed sensing, various features for combining this with AFM imaging, and mechanisms for validating function input and storing meta-data to aid reproducibility.

The Magni package was designed and developed with a strong focus on well-tested, -validated and -documented code.

The Magni package is a product of the FastAFM research project.

Download

  • The package can be found on GitHub where we continually release new versions: GitHub – release 1.7.0 here.
  • The package documentation can be read here: Magni documentation
  • The package can be installed from PyPI or from Anaconda.

Magni 1.6.0 released

Our newest version of the Magni software package was just released on the 2nd of November. This particular release has some interesting features we (the team behind the Magni package) hope some of you find particularly interesting.

The major new features in this release are approximate message passing (AMP) and generalised approximate message passing (GAMP) estimation algorithms for signal reconstruction. These new algorithms can be found in the magni.cs.reconstruction.amp and magni.cs.reconstruction.gamp modules, respectively. Note that the magni.cs sub-package contains algorithms applicable to compressed sensing (CS) and CS-like reconstruction problems in general – and not just atomic force microscopy (AFM).

If you are not familiar with the Magni package and are interested in compressed sensing and/or atomic force microscopy, we invite you to explore the functionality the package offers. It also contains various iterative thresholding reconstruction algorithms, dictionary and measurement matrices for 1D and 2D compressed sensing, various features for combining this with AFM imaging, and mechanisms for validating function input and storing meta-data to aid reproducibility.

The Magni package was designed and developed with a strong focus on well-tested, -validated and -documented code.

The Magni package is a product of the FastAFM research project.

Download

  • The package can be found on GitHub where we continually release new versions: GitHub – release 1.6.0 here.
  • The package documentation can be read here: Magni documentation
  • The package can be installed from PyPI or from Anaconda.

Thoughts about Scholarly HTML

The company science.ai is working on a draft standard (or what I guess they hope will eventually become a standard) called Scholarly HTML. The purpose of this seems to be to standardise the way scholarly articles are structured as HTML in order to use that as a more semantic alternative to for example PDF which may look nice but does nothing to help understand the structure of the content, probably more the contrary.
They present their proposed standard in this document. They also seem to have formed a community group at the World Wide Web Consortium. It appears this is not a new initiative. There was already a previous project called Scholarly HTML, but science.ai seem to be trying to help take the idea further from there. Martin Fenner wrote a bit of background story behind the original Scholarly HTML.
I read science.ai’s proposal. It seems like a very promising initiative because it would allow scholarly articles across publishers to be understood better by, not least, algorithms for content mining, automated literature search, recommender systems etc. It would be particularly helpful if all publishers had a common standard for marking up articles and HTML seems a good choice since you only need a web browser to display it. This is also another nice feature about it. I tend to read a lot on my mobile phone and tablet and it really is a pain when the content does not fit the screen. This is often the case with PDF which does not reflow too well in the apps I use for viewing. Here HTML would be much better, not being physical page-focused like PDF.
I started looking at this proposal because it seemed like a natural direction to look further in from my crude preliminary experiments in Publishing Mathematics in e-books.
After reading the proposal, a few questions arose:

  1. The way the formatting of references is described, it seems to me as if references can be of type “schema:Book” or “schema:ScholarlyArticle”. Does this mean that they do not consider a need to cite anything but books or scholarly articles? I know that some people hold the IMO very conservative view that the reference list should only refer to peer-reviewed material, but this is too constrained and I certainly think it will be relevant to cite websites, data sets, source code etc. as well. It should all go into the reference list to make it easier to understand what the background material behind a paper is. This calls for a much richer selection of entry types. For example Biblatex’ entry types could serve as inspiration.
  2. The authors and affiliations section is described here. Author entries are described as having:

    property=”schema:author” or property=”schema:contributor” and a typeof=”sa:ContributorRole”

    I wonder if this way of specifying authors/contributors makes it possible to specify more granular roles or multiple roles for each author like for example Open Research Badges?

  3. Under article structure, they list the following types of sections:

    Sections are expected to be typed using the typeof attribute. The following typeof values are currently understood:

    sa:Funding (which has its specific structure)
    sa:Abstract
    sa:MaterialsAndMethods
    sa:Results
    sa:Conclusion
    sa:Acknowledgements
    sa:ReferenceList

    I think there is a need for more types of sections. I for example also see articles containing Introduction, Analysis, and Discussion sections and I am sure there must be more that I have not thought of.

Publishing mathematics in ebooks – part 1

This is the first part of what I hope will be a series of posts on my explorations of how to author maths-heavy writing in ebook format.

I have for quite some time now been annoyed with PDFs on mobile phones and tablets. Although there are some fine PDF viewers avaible, it usually still takes a lot of annoying scrolling to read a scientific paper on my phone or tablet. On the other hand, I have recently read a few novels as ebooks on my phone and my tablet and this has been an entirely different, enjoyable experience. The main difference is that the text in ebooks is re-flowable so as to make it easily adaptable to the screen size and preferred font size. This makes ebooks seem like a promising choice as an alternative to PDF for distributing scientific papers in more screen-friendly format. There is just one hurdle: mathematicsRead the rest of this entry »

Teaching with the IPython Notebook

I have been teaching introductory Python for modelling and simulation and for scientific computing for a couple of years now. I am still somewhat new to Python myself, having “converted” from Matlab a couple of years ago. I find the open approach of using free and open source software instead of expensive proprietary software very motivating and I was easily talked into using it by my colleagues and quickly decided to base my teaching on it as well.
Read the rest of this entry »

Magni: A Python Package for Compressive Sampling and Reconstruction of Atomic Force Microscopy Images

Our new software metapaper Magni: A Python Package for Compressive Sampling and Reconstruction of Atomic Force Microscopy Images has just been published in Journal of Open Research Software. The paper describes our new software package Magni:

Magni is an open source Python package that embraces compressed sensing and Atomic Force Microscopy (AFM) imaging techniques. It provides AFM-specific functionality for undersampling and reconstructing images from AFM equipment and thereby accelerating the acquisition of AFM images. Magni also provides researchers in compressed sensing with a selection of algorithms for reconstructing undersampled general images, and offers a consistent and rigorous way to efficiently evaluate the researchers own developed reconstruction algorithms in terms of phase transitions. The package also serves as a convenient platform for researchers in compressed sensing aiming at obtaining a high degree of reproducibility of their research.

The software itself is on GitHub as well as on Aalborg University’s repository: DOI 10.5278/VBN/MISC/Magni

Go ahead and check it out if you are into compressed sensing or atomic force microscopy. Pull requests welcome if you have ideas.

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