Mendeley crashes on Ubuntu laptop with NVIDIA GPU

On a Ubuntu laptop, with a NVIDIA GPU, when trying to open Mendeley, you get this rather unhelpful error:

The application Mendeley Desktop has closed unexpectedly.

I’m sure there are many causes for this error, but one unexpected reason you might get this error is related to your graphics card.

If you have a NVIDIA GPU on your laptop, try to switch to your Intel graphics card instead of NVIDIA..

To switch to your Intel graphics card, open your terminal and type:

sudo prime-select intel

Then restart Mendeley. Like magic and deep learning, it just seems to work.

(if you need to switch back to your NVIDIA card, just type sudo prime-select nvidia)

TensorFlow – failed call to cuInit: CUDA_ERROR_UNKNOWN

Scenario: You’re trying to get your GPU to work in TensorFlow on a Ubuntu Laptop. You’ve already installed Tensorflow, Cuda, and Nvidia drivers.

You run python and import TensorFlow:

import tensorflow as tf

And you see encouraging messages like: "successfully opened CUDA library locally"

But in Python, when you run,


You get this cryptic error:

failed call to cuInit: CUDA_ERROR_UNKNOWN

Here’s how to fix this.
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How to normalize vectors to unit norm in Python

There are so many ways to normalize vectors… A common preprocessing step in machine learning is to normalize a vector before passing the vector into some machine learning algorithm e.g., before training a support vector machine (SVM).

One way to normalize the vector is to apply l2-normalization to scale the vector to have a unit norm. “Unit norm” essentially means that if we squared each element in the vector, and summed them, it would equal 1.

(note this normalization is also often referred to as, unit norm or a vector of length 1 or a unit vector)

So given a matrix X, where the rows represent samples and the columns represent features of the sample, you can apply l2-normalization to normalize each row to a unit norm. This can be done easily in Python using sklearn.

Here’s how to l2-normalize vectors to a unit vector in Python

import numpy as np
from sklearn import preprocessing
# Two samples, with 3 dimensions.
# The 2 rows indicate 2 samples, 
# and the 3 columns indicate 3 features for each sample.
X = np.asarray([[-1,0,1],
                [0,1,2]], dtype=np.float) # Float is needed.
# Before-normalization.
print X
# Output,
# [[-1.  0.  1.]
#  [ 0.  1.  2.]]
# l2-normalize the samples (rows). 
X_normalized = preprocessing.normalize(X, norm='l2')
# After normalization.
print X_normalized
# Output,
# [[-0.70710678  0.          0.70710678]
#  [ 0.          0.4472136   0.89442719]]

Now what did this do?
Continue reading “How to normalize vectors to unit norm in Python”

How to upload sitemap.xml to google app engine

Ah the world wide web… the old www. So many factors to consider when developing web applications, especially if you’re used to developing in a relatively simple research environment.

One thing you will think about is how to get Google to include your page in it’s searchers (i.e., get indexed). To do this, we’ll submit a sitemap to Google. Basically a sitemap lists the links that you want Google to start indexing (so other people can find it when they search the web).

If you’re using WordPress, this is pretty simple, and you can just download a plugin and skip to the last step below (step 6).

However, if you’re using Google App Engine to run your site, then you need to do a few more steps. So here’s instructions for how to do this.
Continue reading “How to upload sitemap.xml to google app engine”

ubuntu – black screen on ubuntu laptop after installing nvidia drivers

I’m running Ubuntu on my Lenovo Y50 laptop, with a Nvidia GPU. And every time I do an update (or restart it?), I see the Ubuntu logo, hear the chime to log in, and then see a blank black screen, or a small white dot in the upper corner.

Other times, after a reboot, I get to the login screen, enter my username and password, then everything flickers violently, and it loops back to asks me to enter in my info again.

Today this post is not about how to permanently fix this (although that would be nice), but rather how to get your GUI back (until you update/restart your machine again).

It seems that on some laptops, the Nvidia drivers and Ubuntu do not always nicely play together. Why? I am not sure.

But anyways, here’s how to get fix your laptop when Ubuntu has a black screen on login (assuming your problem is related to the Nvidia drivers).
Continue reading “ubuntu – black screen on ubuntu laptop after installing nvidia drivers”

Using numpy on google app engine with the anaconda python distribution

– you are using the Google App Engine (GAE) development server with Python
– you installed the Anaconda Python distribution
– you want to use the Numpy library with GAE

On Ubuntu and on Mac (but not Windows for some reason), you get this error when trying to deploy:
google app engine ImportError: No module named _ctypes

The tldr; solution
Create an Anaconda environment using numpy 1.6 and python 2.7:

conda create -n np16py27 anaconda numpy=1.6 python=2.7

Load this specific environment from the command line:

source activate np16py27

Run your GAE dev server: my_gae_project

That’s it! You can read more details below if you are interested.
Continue reading “Using numpy on google app engine with the anaconda python distribution”

how to compute true/false positives and true/false negatives in python for binary classification problems

Here’s how to compute true positives, false positives, true negatives, and false negatives in Python using the Numpy library.

Note that we are assuming a binary classification problem here. That is a value of 1 indicates a positive class, and a value of 0 indicates a negative class. For multi-class problems, this doesn’t really hold.

Continue reading “how to compute true/false positives and true/false negatives in python for binary classification problems”

How to debug a Jupyter/iPython notebook

Here’s how to debug your code when using a Jupyter/iPython notebook.

Use Tracer()(). Here’s an example using a simple function (based on this lucid explanation).

def test_debug(y):
    x = 10
    # One-liner to start the debugger here.
    from IPython.core.debugger import Tracer; Tracer()() 
    x = x + y 	 
    for i in range(10):
        x = x+i
    return x

When the debugger reaches the Tracer()() line, a small line to type in commands will appear under your cell.

Simply type in the variable names to check the values or run other commands. Below I’ve listed some practical Python PBD commands. More can be found here.
Continue reading “How to debug a Jupyter/iPython notebook”

gae python – importerror: no module named webapp2

– Google app engine with Python on Ubuntu
– Running the local development server.

If you start getting this error:

"importerror: no module named webapp2"

after running,
$ helloworld/

You might want to go back to an earlier version for local development.

After downloading “

I got errors with import webapp2

Luckily, I had a previous version “”

So I deleted 1.9.37. And used 1.9.34 instead.

Maybe this will work for you.

How to run an IPython/Jupyter Notebook on a remote machine

Here’s how to run an IPython Notebook (now called a Jupyter Notebook) on a remote linux machine without using VNC.

These instructions are expanded on from here,
and it’s worth reading through to get more details.

Let’s assume,
you have two machines:
local_machine that you are physically working on
remote_machine that you want to run code on.

And you want to work in the browser on your local_machine, but have the code execute on the remote_machine.

Continue reading “How to run an IPython/Jupyter Notebook on a remote machine”