Category Archives: linux

Generating Graphs on Server with no UI in Pyhton

So you run the analysis on Linux server because the data is  huge. Now you want to generate a nice graph or plot to see whats going on.

The script

Using the Iris Dataset I want to generate a plot showing the distribution of the flower examples like this:

Iris plot
Iris plot

To reduce features from 4 to 2 I use sklearn’s  truncated singular value decomposition (which also works on sparse matrices):

import matplotlib.pyplot as plt
from sklearn import datasets 
from sklearn.decomposition import TruncatedSVD 

iris = datasets.load_iris() 
X = 
y =  # Labels

# Visualize result using SVD
svd = TruncatedSVD(n_components=2) 
X_reduced = svd.fit_transform(X)

# Initialize scatter plot with x and y axis values
plt.scatter(X_reduced[:, 0], X_reduced[:, 1], c=y, s=25)

When running this script on Windows everything seems fine.

Setting up server

On a Linux server with no graphical interface or UI there are no tools for the server to generate a picture. On a clean server I need to install sklearn and its dependencies as well as mathplotlib. To make this easier I use Anaconda:

bash -b -p $HOME/anaconda
echo 'export PATH="$HOME/anaconda/bin:$PATH"' >> ~/.bashrc

However, running the script now trows an error:

# ImportError: cannot open shared object file: No such file or directory

So I install also these two libs:

# sudo apt-get install -y libsm6 libxrender1

After this running the script trows:

# RuntimeError: Invalid DISPLAY variable

Generate plot

To enable the server to generate the plot I switch to a different ‘backend’. Pyplot enables various backends for different file formats. To generate and save a .png image I use ‘agg’ backend:


With this I can create my plot and save it. As a side note the .show() method will not be executed when the backend is set to ‘agg’.

The full script code can be seen below or on github:

Iris Dataset and Xgboost Simple Tutorial

I had the opportunity to start using xgboost machine learning algorithm, it is fast and shows good results. Here I will be using multiclass prediction with the iris dataset from scikit-learn.

Installing Anaconda and xgboost

In order to work with the data, I need to install various scientific libraries for python. The best way I have found is to use Anaconda. It simply installs all the libs and helps to install new ones. You can download the installer for Windows, but if you want to install it on a Linux server, you can just copy-paste this into the terminal:

bash -b -p $HOME/anaconda
echo 'export PATH="$HOME/anaconda/bin:$PATH"' >> ~/.bashrc

After this, use conda to install pip which you will need for installing xgboost. It is important to install it using Anaconda (in Anaconda’s directory), so that pip installs other libs there as well:

conda install -y pip libgcc

Now, a very important step: install xgboost Python Package dependencies beforehand. I install these ones from experience:

sudo apt-get install -y make g++ build-essential gfortran libatlas-base-dev liblapacke-dev python-dev python-setuptools libsm6 libxrender1

I upgrade my python virtual environment to have no trouble with python versions:

pip install --upgrade virtualenv

And finally I can install xgboost with pip (keep fingers crossed):

pip install xgboost

This command installs the latest xgboost version, but if you want to use a previous one, just specify it with:

pip install xgboost==0.4a30

Now test if everything is has gone well – type python in the terminal and try to import xgboost:

import xgboost as xgb

If you see no errors – perfect.

Xgboost Demo with the Iris Dataset

Here I will use the Iris dataset to show a simple example of how to use Xgboost.

First you load the dataset from sklearn, where X will be the data, y – the class labels:

from sklearn import datasets

iris = datasets.load_iris()
X =
y =

Then you split the data into train and test sets with 80-20% split:

from sklearn.cross_validation import train_test_split

X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)

Next you need to create the Xgboost specific DMatrix data format from the numpy array. Xgboost can work with numpy arrays directly, load data from svmlignt files and other formats. Here is how to work with numpy arrays:

import xgboost as xgb

dtrain = xgb.DMatrix(X_train, label=y_train)
dtest = xgb.DMatrix(X_test, label=y_test)

If you want to use svmlight for less memory consumption, first dump the numpy array into svmlight format and then just pass the filename to DMatrix:

import xgboost as xgb
from sklearn.datasets import dump_svmlight_file

dump_svmlight_file(X_train, y_train, 'dtrain.svm', zero_based=True)
dump_svmlight_file(X_test, y_test, 'dtest.svm', zero_based=True)
dtrain_svm = xgb.DMatrix('dtrain.svm')
dtest_svm = xgb.DMatrix('dtest.svm')

Now for the Xgboost to work you need to set the parameters:

param = {
    'max_depth': 3,  # the maximum depth of each tree
    'eta': 0.3,  # the training step for each iteration
    'silent': 1,  # logging mode - quiet
    'objective': 'multi:softprob',  # error evaluation for multiclass training
    'num_class': 3}  # the number of classes that exist in this datset
num_round = 20  # the number of training iterations

Different datasets perform better with different parameters. The result can be really low with one set of params and really good with others. You can look at this Kaggle script how to search for the best ones. Generally try with eta 0.1, 0.2, 0.3, max_depth in range of 2 to 10 and num_round around few hundred.


Finally the training can begin. You just type:

bst = xgb.train(param, dtrain, num_round)

To see how the model looks you can also dump it in human readable form:


And it looks something like this (f0, f1, f2 are features):

0:[f2<2.45] yes=1,no=2,missing=1
0:[f2<2.45] yes=1,no=2,missing=1
    2:[f3<1.75] yes=3,no=4,missing=3
        3:[f2<4.95] yes=5,no=6,missing=5
        4:[f2<4.85] yes=7,no=8,missing=7

You can see that each tree is no deeper than 3 levels as set in the params.

Use the model to predict classes for the test set:

preds = bst.predict(dtest)

But the predictions look something like this:

[[ 0.00563804 0.97755206 0.01680986]
 [ 0.98254657 0.01395847 0.00349498]
 [ 0.0036375 0.00615226 0.99021029]
 [ 0.00564738 0.97917044 0.0151822 ]
 [ 0.00540075 0.93640935 0.0581899 ]

Here each column represents class number 0, 1, or 2. For each line you need to select that column where the probability is the highest:

import numpy as np
best_preds = np.asarray([np.argmax(line) for line in preds])

Now you get a nice list with predicted classes:

[1, 0, 2, 1, 1, ...]

Determine the precision of this prediction:

from sklearn.metrics import precision_score

print precision_score(y_test, best_preds, average='macro')
# >> 1.0

Perfect! Now save the model for later use:

 from sklearn.externals import joblib

joblib.dump(bst, 'bst_model.pkl', compress=True)
# bst = joblib.load('bst_model.pkl') # load it later

Now you have a working model saved for later use, and ready for more prediction.

See the full code on github or  below: