Danny's tech notebook | 丹尼技術手札: 2017

Wednesday, August 30, 2017

[Caffe] Try out Caffe with Python code

This document is just a testing record to try out on Caffe with Python code. I refer to this blog. For using Python, we can easily to access every data flow blob in layers, including diff blob, weight blob and bias blob. It is so convenient for us to understand the change of training phase's weights and what have done in each step.

[Caffe] How to use Caffe to solve the regression problem?

There is a question coming up to my mind recently. How to use Caffe to solve the regression problem? We used to see a bunch of examples related to image recognition with labels and they are classification problem. In my experience, I have done this problem using TensorFlow, not Caffe. But, I think in theory they are both the same. The key point is using EuclideanLossLayer as the final Loss Layer and it's the detail from the official web site:

[Raspberry Pi] Use Wireless and Ethernet together

The following content is my Raspberry Pi 3's setting in /etc/network/interface as follows. In my case, I both use wireless and ethernet device at the same time.

# Include files from /etc/network/interfaces.d:
source-directory /etc/network/interfaces.d

auto lo
iface lo inet loopback

auto wlan0
allow-hotplug wlan0
iface wlan0 inet manual
    Wpa-conf /etc/wpa_supplicant/wpa_supplicant.conf

allow-hotplug eth0
iface eth0 inet static
    address 140.96.29.224
    netmask 255.255.255.0
    up ip route add 100.85.0.0/24 via 140.96.29.254 dev eth0
    up ip route add 140.96.29.0/24 via 140.96.29.254 dev eth0
    up ip route add 140.96.98.0/24 via 140.96.29.254 dev eth0

[Debug] Debugging Python and C++ exposed by boost together

During the studying of Caffe, I was curious about how Caffe provides Python interface and what kind of tool uses for wrapping. Then, the answer is Boost.Python. I think for C++ developer, it is worth time to learn and I will study it sooner. In this post, I want to introduce the debugging skill which I found in this post and I believe these are very useful such as debugging Caffe with Python Layer. Here is the link:
https://stackoverflow.com/questions/38898459/debugging-python-and-c-exposed-by-boost-together

[PCIe] lspci command and the PCIe devices in my server

The following content is about my PCIe devices/drivers and the lspci command results.

$ cd /sys/bus/pci_express/drivers

$ ls -al

drwxr-xr-x 2 root root 0 7月 6 15:33 aer/

drwxr-xr-x 2 root root 0 7月 6 15:33 pciehp/

drwxr-xr-x 2 root root 0 7月 6 15:33 pcie_pme/

[Caffe] Install Caffe and the depended packages

This article is just for me to quickly record the all the steps to install the depended packages for Caffe. So, be careful that it maybe is not good for you to walk through them in your environment. ^_^

# Install CCMAKE

$ sudo apt-get install cmake-curses-gui

[NCCL] Build and run the test of NCCL

NCCL requires at least CUDA 7.0 and Kepler or newer GPUs. Best performance is achieved when all GPUs are located on a common PCIe root complex, but multi-socket configurations are also supported.

Note: NCCL may also work with CUDA 6.5, but this is an untested configuration.

Build & run

To build the library and tests.

$ cd nccl
$ make CUDA_HOME=<cuda install path> test
Test binaries are located in the subdirectories nccl/build/test/{single,mpi}.

$ ~/git/nccl$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:./build/lib
$ ~/git/nccl$ ./build/test/single/all_reduce_test 100000000
# Using devices
# Rank 0 uses device 0 [0x04] GeForce GTX 1080 Ti
# Rank 1 uses device 1 [0x05] GeForce GTX 1080 Ti
# Rank 2 uses device 2 [0x08] GeForce GTX 1080 Ti
# Rank 3 uses device 3 [0x09] GeForce GTX 1080 Ti
# Rank 4 uses device 4 [0x83] GeForce GTX 1080 Ti
# Rank 5 uses device 5 [0x84] GeForce GTX 1080 Ti
# Rank 6 uses device 6 [0x87] GeForce GTX 1080 Ti
# Rank 7 uses device 7 [0x88] GeForce GTX 1080 Ti

# out-of-place in-place
# bytes N type op time algbw busbw res time algbw busbw res
100000000 100000000 char sum 30.244 3.31 5.79 0e+00 29.892 3.35 5.85 0e+00
100000000 100000000 char prod 30.493 3.28 5.74 0e+00 30.524 3.28 5.73 0e+00
100000000 100000000 char max 29.745 3.36 5.88 0e+00 29.877 3.35 5.86 0e+00
100000000 100000000 char min 29.744 3.36 5.88 0e+00 29.868 3.35 5.86 0e+00
100000000 25000000 int sum 29.692 3.37 5.89 0e+00 29.754 3.36 5.88 0e+00
100000000 25000000 int prod 30.733 3.25 5.69 0e+00 30.697 3.26 5.70 0e+00
100000000 25000000 int max 29.871 3.35 5.86 0e+00 29.700 3.37 5.89 0e+00
100000000 25000000 int min 29.809 3.35 5.87 0e+00 29.852 3.35 5.86 0e+00
100000000 50000000 half sum 28.590 3.50 6.12 1e-02 27.545 3.63 6.35 1e-02
100000000 50000000 half prod 27.416 3.65 6.38 1e-03 27.375 3.65 6.39 1e-03
100000000 50000000 half max 30.811 3.25 5.68 0e+00 30.670 3.26 5.71 0e+00
100000000 50000000 half min 30.818 3.24 5.68 0e+00 30.931 3.23 5.66 0e+00
100000000 25000000 float sum 29.719 3.36 5.89 1e-06 29.750 3.36 5.88 1e-06
100000000 25000000 float prod 29.741 3.36 5.88 1e-07 30.029 3.33 5.83 1e-07
100000000 25000000 float max 28.400 3.52 6.16 0e+00 28.400 3.52 6.16 0e+00
100000000 25000000 float min 28.364 3.53 6.17 0e+00 28.434 3.52 6.15 0e+00
100000000 12500000 double sum 33.989 2.94 5.15 0e+00 34.104 2.93 5.13 0e+00
100000000 12500000 double prod 33.895 2.95 5.16 2e-16 33.833 2.96 5.17 2e-16
100000000 12500000 double max 30.228 3.31 5.79 0e+00 30.273 3.30 5.78 0e+00
100000000 12500000 double min 30.324 3.30 5.77 0e+00 30.341 3.30 5.77 0e+00
100000000 12500000 int64 sum 29.914 3.34 5.85 0e+00 30.036 3.33 5.83 0e+00
100000000 12500000 int64 prod 30.975 3.23 5.65 0e+00 31.083 3.22 5.63 0e+00
100000000 12500000 int64 max 29.954 3.34 5.84 0e+00 29.949 3.34 5.84 0e+00
100000000 12500000 int64 min 29.946 3.34 5.84 0e+00 29.952 3.34 5.84 0e+00
100000000 12500000 uint64 sum 29.981 3.34 5.84 0e+00 30.100 3.32 5.81 0e+00
100000000 12500000 uint64 prod 30.911 3.24 5.66 0e+00 30.800 3.25 5.68 0e+00
100000000 12500000 uint64 max 29.890 3.35 5.85 0e+00 29.947 3.34 5.84 0e+00
100000000 12500000 uint64 min 29.929 3.34 5.85 0e+00 29.964 3.34 5.84 0e+00

Out of bounds values : 0 OK
Avg bus bandwidth : 5.81761

[Mpld3] Render Matplotlib chart to web using Mpld3

The following example is about rendering a matplotlib chart on web, which is based on Django framework to build up. I encountered some problems before, such as, not able to see chart on the web page or having a run-time error after reloading the page. But, all the problems are solved.

<< demo/views.py>>

import matplotlib.pyplot as plt
import numpy as np
import mpld3

def plot_test1(request):
context = {}
fig, ax = plt.subplots(subplot_kw=dict(axisbg='#EEEEEE'))
N = 100

"""
Demo about using matplotlib and mpld3 to rendor charts
"""
scatter = ax.scatter(np.random.normal(size=N),
np.random.normal(size=N),
c=np.random.random(size=N),
s=1000 * np.random.random(size=N),
alpha=0.3,
cmap=plt.cm.jet)
ax.grid(color='white', linestyle='solid')

ax.set_title("Scatter Plot (with tooltips!)", size=20)

labels = ['point {0}'.format(i + 1) for i in range(N)]
tooltip = mpld3.plugins.PointLabelTooltip(scatter, labels=labels)
mpld3.plugins.connect(fig, tooltip)
#figure = mpld3.fig_to_html(fig)
figure = json.dumps(mpld3.fig_to_dict(fig))
context.update({ 'figure' : figure })

"""
Demo about using tensorflow to predict the result
"""
num = np.random.randint(100)
prediction = predict_service.predict(num)
context.update({ 'num' : num })
context.update({ 'prediction' : prediction })

return render(request, 'demo/demo.html', context)

<<demo/demo.html>>

So, we can see the result as follows:

[Hadoop] To build a Hadoop environment (a single node cluster)

For the purpose of studying Hadoop, I have to build a testing environment to do. I found some resource links are good enough to build a single node cluster of Hadoop MapReduce as follows. And there are additional changes from my environment that I want to add some comments for my reference.

http://www.thebigdata.cn/Hadoop/15184.html
http://www.powerxing.com/install-hadoop/

Login the user "hadoop"

$ sudo su - hadoop

Go to the location of Hadoop

$ /usr/local/hadoop

Add the variables in ~/.bashrc

export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64 export HADOOP_HOME=/usr/local/hadoop export HADOOP_CONF_DIR=$HADOOP_HOME/etc/hadoop export HADOOP_INSTALL=/usr/local/hadoop export PATH=$PATH:$HADOOP_INSTALL/bin export PATH=$PATH:$HADOOP_INSTALL/sbin export HADOOP_MAPRED_HOME=$HADOOP_INSTALL export HADOOP_COMMON_HOME=$HADOOP_INSTALL export HADOOP_HDFS_HOME=$HADOOP_INSTALL export YARN_HOME=$HADOOP_INSTALL

Modify $JAVA_HOME in etc/hadoop/hadoop-env.sh

export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64

Start dfs and yarn

$ sbin/start-dfs.sh
$ sbin/start-yarn.sh

Finally, we can try the Hadoop MapReduce example as follows:
$ bin/hadoop jar share/hadoop/mapreduce/hadoop-mapreduce-examples-2.7.0.jar grep input output 'dfs[a-z.]+'

[Spark] To install Spark environment based on Hadoop

This document is to record how to install Spark environment based on Hadoop as the previous one. For running Spark in Ubuntu machine, it should install Java first. Using the following command is easily to install Java in Ubuntu machine.

$ sudo apt-get install openjdk-7-jre openjdk-7-jdk
$ dpkg -L openjdk-7-jdk | grep '/bin/javac'
$ /usr/lib/jvm/java-7-openjdk-amd64/bin/javac

So, we can setup the JAVA_HOME environment variable as follows:
$ vim /etc/profile
append this ==> export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64

$ sudo tar -zxf ~/Downloads/spark-1.6.0-bin-without-hadoop.tgz -C /usr/local/
$ cd /usr/local
$ sudo mv ./spark-1.6.0-bin-without-hadoop/ ./spark
$ sudo chown -R hadoop:hadoop ./spark

$ sudo apt-get update
$ sudo apt-get install scala
$ wget http://apache.stu.edu.tw/spark/spark-1.6.0/spark-1.6.0-bin-hadoop2.6.tgz
$ tar xvf spark-1.6.0-bin-hadoop2.6.tgz
$ cd /spark-1.6.0-bin-hadoop2.6/bin
$ ./spark-shell

$ cd /usr/local/spark
$ cp ./conf/spark-env.sh.template ./conf/spark-env.sh
$ vim ./conf/spark-env.sh
append this ==> export SPARK_DIST_CLASSPATH=$(/usr/local/hadoop/bin/hadoop classpath)

[picamera] Solving the problem of video display using Raspberry Pi Camera

When I tried to use Raspberry Pi Camera to display video or image, I encountered a problem that there is no image frame and the GUI showed a black frame on the screen. It took me a while to figure out this issue.
After searching the similar error on the Internet, I found it is related with using picamera library v1.11 and Python 2.7. So I try downgrading to picamera v1.10 and this should resolve the blank/black frame issue:

The linux command is as follows:
$ sudo pip uninstall picamera
$ sudo pip install 'picamera[array]'==1.10

So, it seems there are some issues with the most recent version of picamera that are causing a bunch of problems for Python 2.7 and Python 3 users.

[Kafka] Install and setup Kafka

Kafka is used for building real-time data pipelines and streaming apps. It is horizontally scalable, fault-tolerant, wicked fast, and runs in production in thousands of companies.

Install and setup Kafka
$ sudo useradd kafka -m
$ sudo passwd kafka
$ sudo adduser kafka sudo
$ su - kafka
$ sudo apt-get install zookeeperd

To make sure that it is working, connect to it via Telnet:
$telnet localhost 2181
$ mkdir -p ~/Downloads
$ wget "http://mirror.cc.columbia.edu/pub/software/apache/kafka/0.8.2.1/kafka_2.11-0.8.2.1.tgz" -O ~/Downloads/kafka.tgz
$ mkdir -p ~/kafka && cd ~/kafka
$ tar -xvzf ~/Downloads/kafka.tgz --strip 1
$ vi ~/kafka/config/server.properties

By default, Kafka doesn't allow you to delete topics. To be able to delete topics, add the following line at the end of the file:
⇒ delete.topic.enable = true

Start Kafka
$ nohup ~/kafka/bin/kafka-server-start.sh ~/kafka/config/server.properties > ~/kafka/kafka.log 2>&1 &

Publish the string "Hello, World" to a topic called TutorialTopic by typing in the following:
$ echo "Hello, World" | ~/kafka/bin/kafka-console-producer.sh --broker-list localhost:9092 --topic TutorialTopic
$ ~/kafka/bin/kafka-console-consumer.sh --zookeeper localhost:2181 --topic TutorialTopic --from-beginning

[InfluxDB] Install and setup InfluxDB

Download the source and install

$ wget https://s3.amazonaws.com/influxdb/influxdb_0.12.1-1_amd64.deb
$ sudo dpkg -i influxdb_0.12.1-1_amd64.deb

Edit influxdb.conf file

$ vim /etc/influxdb/influxdb.conf

螢幕快照 2016-04-13 下午2.42.58.png

Restart influxDB

$ sudo service influxdb restart
influxdb process was stopped [ OK ]
Starting the process influxdb [ OK ]
influxdb process was started [ OK ]

$ sudo netstat -naptu | grep LISTEN | grep influxd
tcp6 0 0 :::8083 :::* LISTEN 3558/influxd
tcp6 0 0 :::8086 :::* LISTEN 3558/influxd
tcp6 0 0 :::8088 :::* LISTEN 3558/influxd

Client command tool

$influx
> show databases

Tuesday, May 9, 2017

[OpenGL] Draw 3D and Texture with BMP image using OpenGL Part I

It has been more than half of year not posting any article in my blogger and that makes me a little bit embarrassed. Well, for breaking this situation, I just quickly explain a simple concept about OpenGL coordinate.

Before taking an adventure to OpenGL, we have to know the coordinate in OpenGL first. Please check out the following graph. As we can see, the perspective of z position is pointed to us and it's so different from OpenCV.

If we take a look closer, the following OpenGL code can be explained in the picture below:

glBegin(GL_QUADS) # Start Drawing The Cube

# Front Face (note that the texture's corners have to match the quad's corners)
glTexCoord2f(1.0, 0.0); glVertex3f(-1.0, -1.0, 1.0) # Bottom Left Of The Texture and Quad
glTexCoord2f(1.0, 1.0); glVertex3f( 1.0, -1.0, 1.0) # Bottom Right Of The Texture and Quad
glTexCoord2f(0.0, 1.0); glVertex3f( 1.0, 1.0, 1.0) # Top Right Of The Texture and Quad
glTexCoord2f(0.0, 0.0); glVertex3f(-1.0, 1.0, 1.0) # Top Left Of The Texture and Quad

# Back Face
glTexCoord2f(1.0, 0.0); glVertex3f(-1.0, -1.0, -1.0) # Bottom Right Of The Texture and Quad
glTexCoord2f(1.0, 1.0); glVertex3f(-1.0, 1.0, -1.0) # Top Right Of The Texture and Quad
glTexCoord2f(0.0, 1.0); glVertex3f( 1.0, 1.0, -1.0) # Top Left Of The Texture and Quad
glTexCoord2f(0.0, 0.0); glVertex3f( 1.0, -1.0, -1.0) # Bottom Left Of The Texture and Quad

# Top Face
glTexCoord2f(0.0, 1.0); glVertex3f(-1.0, 1.0, -1.0) # Top Left Of The Texture and Quad
glTexCoord2f(0.0, 0.0); glVertex3f(-1.0, 1.0, 1.0) # Bottom Left Of The Texture and Quad
glTexCoord2f(1.0, 0.0); glVertex3f( 1.0, 1.0, 1.0) # Bottom Right Of The Texture and Quad
glTexCoord2f(1.0, 1.0); glVertex3f( 1.0, 1.0, -1.0) # Top Right Of The Texture and Quad

# Bottom Face
glTexCoord2f(1.0, 1.0); glVertex3f(-1.0, -1.0, -1.0) # Top Right Of The Texture and Quad
glTexCoord2f(0.0, 1.0); glVertex3f( 1.0, -1.0, -1.0) # Top Left Of The Texture and Quad
glTexCoord2f(0.0, 0.0); glVertex3f( 1.0, -1.0, 1.0) # Bottom Left Of The Texture and Quad
glTexCoord2f(1.0, 0.0); glVertex3f(-1.0, -1.0, 1.0) # Bottom Right Of The Texture and Quad

# Right face
glTexCoord2f(1.0, 0.0); glVertex3f( 1.0, -1.0, -1.0) # Bottom Right Of The Texture and Quad
glTexCoord2f(1.0, 1.0); glVertex3f( 1.0, 1.0, -1.0) # Top Right Of The Texture and Quad
glTexCoord2f(0.0, 1.0); glVertex3f( 1.0, 1.0, 1.0) # Top Left Of The Texture and Quad
glTexCoord2f(0.0, 0.0); glVertex3f( 1.0, -1.0, 1.0) # Bottom Left Of The Texture and Quad

# Left Face
glTexCoord2f(0.0, 0.0); glVertex3f(-1.0, -1.0, -1.0) # Bottom Left Of The Texture and Quad
glTexCoord2f(1.0, 0.0); glVertex3f(-1.0, -1.0, 1.0) # Bottom Right Of The Texture and Quad
glTexCoord2f(1.0, 1.0); glVertex3f(-1.0, 1.0, 1.0) # Top Right Of The Texture and Quad
glTexCoord2f(0.0, 1.0); glVertex3f(-1.0, 1.0, -1.0) # Top Left Of The Texture and Quad

glEnd(); # Done Drawing The Cube

So, right now, if we just look at the first section of the code as follows, it represents the blue quadrilateral for the front face.

And, the texture coordinate represents the direction of the image.

In sum, we can see the result just like this:

Danny's tech notebook | 丹尼技術手札