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Snamuye at 20:23, 28 July 2015

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Snamuye: Created page with "=== Project: Pi Based Cluster === Course: APT 4030 - Parallel Computing About: In this project, we will build a cluster of identical raspberry pi nodes, networked..."

2015-07-28T20:20:52Z

Created page with "=== [[|Project: Pi Based Cluster]] === Course: APT 4030 - Parallel Computing [[|About:]] In this project, we will build a cluster of identical raspberry pi nodes, networked..."

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=== [[Project: Pi Based Cluster (USIU)|Project: Pi Based Cluster]] ===

Course: APT 4030 - Parallel Computing

[[About: (USIU)|About:]]

In this project, we will build a cluster of identical raspberry pi nodes, networked together and running parallel processing software that allows each node in the cluster to share data and computation.

[[Objective(s): (USIU)|Objective(s):]]

Building a cluster computer powered by raspberry Pi that could be used to develop and run parallel and distributed programs. In doing so, the following goals could be achieved.

*Practical understanding of building parallel systems.
*Experiment with different configurations to achieve better performance.
*Familiarity with MPI (Message Passing Interface) API for parallel programming.
*Familiarity with raspberry pi micro computers useful for rapid hardware prototyping.

[[Building the system: (USIU)|Building the system:]]

[[Components: (USIU)|Components:]]

Computer hardware -

Raspberry Pi Model B

Storage - SD cards

Ethernet cables

Power supply

Linux OS

There is an array of different possibilities.

MPI library

MPICH or OpenMPI

Ethernet switch and Router

A switch that we can use without interruption during the lab works.

[[Implementation: (USIU)|Implementation:]]

Ideally the project will be implemented in stages, starting with configuring the first two nodes and then scaling to add all other additional nodes.

[[Resources: (USIU)|Resources:]]

There are many resources that we will use including Raspberry Pi Foundation[https://www.raspberrypi.org/ https://www.raspberrypi.org/]

Prof Simon Cox, Making a Raspberry pi super computer, University of Southampton [http://coen.boisestate.edu/ece/raspberry-pi/ http://coen.boisestate.edu/ece/raspberry-pi/]

[[Configuring the nodes, step by step guide (USIU)|Configuring the nodes, step by step guide]]

[[First, configure the first node (USIU)|First, configure the first node]]

When this is done, its easier to clone as many nodes as wanted.

#Get the OS image raspberrypi.org/download

After many false starts, we were content to just use Rasbian Weezy 5.5

#Get image into a the sdcard

On Linux:

#dd if=/media/yourMachine/Images/2015-05-05-raspbian-wheezy.img of=/dev/sdb bs=512 conv=noerror,sync

#Boot the Pi

Great suspense it anything did not go as planned.

If there is an error with the card or any other thing, nothing will show up on the screen, if the Pi is overwhelmed it will take forever to boot. Rasbian is ideal because it has been tested and has a descent first boot time.

#Configuration on first boot

These configurations can be done later with raspi-config or ideally done on the first boot.

*Expand image to fill card
*Change the password

laxmi

*Change hostname (node1 or nodex)

#Re boot

user: pi (has root priviledges) password: laxmi

Refresh update repo packages and update the software

[[|#sudo apt-get update && sudo apt-get upgrade -y]]

Choose your poison: I prefer having my emacs

[[|#sudo apt-get install emacs]]

(:( you only get version 23, will have to compile to use version 24)

#Refresh and update the softwares, if not done yet.

[[|#sudo apt-get update && sudo apt-get upgrade -y]]

#Get Fortran, (strange but we need it)

[[|#sudo apt-get install gfortran]]

#Before getting Argonne MPICH

Resource:[http://www.mpich.org/documentation/guides/ http://www.mpich.org/documentation/guides/]

The have great resources not just the the MPICH library

[[|#mkdir /home/pi/mpich3 $ cd ~/mpich3]]

#Get MPICH sources from Argonne

#wget [http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz]

Resource: [http://www.mpich.org/downloads http://www.mpich.org/downloads] - Get latest stable

#Unpack them.

#tar xfz mpichXXX.tar.gz

#Planning a clean place for install

[[|#sudo mkdir /home/rpimpi/]]

#sudo mkdir /home/rpimpi/mpich3-install

#Make a build directory, and go to the build

[[|#mkdir /home/pi/mpich_build $ cd /home/pi/mpich_build]]

#Configure the build

This will take a while, you can get the cards ready, you can play while the configurations takes place.

[[|#sudo /home/pi/mpich3/mpichXXX/configure -prefix=/home/rpimpi/mpich3- install]]

#Make

What ever it took the last, you can +1

[[|# ]]sudo make

#Install the files

It can take a bit of time, but not any way close to the last two stages.

[[$ sudo make install (USIU)|$ sudo make install]]

#Add the place that you put the install to your PATH

[[$ export PATH=$PATH:/home/rpimpi/mpich3-mstall/bin (USIU)|$ export PATH=$PATH:/home/rpimpi/mpich3-mstall/bin]]

#Or Note to permanently put this on the PATH you will need to edit .profile

[[$emacs -/.profile (USIU)|$emacs -/.profile]]

and add lines below:

# Add MPI to path (This is just a comment for later) PATH="$PATH:/home/rpimpi/mpich3-install/bin"

#Verify if the install were succesful

[[|#which mpicc]]

/home/rpimpi/mpich3-install/mpicc $ which mpiexec

#Go /home and set a place for your first test

[[|#cd ~]]

#mkdir mpi_first_test $ cd mpi_first_test

#Now testing MPI on single node

[[|#mpiexec -f machinefile -n <number> hostname]]

where machine file contains a list of IP addresses (in this case just one) for the machines

#How this supposed to be done
<ol style="list-style-type:lower-alpha;">
<li>Get your IP address</li>
</ol>

[[|#ifconfig]]
<ol style="list-style-type:lower-alpha;">
<li>Put this into a single file called machinefile</li>
</ol>

[[|#emacs machinefile]]
<ol style="list-style-type:lower-alpha;">
<li>Add this line:</li>
</ol>

192.168.1.161 [or the ip is ... ]

#Now test if the machinefile

[[|# mpiexec -f machinefile ~n 1 hostname]]

Output should be: node1 ('hostname')

#Little C code using MPI on Pi to calculate Pi

Don't worry, we shall not write the c code our selves, but MPICH has some example codes we can run.

[[|# cd /home/pi/mpi_fist_test]]

[[|# mpiexec -f machinefile -n 2 /home/pi/mpich3/examples/cpi]]

Output is should be

Process 0 of 2 is on raspberrypi Process 1 of 2 is on raspberrypi

pi is approximately 3.141 5926544231318, Error is 0.0000000008333387

#[[Celebrate! (USIU)|Celebrate!]]

This calls for a celebration! (Seriously!)

Order a bottle from Bourgogne and celebrate (and clone the node).

#[[Shut down (USIU)|Shut down]]

[[|# sudo poweroff]]

@@ Line 1: / Line 1: @@
 === Project: Pi Based Cluster ===
-<u>Course: APT 4030 - Parallel Computing</u>
+''Course: DST4030 - Parallel Computing''
 '''About:'''
@@ Line 103: / Line 113: @@
 <span style="font-family:courier new,courier,monospace">#sudo apt-get update && sudo apt-get upgrade -y</span>
-<span style="font-family:courier new,courier,monospace"></span>
@@ Line 111: / Line 121: @@
 <span style="font-family:courier new,courier,monospace">#sudo apt-get install gfortran</span>
-<span style="font-family:courier new,courier,monospace"></span>
@@ Line 137: / Line 147: @@
 <span style="font-family:courier new,courier,monospace">#tar xfz mpichXXX.tar.gz</span>
-<span style="font-family:courier new,courier,monospace"></span>
@@ Line 147: / Line 157: @@
 <span style="font-family:courier new,courier,monospace">#sudo mkdir /home/rpimpi/mpich3-install</span>
-<span style="font-family:courier new,courier,monospace"></span>
@@ Line 155: / Line 165: @@
 <span style="font-family:courier new,courier,monospace">#mkdir /home/pi/mpich_build $ cd /home/pi/mpich_build</span>
-<span style="font-family:courier new,courier,monospace"></span>
@@ Line 165: / Line 175: @@
 <span style="font-family:courier new,courier,monospace">#sudo /home/pi/mpich3/mpichXXX/configure -prefix=/home/rpimpi/mpich3- install</span>
-<span style="font-family:courier new,courier,monospace"></span>
@@ Line 175: / Line 185: @@
 <span style="font-family:courier new,courier,monospace">#sudo make</span>
-<span style="font-family:courier new,courier,monospace"></span>
@@ Line 185: / Line 195: @@
 <span style="font-family:courier new,courier,monospace">#sudo make install</span>
-<span style="font-family:courier new,courier,monospace"></span>

@@ Line 62: / Line 62: @@
 <span style="font-family:courier new,courier,monospace">#dd if=/media/yourMachine/Images/2015-05-05-raspbian-wheezy.img of=/dev/sdb bs=512 conv=noerror,sync</span>
-<span style="font-family:courier new,courier,monospace"></span>
 '''3. Boot the Pi'''
@@ Line 104: / Line 104: @@
 <span style="font-family:courier new,courier,monospace"></span>
 '''7. Get Fortran, (strange but we need it)'''
@@ Line 110: / Line 112: @@
 <span style="font-family:courier new,courier,monospace"></span>
 '''8. Before getting Argonne MPICH'''
@@ Line 119: / Line 123: @@
 <span style="font-family:courier new,courier,monospace">#mkdir /home/pi/mpich3 $ cd ~/mpich3</span>
-<span style="font-family:courier new,courier,monospace"></span>
 '''9. Get MPICH sources from Argonne'''
@@ Line 134: / Line 138: @@
 <span style="font-family:courier new,courier,monospace"></span>
 '''11. Planning a clean place for install'''
@@ Line 142: / Line 148: @@
 <span style="font-family:courier new,courier,monospace"></span>
 '''12. Make a build directory, and go to the build'''
@@ Line 148: / Line 156: @@
 <span style="font-family:courier new,courier,monospace"></span>
 '''13. Configure the build'''
@@ Line 156: / Line 166: @@
 <span style="font-family:courier new,courier,monospace"></span>
 '''14. Make'''
@@ Line 164: / Line 176: @@
 <span style="font-family:courier new,courier,monospace"></span>
 '''15. Install the files'''
@@ Line 172: / Line 186: @@
 <span style="font-family:courier new,courier,monospace"></span>
 '''16. Add the place that you put the install to your PATH'''
@@ Line 177: / Line 193: @@
 <span style="font-family:courier new,courier,monospace">#export PATH=$PATH:/home/rpimpi/mpich3-mstall/bin</span>
-<span style="font-family:courier new,courier,monospace"></span>
 '''17. Or Note to permanently put this on the PATH you will need to edit .profile'''
@@ Line 187: / Line 203: @@
 <span style="font-family:courier new,courier,monospace">#Add MPI to path (This is just a comment for later) PATH="$PATH:/home/rpimpi/mpich3-install/bin"</span>
-<span style="font-family:courier new,courier,monospace"></span>
 '''18. Verify if the install were succesful'''
@@ Line 193: / Line 209: @@
 <span style="font-family:courier new,courier,monospace">#which mpicc /home/rpimpi/mpich3-install/mpicc $ which mpiexec</span>
-<span style="font-family:courier new,courier,monospace"></span>
 '''19. Go /home and set a place for your first test'''
@@ Line 201: / Line 217: @@
 <span style="font-family:courier new,courier,monospace">#mkdir mpi_first_test $ cd mpi_first_test</span>
-<span style="font-family:courier new,courier,monospace"></span>
 '''20. Now testing MPI on single node'''
@@ Line 225: / Line 241: @@
 <span style="font-family:courier new,courier,monospace">192.168.1.161 [or the ip is ... ]</span>
-<span style="font-family:courier new,courier,monospace"></span>
 '''22. Now test if the machinefile'''

@@ Line 1: / Line 1: @@
-=== [[Project: Pi Based Cluster (USIU)|Project: Pi Based Cluster]] ===
+=== [[Raspberry Pi Min-Grant project:Pi Based Cluster (USIU)|Project: Pi Based Cluster]] ===
 Course: APT 4030 - Parallel Computing
@@ Line 22: / Line 22: @@
 Computer hardware -
-Raspberry Pi Model B
+*Raspberry Pi Model B
+*Storage - SD cards
-Storage - SD cards
+*Ethernet cables
+*Power supply
-Ethernet cables
+*Linux OS (Wheezy)
+*There is an array of different possibilities.
-Power supply
+*MPI library
+*MPICH or OpenMPI
-Linux OS
+*Ethernet switch and Router
+*A switch that we can use without interruption during the lab works.
 [[Implementation: (USIU)|Implementation:]]
@@ Line 91: / Line 82: @@
 Refresh update repo packages and update the software
-[[|#sudo apt-get update && sudo apt-get upgrade -y]]
+&#x5B;&#x5B;|#sudo apt-get update && sudo apt-get upgrade -y&#x5D;&#x5D;
 Choose your poison: I prefer having my emacs
-[[|#sudo apt-get install emacs]]
+&#x5B;&#x5B;|#sudo apt-get install emacs&#x5D;&#x5D;
 (:( you only get version 23, will have to compile to use version 24)
@@ Line 101: / Line 92: @@
 #Refresh and update the softwares, if not done yet.
-[[|#sudo apt-get update && sudo apt-get upgrade -y]]
+&#x5B;&#x5B;|#sudo apt-get update && sudo apt-get upgrade -y&#x5D;&#x5D;
 #Get Fortran, (strange but we need it)
-[[|#sudo apt-get install gfortran]]
+&#x5B;&#x5B;|#sudo apt-get install gfortran&#x5D;&#x5D;
 #Before getting Argonne MPICH
@@ Line 113: / Line 104: @@
 The have great resources not just the the MPICH library
-[[|#mkdir /home/pi/mpich3 $ cd ~/mpich3]]
+&#x5B;&#x5B;|#mkdir /home/pi/mpich3 $ cd ~/mpich3&#x5D;&#x5D;
 #Get MPICH sources from Argonne
@@ Line 127: / Line 118: @@
 #Planning a clean place for install
-[[|#sudo mkdir /home/rpimpi/]]
+&#x5B;&#x5B;|#sudo mkdir /home/rpimpi/&#x5D;&#x5D;
 #sudo mkdir /home/rpimpi/mpich3-install
@@ Line 133: / Line 124: @@
 #Make a build directory, and go to the build
-[[|#mkdir /home/pi/mpich_build $ cd /home/pi/mpich_build]]
+&#x5B;&#x5B;|#mkdir /home/pi/mpich_build $ cd /home/pi/mpich_build&#x5D;&#x5D;
 #Configure the build
@@ Line 139: / Line 130: @@
 This will take a while, you can get the cards ready, you can play while the configurations takes place.
-[[|#sudo /home/pi/mpich3/mpichXXX/configure -prefix=/home/rpimpi/mpich3- install]]
+&#x5B;&#x5B;|#sudo /home/pi/mpich3/mpichXXX/configure -prefix=/home/rpimpi/mpich3- install&#x5D;&#x5D;
 #Make
@@ Line 145: / Line 136: @@
 What ever it took the last, you can +1
-[[|# ]]sudo make
+&#x5B;&#x5B;|# &#x5D;&#x5D;sudo make
 #Install the files
@@ Line 163: / Line 154: @@
 and add lines below:
-# Add MPI to path (This is just a comment for later) PATH="$PATH:/home/rpimpi/mpich3-install/bin"
+#Add MPI to path (This is just a comment for later) PATH="$PATH:/home/rpimpi/mpich3-install/bin"
 #Verify if the install were succesful
-[[|#which mpicc]]
+&#x5B;&#x5B;|#which mpicc&#x5D;&#x5D;
 /home/rpimpi/mpich3-install/mpicc $ which mpiexec
@@ Line 173: / Line 164: @@
 #Go /home and set a place for your first test
-[[|#cd ~]]
+&#x5B;&#x5B;|#cd ~&#x5D;&#x5D;
 #mkdir mpi_first_test $ cd mpi_first_test
@@ Line 179: / Line 170: @@
 #Now testing MPI on single node
-[[|#mpiexec -f machinefile -n <number> hostname]]
+&#x5B;&#x5B;|#mpiexec -f machinefile -n &lt;number&gt; hostname&#x5D;&#x5D;
 where machine file contains a list of IP addresses (in this case just one) for the machines
@@ Line 188: / Line 179: @@
 </ol>
-[[|#ifconfig]]
+&#x5B;&#x5B;|#ifconfig&#x5D;&#x5D;
 <ol style="list-style-type:lower-alpha;">
 <li>Put this into a single file called machinefile</li>
 </ol>
-[[|#emacs machinefile]]
+&#x5B;&#x5B;|#emacs machinefile&#x5D;&#x5D;
 <ol style="list-style-type:lower-alpha;">
 <li>Add this line:</li>
@@ Line 202: / Line 193: @@
 #Now test if the machinefile
-[[|# mpiexec -f machinefile ~n 1 hostname]]
+&#x5B;&#x5B;|# mpiexec -f machinefile ~n 1 hostname&#x5D;&#x5D;
 Output should be: node1 ('hostname')
@@ Line 210: / Line 201: @@
 Don't worry, we shall not write the c code our selves, but MPICH has some example codes we can run.
-[[|# cd /home/pi/mpi_fist_test]]
+&#x5B;&#x5B;|# cd /home/pi/mpi_fist_test&#x5D;&#x5D;
-[[|# mpiexec -f machinefile -n 2 /home/pi/mpich3/examples/cpi]]
+&#x5B;&#x5B;|# mpiexec -f machinefile -n 2 /home/pi/mpich3/examples/cpi&#x5D;&#x5D;
 Output is should be
@@ Line 228: / Line 219: @@
 #[[Shut down (USIU)|Shut down]]
-[[|# sudo poweroff]]
+&#x5B;&#x5B;|# sudo poweroff&#x5D;&#x5D;