Ruby/Sinatra server with Neo4j DB on pcDuino

The original post can be found at: https://github.com/cjdaly/napkin/wiki/Server-on-pcduino

Hardware setup

The image below shows my pcDuino hardware setup. Some notes:

• USB power (center left) is connected to 5V, 2 Amp power adapter.
• Ethernet (lower left) connection to LAN.
• FTDI basic 3.3V, connect RXI, TXO and GND to the pcduino debug port (lower right) at 115200 baud (8/1/N). Use this to watch boot process and as a root shell.

Ubuntu initial setup

Used PhoenixCard to install this 2013-1126 kernel and then installed the matchingUbuntu image into the NAND flash as described in the pcDuino documentation.

The console cable connection provides a root shell. The commands below assume the root user is running them. If a non-root user is doing the setup, prepend sudo and otherwise adjust as necessary.

Micro SD card setup notes

• Insert (new) SD card after boot sequence complete.
• Beware of data loss!
  • Use fdisk /dev/mmcblk0 to edit partitions of SD card.
  • Delete existing partitions; add new primary partition (defaults); write; quit.
  • Format the new partition with mkfs.ext4 /dev/mmcblk0p1.
• Edit the /etc/fstab file and add a line:
  • /dev/mmcblk0p1 /media/sd ext4 rw,nosuid,nodev 0 0
• Reboot with sudo shutdown -r now.
  • Do ls -l /media/sd to verify SD card is now mounted in expected place.
  • Use chmod ugo+w /media/sd to allow normal users to create files and directories on the SD card.

Package installation

Run the following commands to install components needed by the Napkin server (some of these may already be present):

<code>apt-get update
apt-get install -y ssh git lsof
</code>

These next 2 dependencies are needed by the software floating point variant of the Java runtime (more on this in the Java setup section below):

<code>apt-get install -y libc6-armel libsfgcc1
</code>

Disable unnecessary services

Edit /etc/rc.local and comment out the lines containing enable_otg, check_factory,dhcpd.

System configuration

To set the system timezone:

<code>dpkg-reconfigure tzdata
</code>

Also need to increase open files limit (the value reported by running: ulimit -n). Edit /etc/security/limits.conf and add lines like this (replace ubuntu below with the userid you will use to run the Napkin server, if different):

<code>ubuntu hard nofile 40000
ubuntu soft nofile 40000
</code>

You can set a password for the ubuntu user account like this:

<code>passwd ubuntu
</code>

Reboot the system after editing the limits.conf file for the changes to take effect:

<code>shutdown -r now
</code>

Login with ssh

For the rest of the configuration, login as the default ubuntu user, or other non-root user. Use ifconfig in console/root shell to determine DHCP assigned IP address.

Setup Java

I have tried both the hardware float and software float Oracle Java 7 JRE packages. With the hflt package, I am stuck on https://github.com/cjdaly/napkin/issues/3 . The sfltpackage seems to work as long as the libc6-armel and libsfgcc1 have been installed with apt-get (see above).

From the Oracle embedded downloads page, download the Java 7 for ARM, server, headless, software floating point download, ejre-7u45-fcs-b15-linux-arm-vfp-sflt-server_headless-26_sep_2013.gz on a separate system (download from web browser) and use sftp (Linux) or WinSCP (Windows) to copy it to the pcDuino.

On the pcDuino:

<code>cd ~
mkdir java
cd java
mkdir sflt
cd sflt
</code>

Use the sftp client to copy the Java download to the directory just created. Then extract the download:

<code>tar xvf ejre-7u45-fcs-b15-linux-arm-vfp-sflt-server_headless-26_sep_2013.gz
</code>

Setup Neo4J

<code>cd ~
mkdir neo4j
cd neo4j
wget -O neo4j-community-2.0.0.tgz 'http://download.neo4j.org/artifact?edition=community&amp;version=2.0.0&amp;distribution=tarball'
tar xvf neo4j-community-2.0.0.tgz
cd neo4j-community-2.0.0/conf
</code>

Edit the neo4j-server.properties file and change the database location property value to use storage on the SD card:

<code>org.neo4j.server.database.location=/media/sd/napkin-neo4j-db
</code>

Edit the neo4j-wrapper.conf file, uncomment and set values for the properties below:

<code>wrapper.java.initmemory=128
wrapper.java.maxmemory=128
</code>

Also, add this line to the neo4j-wrapper.conf file:

<code>wrapper.java.additional=-XX:MaxPermSize=48M
</code>

Now edit the neo4j.properties file and uncomment and set these values to constrain usage of memory mapped IO:

<code>neostore.nodestore.db.mapped_memory=0M
neostore.relationshipstore.db.mapped_memory=0M
neostore.propertystore.db.mapped_memory=0M
neostore.propertystore.db.strings.mapped_memory=0M
neostore.propertystore.db.arrays.mapped_memory=0M
</code>

See Neo4j issue 1384 for more details on how these configuration settings were determined.

Setup JRuby (part 1)

<code>cd ~
mkdir jruby
cd jruby
wget -O jruby-bin-1.7.9.tar.gz 'http://jruby.org.s3.amazonaws.com/downloads/1.7.9/jruby-bin-1.7.9.tar.gz'
tar xvf jruby-bin-1.7.9.tar.gz
</code>

Clone Napkin

Next, clone the napkin code from github:

<code>cd ~
git clone https://github.com/cjdaly/napkin.git
</code>

Now add java, neo4j and jruby to the path, and confirm each one gives a reasonable version/status message.

<code>source ~/napkin/server/sinatra/server-setup.sh
</code>

Setup JRuby (part 2)

Now install gems used by Napkin:

<code>gem install --no-rdoc --no-ri rest-client sinatra json kramdown
</code>

Typical startup

<code>cd ~/napkin/server/sinatra
source server-setup.sh
./napkin.sh -start systems/pcduino1
tail -f napkin.log
</code>

Typical shutdown

<code>./napkin.sh -status
./napkin.sh -stop
</code>

.Net Gadgeteer serial sidekick

The pcduino1 Napkin system configuration is a pcDuino v1 model which is powering and talking to (via /dev/ttyS1 UART) the Fez Cerberus .Net Gadgeteer system originally known as cerb2.

Fez Cerberus hardware

• socket 1: empty
• socket 2: Barometer
• socket 3: Button
• socket 4: GasSense
• socket 5: LCD 7
• socket 6: Breakout Module connected to pcDuino Arduino-ish RX, TX and GND pins per Gadgeteer U socket documentation
• socket 7: 2×16 LCD
• socket 8: USB client SP (power)

Serial port setup

Some black magic is involved in configuring the Arduino-ish RX and TX pins to work as the serial port /dev/ttyS1. I had the best success with the setuart2.c provided bybgreat in this forum post. I compiled this with gcc -o setuart2 setuart2.c. Currently need to run setuart2 on as root after each reboot to enable the serial port. Use cat /dev/ttyS1 to confirm Gadgeteer is periodically spewing out sensor data.

Here is a view from the back of the enclosure: