Cortex

Cortex is a cluster of 6 servers used by VisLab for development purposes (the other cluster, iCubBrain, is used for demos).

An older version of this article can be found at Cortex/Archive.

Specifications and setup

The Cortex computation rack actually contains 7 machines:

• 1 server that manages startup, shutdown and the file system of the clients;
• 6 clients (named cortex1...cortex6) that run user processes.

All clients numbered 1 to 5 mount the same file system. Therefore, performing changes in the file system of cortex[1-5] will reflect to all other four clients. Beware, though, that because of the way the file systems are mounted, there is some caching going on. This improves disk access performance, but strange phenomena might happen, i.e., after a file is modified and saved on one client, other clients can continue to see the old version of it for some time (probably less than one minute). The client cortex6 is separate for now, because it runs a 64 bit Linux.

Memory: 2GB for each machine (sudo dmidecode --type 17 to see RAM speed and type).

Network setup

Connectivity

Cortex machines are connected to Cortex Switch, that links to VisLab switch with a fiber optic connection of 4Gbit/s.

Cortex nodes

Cortex server and clients have the following IPs and domain names:

• Server: 10.10.1.240, server.visnet
• Client 1: 10.10.1.1, cortex1.visnet
• Client 2: 10.10.1.2, cortex2.visnet
• Client 3: 10.10.1.3, cortex3.visnet
• Client 4: 10.10.1.4, cortex4.visnet
• Client 5: 10.10.1.5, cortex5.visnet
• Client 6: 10.10.1.6, cortex6.visnet

For further details, see the Vislab#Network and the VisLab network articles.

Additional setup

Boot procedure

The clients boot via the network, using the PXE system. Each machine determines its own identity and asks the server for a kernel image and an initial ram disk. Kernel images and initial ram disks are stored on the server in the /tftpboot/ directory. Kernels can be stock kernels, but the initial ram disk must be created in a way that enables booting from the network. This is not as bad as it sounds. It involves invoking the command mkinitramfs.

The server decides which kernel and initramdisk to send to each machine based on the information stored in the two files: /tftpboot/pxelinux.cfg/default(for cortexes 1-5) and /tftpboot/pxelinux.cfg/01-00-19-d1-9e-e9-53 (for cortex6).

The roots and the homes of the users are also stored on the server machine, so they are mounted by each client at boot time.

Mounting of root directory

We are not sure which mechanism mounts the root filesystem, exactly. Here is the relevant line from /etc/fstab:

 # <file system> <mount point>   <type>  <options>       <dump>  <pass>
 /dev/nfs        /               nfs     defaults        1       1

Mounting of home directory

The home directory is mounted via the Upstart system a few seconds after booting. When rebooting the system, it is possible to login while /home is still not mounted. In that case, log out and log in again, in order for your environment variables to be set correctly.

In November 2010, we created a file called /etc/init/mountHome-net.conf containing:

 description     "Mount network filesystems"
 start on started networking or runlevel 2
 exec /usr/local/bin/mountHome.sh

and /usr/local/bin/mountHome.sh containing:

 MOUNTED=$(mount | grep home)
 while [ -z "$MOUNTED" ]
 do
       su icub -c 'mount /home' &> /var/tmp/mountHomeUpstartOut.txt
       MOUNTED=$(mount | grep home)
       echo $MOUNTED
       sleep 1
 done
 ls /home > /var/tmp/mountHomeUpstartLs.txt
 runlevel > /var/tmp/mountHomeUpstartRunlevel.txt

After a successful mount, we should see something like

 $ mount | grep home
 10.10.1.240:/nfsroot.home on /home type nfs (rw,user=icub,addr=10.10.1.240)

If /home is wrongly mounted with the noexec flag, users won't be able to execute binaries located inside it.

Server machine

The server has:

• a boot folder for the clients at /tftpboot/pxelinux.cfg. It contains the files:
  • default - default boot file;
  • <mac_address> - specific for a machine with the given mac address.
• startup scripts for each machine at /nfsroot/app

Client machines

The clients have:

• A superuser account (compurack) to administer system-wide settings (configurations, libraries, etc.)
• Normal user accounts. By default, the login script runs the contents of file $HOME/.bash_env, where users can set their environment variables, e.g., export ICUB_ROOT=$HOME/iCub. This works for both interactive shell sessions and non-interactive ones (i.e., commands remotely invoked by yarprun).
• A yarp account to update and install the YARP library. Variable YARP_ROOT is set by default to /home/yarp/yarp2 for all users (in /etc/bash.bashrc) <-- change this policy
• An icub account with sudo privileges (created with sudo adduser icub admin on 2009-06-30) <-- change this policy
• cortex6's /etc/hosts file can include the following line:

 127.0.0.1	cortex6

System-wide libraries and repositories

YARP

yarp2 is installed for user icub, similarly to iCubBrain server configuration.

For now, we don't use system-wide installation (sudo make install). We could use it again after we verify that a user can easily override global settings.

iCub

iCub is installed for user icub, similarly to iCubBrain server configuration.

For now, we don't use system-wide installation (sudo make install). We could use it again after we verify that a user can easily override global settings.

Other libraries, manually installed

Please list here the system-wide libraries and applications that were installed by the superuser, especially the ones that do not have a clean 'make install' procedure but were manually installed into /opt:

• ARToolKit
• Ipopt-3.5.5-linux-x86_32-gcc4.2.4

CMake 2.6 does not come with the version of Ubuntu currently installed, but it is needed by the latest version of yarp, so we installed it via this archive.

• cmake 2.6

Other libraries, installed with Ubuntu packages

These packages were installed with apt-get install

 libncurses5-dev
 libace-dev
 libgsl0-dev
 libgtk2.0-dev libgtkmm-2.4-dev libglademm-2.4-dev
 glew-utils libglew1.5-dev
 libglut-dev
 git-core

OpenCV:

 libcv-dev libhighgui-dev libcvaux-dev

User repositories

Each user should manage his own yarp2 and iCub repositories. <-- then we shouldn't have done sudo make install here :)

We recommend to set your environment variables in a new file, called ~/.bash_env and containing:

 export YARP_ROOT=~/yarp2
 export YARP_DIR=$YARP_ROOT/build
 export ICUB_ROOT=~/iCub
 export ICUB_DIR=$ICUB_ROOT/main/build
 export PATH=$PATH:$YARP_DIR/bin:$ICUB_DIR/bin

Refer to the RobotCub software article for further instructions.

Other configuration

Subversion

We have set the following parameter in /etc/subversion/config:

 store-passwords = no

This implies that SVN will ask you for your password every time you do a commit. (Don't worry about changing your personal ~/.subversion/config file: the parameter is not actually set there, so the global /etc setting is used.)

Network tuning

  sysctl -w net.core.rmem_max=8388608
  sysctl -w net.core.wmem_max=8388608
  sysctl -w net.core.rmem_default=65536
  sysctl -w net.core.wmem_default=65536
  sysctl -w net.ipv4.tcp_rmem='4096 87380 8388608'
  sysctl -w net.ipv4.tcp_wmem='4096 65536 8388608'
  sysctl -w net.ipv4.tcp_mem='8388608 8388608 8388608'
  sysctl -w net.ipv4.route.flush=1

Prompt ($PS1)

The prompt is set to user@cortex?:pwd$ in /etc/bash.bashrc. With those settings, if you log in to Cortex1, the prompt will be user@cortex1:~$. We chose to do so because sometimes it's convenient to have the number of the Cortex machine you're working on embedded in the prompt. By default, though, this configuration is overridden in the users' ~/.bashrc file, and the prompt is set to user@source regardless of the Cortex machine you log in to.
If you want to inhibit this behaviour in ~/.bashrc and thus have a prompt like user@cortex?:pwd, just comment these lines in your ~/.bashrc:

  # set a fancy prompt (non-color, unless we know we "want" color)
  case "$TERM" in
  xterm-color)
      PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
      ;;
  *)
      PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
      ;;
  esac

However, for users created after 2009-05-07, the prompt is already set to user@cortex?:pwd$ by default.

Helper commands

• Check the kernel: uname -m
• Check the file versions: file
• Set bash shell in /etc/passwd
• Check disk space: du –sh /home
• Check per-user processes: ps -U <user>