MAS OS setup

Supported operating systems

• Ubuntu 9.10, 9.04, 8.10, 8.04, 7.10, 6.06.
• New users should feel free to install 9.10. We will upgrade to 10.04 (a Long Term Release) and then start getting conservative for a while.

Ubuntu 9.10

Starting with Ubuntu 9.10, some effort has been made to automate the installation. After installing Ubuntu 9.10 (desktop), get the install tarball:

cd ~
wget http://e-mode.phas.ubc.ca/~mhasse/mce/ubuntu_09.10/install.tar.gz
tar -xzf install.tar.gz
cd install/

Install additional ubuntu packages

From that install folder, run

bash install.bash

Bigphysarea kernel patch

You can either download the compiled kernels or build them from scratch.

From install folder, run EITHER

bash kernel_download.bash

or

bash kernel_build.bash

Then when one or the other of those has succeeded, install them:

bash kernel_install.bash

You can now proceed to the section below titled "Configure the system for MCE users"

Ubuntu 6.06 - 9.04

Disable CDROM seeking

The package manager knows that you have the Ubuntu disk and will say things like

Media change: please insert the disc labeled
'Ubuntu-Server 6.06.1 _Dapper Drake_ - Release i386 (20060807.1)'

To disable this (and download packages from the internet instead), open /etc/apt/sources.list

sudo pico /etc/apt/sources.list

and remove (comment) the line

deb cdrom:[Ubuntu-Server 6.06.1 _Dapper Drake_ - Release i386 (20060807.1)]/ dapper main restricted

Install required packages

sudo apt-get update
sudo apt-get install build-essential subversion emacs21 libreadline5-dev 

Enable universe repository and install GGV

Uncomment the line in /etc/apt/sources.list so it says

deb http://us.archive.ubuntu.com/ubuntu/ dapper universe

Then run

sudo apt-get update
sudo apt-get install gnome-gv

gnome-gv doesn't exist on 7.10, you'll have to settle for

sudo apt-get install gv

Install packages that you shouldn't even want to install (soon to be optional)

sudo apt-get install tcsh

Install desktop manager (optional)

sudo apt-get install ubuntu-desktop gdm

Install python stuff

The 'pyth' branch MAS has experimental support for python using wx and matplotlib:

sudo apt-get install python-dev python-wxglade python-matplotlib python-numarray-ext swig

numpy and scipy

For loading / plotting MCE data in python using mce_data.py, you will want numpy / scipy. The Ubuntu packages can be a bit out of date, but should be enough for basic data manipulation and plotting. Just run:

sudo apt-get install python-numpy python-scipy 

For Ubuntu 6.06, numpy and scipy can be obtained following instructions from this page:

http://debs.astraw.com/dapper/

There are some very useful numpy features that are not available on older Ubuntu default packages. To access such features it is not too hard to install more recent versions of numpy (and scipy) from sourceforge:

1. Remove Ubuntu numpy and scipy packages; install dependencies for the source.

sudo apt-get remove python-numpy python-scipy
sudo apt-get install libblas-dev lapack-dev

2. Get source tarballs from links below... unzip the contents.

http://sourceforge.net/projects/numpy
http://sourceforge.net/projects/scipy

3. Compile the source packages. That means that in each folder you have to do:

./setup.py config
./setup.py build
sudo ./setup.py install

The config step complains a fair bit, but it's really obvious when there is an error rather than a warning. The scipy package takes a long time to compile.

Install unpackaged libraries

MAS uses libconfig to manage its configuration files. The webpage is here: [ http://www.hyperrealm.com/libconfig/ ]. To install libconfig run the following:

 wget http://www.hyperrealm.com/libconfig/libconfig-1.3.2.tar.gz
 tar -xzf libconfig-1.3.2.tar.gz
 cd libconfig-1.3.2
 ./configure
 make
 sudo make install

To make the system aware of this library, add "/usr/local/lib" to /etc/ld.so.conf and run "sudo ldconfig". i.e.

 echo /usr/local/lib | sudo tee -a /etc/ld.so.conf
 sudo ldconfig

On newer systems (Ubuntu 7.10) you can do this instead:

 echo /usr/local/include | sudo tee /etc/ld.so.conf.d/libconfig.conf
 sudo ldconfig

Download and install MAS kernel patch

Download

If you're not compiling the kernel from scratch, download the binary packages from UBC:

wget http://e-mode.phas.ubc.ca/~mhasse/mce/kernel-headers-2.6.15.7-bigphys_10.00.Custom_i386.deb
wget http://e-mode.phas.ubc.ca/~mhasse/mce/kernel-image-2.6.15.7-bigphys_10.00.Custom_i386.deb
wget http://e-mode.phas.ubc.ca/~mhasse/mce/extras.patch

For Ubuntu 7.10, get these instead:

wget http://e-mode.phas.ubc.ca/~mhasse/mce/linux-headers-2.6.22.9-bigphys_10.00.Custom_i386.deb
wget http://e-mode.phas.ubc.ca/~mhasse/mce/linux-image-2.6.22.9-bigphys_10.00.Custom_i386.deb

On Ubuntu 7.10 machines without PAE hardware (i.e. a maximum of 4G of system memory) use:

wget http://e-mode.phas.ubc.ca/~mhasse/mce/linux-headers-2.6.22.14-bigphys_2.6.22.14-bigphys-10.00.Custom_i386.deb
wget http://e-mode.phas.ubc.ca/~mhasse/mce/linux-image-2.6.22.14-bigphys_2.6.22.14-bigphys-10.00.Custom_i386.deb

Install

Then, install the packages using dpkg:

sudo dpkg -i kernel-headers-2.6.15.7-bigphys_10.00.Custom_i386.deb
sudo dpkg -i kernel-image-2.6.15.7-bigphys_10.00.Custom_i386.deb

The "image" file might complain about symbolic links, no big deal.

On Ubuntu 7.10, instead install these:

sudo dpkg -i linux-headers-2.6.22.9-bigphys_10.00.Custom_i386.deb
sudo dpkg -i linux-image-2.6.22.9-bigphys_10.00.Custom_i386.deb

Why are these ones called "linux" instead of "kernel"? I think it's because I got them from Ubuntu repositories instead of kernel.org.

On Ubuntu 7.10 machines without PAE install these:

sudo dpkg -i linux-headers-2.6.22.14-bigphys_2.6.22.14-bigphys-10.00.Custom_i386.deb
sudo dpkg -i linux-image-2.6.22.14-bigphys_2.6.22.14-bigphys-10.00.Custom_i386.deb

The Ubuntu 8.04 kernel has a sound-card driver that lays claim to the Motorola DSP on the PCI card. We have to blacklist this module to prevent it from trying to configure the card as a sound card. Add the following to the bottom of /etc/modprobe.d/blacklist :

# Conflicts with Astro-cam PCI card!!
blacklist snd_asihpi

Patch

This makes it possible to compile against the kernel package as though it had been locally compiled originally.

cd /usr/src/kernel-headers-2.6.15.7-bigphys/
sudo patch -p1 < ~/extras.patch

This step is not necessary for Ubuntu 7.10. It may be necessary to link the kernel headers into /lib/modules:

 sudo ln -s /usr/src/linux-headers-2.6.22.9-bigphys/ /lib/modules/2.6.22.9-bigphys/build

Boot menu

We need to add the kernel option that causes bigphys to allocate boot memory for our driver. In older versions of MAS (especially ACT's stable release) we also need to disable "acpi". It's a good idea to not run any DSP/MCE commands until all of your kernel options are in place.

Having installed the kernel "image" package, the kernel should show up in the boot loader (grub)'s kernel list.

Editing the kernel list

As root (or using sudo), edit the file /boot/grub/menu.lst .

sudo pico /boot/grub/menu.lst

Go to the list of kernels, below the line "## ## End Default Options ##", and find the new kernel entry. On Ubuntu 6.06, it should be the third block (index 2), and look like this:

title           Ubuntu, kernel 2.6.15.7-bigphys
root            (hd0,0)
kernel          /vmlinuz-2.6.15.7-bigphys root=/dev/sda3 ro quiet splash
initrd          /initrd.img-2.6.15.7-bigphys
savedefault
boot

Add the kernel options to the "kernel" line, producing either this (recent MAS):

kernel          /vmlinuz-2.6.15.7-bigphys root=/dev/sda3 ro quiet splash bigphysarea=8192

or this (old MAS, esp. ACT):

kernel          /vmlinuz-2.6.15.7-bigphys root=/dev/sda3 ro quiet splash bigphysarea=8192 acpi=off

Save and close the file, and reboot to test this kernel. If the kernel "works", you can edit menu.lst again and change the value of the "default" option to point to this kernel:

default    2

Ubuntu 7.10 and later: the kernel packages install a bit differently so the block will likely be the first one in the list. The 'kernel' line must change from something like

kernel          /boot/vmlinuz-2.6.22.9-bigphys root=UUID=1b6e7b54-894d-4571-9f0a-527fe0103975 ro quiet splash

to

kernel          /boot/vmlinuz-2.6.22.9-bigphys root=UUID=1b6e7b54-894d-4571-9f0a-527fe0103975 ro quiet splash bigphysarea=8192

Note that the long hexadecimal serial numbers are system specifc and yours are probably different than these ones. Leave them as they are and just add the new kernel options. The "default" option will probably be

default    0

but it's a good idea to count these things out for yourself.

Configure the system for MCE users

Permissions and umask

Set the umask for all users to give write access for their group by default.

Edit /etc/profile and change the "umask 022" line to

umask 002

Edit /etc/login.defs and find the line that start "# UMASK" and change it to

UMASK           002

Any users wishing to use MCE under their own accounts should be added to the "mce" group and should have "mce" as their primary group. Their umask must be set properly, or other users will not be free to manipulate shared files.

To setup additional system users, see the page on MAS user setup.

Folders

This is the sort of thing that should be done by an install script...

Data directory:

sudo mkdir /data
sudo chown mce:mce /data
sudo chmod g+ws /data
mkdir /data/cryo/

Configuration directory:

sudo mkdir /etc/mce
sudo chgrp mce /etc/mce
sudo chmod g+ws /etc/mce

If necessary, branch MAS and mce_script

You can work with a complete checked-out tree, or not.

In the first case:

svn checkout svn://e-mode.phas.ubc.ca/mas
svn copy mas/trunk mas/branch/{your_project_name}
svn commit mas

Alternately, do the copy directly on the svn server (it is automatically committed):

svn copy svn://e-mode.phas.ubc.ca/mas/trunk svn://e-mode.phas.ubc.ca/mas/branch/{your_project_name}

For mce_script, replace "mas" with "mce_script".

Then check out the appropriate branch (or the whole tree) on the new machine.

Download (checkout) MAS and mce_script

See the page on MAS svn repository

Compile and install MAS

./configure

MAS uses autoconf for some basic configuration stuff. The biggest thing you usually need to tell it is what the basic username and group should be for mce data. Also, there are a few options for the driver and some stupid python stuff.

From the MAS source folder, run

./configure

Useful options:

 --without-driver        suppress driver compilation/installation
 --without-bigphysarea   compile driver without bigphysarea support
 --with-user=USER        set default MCE user
 --with-group=GROUP      set default MCE group

It will complain if it cannot find something.

make

This often works.

make clean; make

Test the driver

It is wise to test that the driver does not kill your machine before installing it to load on boot. After compiling do:

cd driver
sudo ./reload

This will load the driver, which should then try to talk to the SDSU PCI card if it is installed. Note that since "reload" first unloads the driver if it is present, and then loads the driver from the current folder, it may report an "ERROR" message if the first step fails, even though the driver is successfully loaded. The definitive way to check that the driver is loaded is

 cat /proc/mce_dsp

If this file does not exist, the driver isn't loaded. If the cat prints out a bunch of low-level driver information, you're in good shape.

sudo make install

If you're satisfied that the driver works, install the whole thing. Go back up to the MAS base folder and run

sudo make install

This should put mce_dsp.ko into /lib/modules/2.6.15.7-bigphys/kernel/drivers/misc/, and re-scan the module dependencies. It will also install the MAS binaries in /usr/mce/bin, and do a bunch of other stuff.

The driver and logging daemon can then be started/restarted as desired through the init.d script "mas":

/etc/init.d/mas restart

The driver will automatically be set to load on boot. To disable this, remove the symbolic link "/etc/rc2.d/S99mas".

Install MCE configuration files

The hardware configuration file ("mce.cfg") describes aspects of the MCE subrack configuration (what cards are present) and the firmware capabilities. Hardware config files live in /etc/mce/. A bunch of files are provided to fit common configurations. These tend to live in /etc/mce/ somewhere.

v4/mce_v1*.cfg   Version 4 series firmware, large subrack (4 readout cards)
v4/mce_v2*.cfg   Version 4 series firmware, small subrack (2 readout cards)
v5/mce_v1*.cfg   Version 5 series firmware, large subrack (4 readout cards)
v5/mce_v2*.cfg   Version 5 series firmware, small subrack (2 readout cards)

You should make /etc/mce/mce.cfg a symbolic link to the config file you like the best.

cd /etc/mce/
rm mce.cfg
ln -s v5/mce_v1.cfg

That's the one I like the best.

Install mce_script

The mce_script files are designed so that users can fairly easily run a different set of scripts. We will install a system default set in /usr/mce/mce_script

cd /usr/mce
svn checkout svn://e-mode.phas.ubc.ca/mce_script/branch/{your_experiment} mce_script

Current experiments include ACT and SPIDER.

mas_env.bash

To set up the environment and path to use these scripts and idl codes, a user should do "source mas_env.bash". (This file used to live in mas/config, but has been moved into mce_script/template.) Non-developer users can source /usr/mce/mce_script/template/mas_env.bash directly; advanced users may want to keep their own copy (or several different copies) in their home folder.

Note that MAS/mce_script scripts should *not* source mas_env.bash! The whole point of it is that paths should be flexible.

.bashrc

To have bash start up with the MAS variables defined, and the paths ready, add the following lines to .bashrc :

export MAS_ROOT=/usr/mce/mce_script/
source $MAS_ROOT/template/mas_env.bash
export IDL_PATH="<IDL_DEFAULT>:$MAS_IDL/mas"

While you're in there, you may want to define a few aliases. In particular, I always uncomment the alias ll='ls-l' line.