MAS OS setup

Ubuntu 6.06 LTS server: This is the most supported OS. The instructions below are mostly for 6.06.

Ubuntu 7.10 server: We can support this now. Patched kernels are available. In the text below, major deviations from the 6.06 installation procedure are identified.

Ubuntu 8.04 LTS server: This version is new enough that the kernel build system isn't producing portable kernel packages. MAS works with 8.04 but I don't want to install too many 8.04 systems until they clean up the build system.

Install additional ubuntu packages

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

For loading / plotting MCE data in python using mce_data.py, you will want numpy / scipy:

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/

On more recent, but not new, Ubuntu (e.g. 8.10), you may want to install a more current version of numpy. The easiest way to do this seems to get source code from

http://sourceforge.net/projects/numpy

unzip and run

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

The config step may complain that it can't find BLAS and ATLAS, but that's ok because the numpy source has scaled-down substitutes.

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

Build the driver

By default, the driver will build with bigphysarea support enabled. To override build options, create a file Makefile.local in the "driver" folder, and add lines like:

# BIGPHYS=0 disables bigphysarea frame-buffering
BIGPHYS = 0

or

# FAKEMCE=1 provides simple emulation of a PCI card/MCE for testing
FAKEMCE = 1

or

# REALTIME=1 makes use of realtime interrupt routines
REALTIME = 1

In Makefiles, there should not be comments on the same line as the variable definitions. On a system running the bigphys kernel with the correct PCI card, Makefile.local will be created at compile time if it does not already exist. It can be left empty.

Anyway, once Makefile.local is setup, type

cd mas
make clean; make

From the driver folder we can test the driver:

cd driver
./reload
./mknodes

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.

If you're satisfied that the driver works, install the driver with the command

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. To get the driver to load on boot you must add manually the following lines to /etc/rc.local:

modprobe mce_dsp
/home/mce/mas/driver/mknodes
sudo -u mce /usr/mce/bin/maslog_server

Install MAS config files

Hardware and binary config files live in /etc/mce/ (created above).

Make sure you use the hardware config (mce_*.cfg) file appropriate for your system. Racks with 4 readout cards should use mce_v1.cfg; small sub-racks with readout card slots should use mce_v2.cfg.

cd ~/mas/config
cp mce_v1.cfg /etc/mce/mce.cfg
cp mas.cfg /etc/mce/mas.cfg

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.