Sage

Installations & upgrades

Initial installation 2.10

Some notes on the installation of Sage (v2.10) in a vserver:

Create a vserver, remove tmpfs /tmp in /etc/vservers/sage/fstab as 16M is too short for compilation

Create an account for the compilation

# adduser --disabled-password --shell /bin/false sage

Install packages needed for the compilation + some for runtime

# apt-get install gcc-4.1-base make m4 bison flex tar perl binutils \
           libstdc++6-dev g++ openssh-client \
           less screen imagemagick

Download and compile sources

# cd /opt
# export http_proxy=http://proxy....:8080 
# wget http://www.sagemath.org/dist/src/sage-2.10.tar
# tar xf sage-2.10.tar
# chown -R sage:sage *
# su -s /bin/bash - sage
sage$ cd /opt/sage-2.10/
sage$ make

Time for triple coffee...

To maintain the installation and install optional packages:

sage$ export http_proxy=http://proxy....:8080 
sage$ ./sage -upgrade
sage$ ./sage -optional
sage$ ./sage -i extra_docs-
sage$ ./sage -i openssl-0.9.8d.p1
sage$ ./sage -i pyopenssl-0.6
sage$ ./sage -i gap_packages-4.4.10_3
sage$ ./sage -i database_gap-4.4.10
...

Create an account to run sage as webserver

# adduser --disabled-password --shell /bin/false saged
# cp /opt/sage-2.10/sage /home/install

Edit the launch script /home/install/sage to point to the right directory:

SAGE_ROOT="/opt/sage-2.10"
# ln -s /home/install/sage /usr/local/bin

To start & stop the webserver as a real daemon, in a screen session, save the following script as /home/install/saged:

#! /bin/sh
# Author: Philippe Teuwen

# Do NOT "set -e"

PATH=/usr/sbin:/usr/bin:/sbin:/bin
DESC="Launching SAGE webserver"
NAME=sage
PIDFILE=/var/run/$NAME.pid
SCRIPTNAME=/etc/init.d/$NAME
DAEMON=/usr/local/bin/sage
HOST="fqdn.of.the.server"
PORT="8000"
ARGS="-c \"notebook(address=\\\"$HOST\\\",port=$PORT,accounts=true)\""
USER=saged
# Exit if mysql client is not installed
[ -x "$DAEMON" ] || exit 0

# Load the VERBOSE setting and other rcS variables
[ -f /etc/default/rcS ] && . /etc/default/rcS

# Define LSB log_* functions.
# Depend on lsb-base (>= 3.0-6) to ensure that this file is present.
. /lib/lsb/init-functions

#
# Function that starts the daemon/service
#
do_start()
{
        if [ -e $PIDFILE ]; then
            if ps -p $(cat $PIDFILE) >/dev/null; then
                echo -n -e "\nError: $NAME seems to be already running!"
                return 1
            else
                rm -f $PIDFILE
            fi
        fi
        screen -d -m -S sage su -s /bin/bash - $USER -c "$DAEMON $ARGS"
        sleep 1
        # PID of screen
        PID=$(screen -ls sage|grep sage|sed 's/[[:space:]]*\([0-9]\+\)\..*/\1/')
        # PID of su
        PID=$(ps --ppid $PID -o pid --no-headers)
        # PID of sage
        PID=$(ps --ppid $PID -o pid --no-headers)
        echo $PID > $PIDFILE
}

#
# Function that stops the daemon/service
#
do_stop()
{
        if [ -e $PIDFILE ]; then
            PID=$(cat $PIDFILE)
            if ps -p $PID > /dev/null; then
                # kill script
                kill $PID
                rm -f $PIDFILE
                return 0
            else
                echo -e "\nWarning: $NAME was not running."
                echo -n -e "\nCleaning PID file"
                rm -f $PIDFILE
                return 1
            fi
        else
            echo -n -e "\nWarning: $NAME was not running"
            return 1
        fi
}

case "$1" in
  start)
        [ "$VERBOSE" != no ] && log_daemon_msg "Starting $DESC" "$NAME"
        do_start
        case "$?" in
                0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
                2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
        esac
        ;;
  stop)
        [ "$VERBOSE" != no ] && log_daemon_msg "Stopping $DESC" "$NAME"
        do_stop
        case "$?" in
                0|1) [ "$VERBOSE" != no ] && log_end_msg 0 ;;
                2) [ "$VERBOSE" != no ] && log_end_msg 1 ;;
        esac
        ;;
  restart|force-reload)
        #
        # If the "reload" option is implemented then remove the
        # 'force-reload' alias
        #
        log_daemon_msg "Restarting $DESC" "$NAME"
        do_stop
        case "$?" in
          0|1)
                do_start
                case "$?" in
                        0) log_end_msg 0 ;;
                        1) log_end_msg 1 ;; # Old process is still running
                        *) log_end_msg 1 ;; # Failed to start
                esac
                ;;
          *)
                # Failed to stop
                log_end_msg 1
                ;;
        esac
        ;;
  *)
        echo "Usage: $SCRIPTNAME {start|stop|restart|force-reload}" >&2
        exit 3
        ;;
esac

:

If you don want anybody to be able to create an account (which gives access to bash!!), remove ",accounts=true" from ARGS.

Install the script:

# ln -s /home/install/saged /etc/init.d
# update-rc.d saged defaults 99 01

Upgrade to 2.10.1

I had many troubles because of a caching proxy
A ticket was filled for this issue: http://trac.sagemath.org/sage_trac/ticket/2043
Meanwhile I tried to get around so I copied manually

http://www.sagemath.org/packages/standard/list           -> /opt/sage-2.10/spkg/standard
http://www.sagemath.org/packages/standard/deps           -> /opt/sage-2.10/spkg/standard
http://www.sagemath.org/packages/standard/newest_version -> /opt/sage-2.10/spkg/standard
http://www.sagemath.org/packages/standard/README         -> /opt/sage-2.10/spkg/standard
http://www.sagemath.org/packages/install                 -> /opt/sage-2.10/spkg

then I had to avoid that download happens during sage -upgrade:

/opt/sage-2.10/local/bin/sage-update lines download_file("standard/list") etc

During sage -upgrade the version control system prompted me, I guess for the sage-update script, I simply quitted the changelog editor and it continued.
But now I see that the upgrade of sage_scripts-2.10.1 was not complete.
The solution to ignore local changes is to delete the directory local/bin/.hg and install again the scripts package:

sage -f sage_scripts-2.10.1 

I had also to install a zlib headers package because libpng compilation failed using the local zlib headers.

apt-get install zlib1g-dev

A ticket was filled for this issue: http://trac.sagemath.org/sage_trac/ticket/2043
I tested it:

apt-get remove zlib1g-dev
cd /opt/sage-2.10/spkg/standard
wget http://sage.math.washington.edu/home/mabshoff/SPKG/libpng-1.2.22.p5.spkg
sage -i libpng-1.2.22.p5

But still the same error, ongoing...

Install 2.10.3

To upgrade to 2.10.3 I simply took the full sources under /opt/sage-2.10.3, did make
and modified the path in /usr/local/bin/sage
For the optional packages, as most didn't change their version, I transferred them from the old install to /opt/sage-2.10.3/spkg/optional before installing them with sage -i package
Note that this full installation relied on the scripts & setup I installed before, cf the initial installation described at the top of the page.

Install 2.11

To upgrade to 2.11 I simply took the full sources under /opt/sage-2.11, did make
and modified the path in /usr/local/bin/sage
I also ran make test and that was ok.
But on a second machine I got an error at compile time, g++ killed. That was due to exhaused memory so I stopped the Sage notebook during the compilation of the new version and it went fine.

TODO: transfer the optional packages

Install 3.0.3

Same as usual, no special comment.

Install 3.1.1

This time I tried successfully the pre-compiled version at http://sage.apcocoa.org/linux/64bit/sage-3.1.1-debian64-opteron-x86_64-Linux.tar.gz and modified the path in /usr/local/bin/sage
Then run sage as the install user

----------------------------------------------------------------------
| SAGE Version 3.1.1, Release Date: 2008-08-17                       |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------
The SAGE install tree may have moved.
Regenerating Python.pyo and .pyc files that hardcode the install PATH (please wait at most a few minutes)...
Please do not interrupt this.

Client tuning

jsMath fonts

If you want to install the jsMath fonts locally on your client for a faster rendering:
Download TEX fonts and install them either in ~/.fonts/ or C:\Windows\Fonts

SSH & X11 PortForwarding

SAGE console via ssh

Some notes to give a console access with python autocompletion:
Put ssh keys in /home/saged/.ssh/authorized_keys
Set /usr/local/bin/sage as shell of user saged in /etc/passwd
Then on the client side:

Host sage
  Hostname blabla
  User saged

SAGE console via ssh with X11 forwarding

Some notes to enable X11 forwarding with the sage console:

apt-get install xbase-clients
vi /etc/ssh/sshd_config
    X11Forwarding yes
    #if you're in a vserver:
    X11UseLocalhost no 
/etc/init.d/ssh restart

Then on the client side:

Host sage
  Hostname blabla
  User saged
  ForwardX11 yes

Maxima plot via X11

Some notes to enable tcl/tk interactive plotting with maxima:
You need X11 forwarding, cf above

apt-get install tk8.4

Test:

ssh sage
Last login: blabla
----------------------------------------------------------------------
| SAGE Version 2.10, Release Date: 2008-01-18                        |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------

sage: maxima.plot2d('cos(2*x) + 2*cos(x)','[x,0,1]','[plot_format,openmath]')

or

sage: maxima.eval('load("plotdf")')
sage: maxima.eval('plotdf(x+y,[trajectory_at,2,-0.1]);')

or

sage: maxima.plot3d("sin(x^2+y^2)","[x,-3,3]","[y,-3,3]",'[plot_format,openmath]')

octave & gnuplot via X11

Some notes to enable octave and gnuplot:
You need X11 forwarding, cf above

apt-get install octave gnuplot

Test:

ssh sage
Last login: blabla
----------------------------------------------------------------------
| SAGE Version 2.10, Release Date: 2008-01-18                        |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------

sage: octave.de_system_plot(['x+y', 'x-y'], [1, -1], [0,2])

singular & surf via X11

Some notes to enable surf for singular:
You need X11 forwarding, cf above

We need to compile surf from the sources:

apt-get install zlib1g-dev libjpeg62-dev libtiff4-dev flex \
   libgmp3-dev libgtk1.2-dev libx11-dev libxmu-headers libxmu-dev
cd /opt
wget "http://downloads.sourceforge.net/surf/surf-1.0.5.tar.gz"
tar xzf surf-1.0.5.tar.gz 
cd surf-1.0.5/
./configure 
make
ln -s  /opt/surf-1.0.5/surf /usr/local/bin

To run the binary, you don't need all the header packages but you still need some libraries (if you compiled from sources you already have it)

apt-get install libgmp3c2 libgtk1.2 

Test:

ssh sage
Last login: blabla
----------------------------------------------------------------------
| SAGE Version 2.10, Release Date: 2008-01-18                        |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------
sage: s = singular.eval
sage: s('LIB "surf.lib";')
'// ** loaded /opt/sage-2.10/local/LIB/surf.lib (1.28,2007/07/13)'
sage: s("ring rr0 = 0, (x1,x2),dp;")

sage: s("ideal I = x1^3 - x2^2;")

sage: s("plot(I);")
"Press q to exit from 'surf'"

or

sage: singular.eval('ring rr1 = 0,(x,y,z),dp;')

sage: singular.eval('ideal I(1) = 2x2-1/2x3 +1-y+1;')

sage: singular.eval('plot(I(1));')
"Press q to exit from 'surf'"

Importing Python packages

System wide Python packages

install the package

# python setup.py install

or add the --record option to make a list of files which where installed for easy removal later

# python setup.py install --record install.log

append the python path in sage

sage: import sys                
sage: sys.path.append('/usr/lib/python2.5/site-packages')

import the package, for example:

sage: import M2Crypto

removal of the package:

cat install.log | xargs rm

Alternative way to install python package

On Red Hat/Fedora:

$ python setup.py bdist_rpm

On Debian/Ubuntu:
Same step then use alien to transform the .rpm into a .deb

=> easy removal of the python package is possible

Import to local Sage Python path

install the script to the Sage Python path

$ sage-python setup.py install

in sage: just import, that's it

sage: import M2Crypto

Import user Python modules

It will be soon possible for a user without administrator privileges on the server to import the path to their module in a more elegant way than the sys.path.append(), cf [1]
I propose offering a workaround, e.g. SAGE_PYTHONPATH which *does* get appended to PYTHONPATH on startup.

Installing development Python packages

This section is Python generic, not specific to SAGE.
During development, it's painful to install the package every time you're doing sth on it.
There are various ways to import a module actually

Basic import from a local directory

In your code, e.g. mycode.py:

from Module1 import Function1

Usage: pointing to the path containing the module

PYTHONPATH=/path/to/src/directory/above/Module1 python mycode.py

Import from a local directory, using egg_info

This is using python-pkg-resources

Installing (locally):

python setup.py egg_info

In your code, e.g. mycode.py:

from pkg_resources import require
require("Module1>=1.0")
from Module1 import Function1

Usage: pointing to the path containing the egg_info

PYTHONPATH=/path/to/src/directory/containing/egg_info python mycode.py

Cleaning:

rm -rf /path/to/src/directory/containing/egg_info/Module1.egg-info

Install a development version

Actually symlinking to the working directory
This is using python-pkg-resources

Installing (symlink):

sudo python setup.py develop

Usage:

python mycode.py

Cleaning:

sudo python setup.py develop --uninstall
rm -rf /path/to/src/directory/containing/egg_info/Module1.egg-info

Create and installing an egg

This is using python-pkg-resources

Installing:

python setup.py bdist_egg
sudo easy_install dist/Module1-1.0-py2.5.egg

Usage:

python mycode.py

Cleaning:

sudo rm /usr/lib/python2.5/site-packages/Module1-1.0-py2.5.egg

Create and using locally an egg

This is using python-pkg-resources

Creating:

python setup.py bdist_egg

In your code, e.g. mycode.py:

from pkg_resources import require
require("Module1>=1.0")
from Module1 import Function1

Usage: pointing to the path containing the egg file

PYTHONPATH=/path/to/your/dist/ python mycode.py

Interfaces to proprietary software

Maple

Some notes if you want to use your Maple 32-bit on a 64-bit arch:

apt-get install ia32-libs
/bin/maple -binary IBM_INTEL_LINUX

Or from Sage:

maple.fsolve('x^2=cos(x)+4', 'x=0..5')

Maple via X11

You need X11 forwarding, cf above
Test:

ssh sage
Last login: blabla
----------------------------------------------------------------------
| SAGE Version 2.10, Release Date: 2008-01-18                        |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------
sage: sh.eval("xmaple")