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.

Install 5.0.1

root@sagemath:~# su -s /bin/bash - sage
sage@sagemath:~$ cd /opt
sage@sagemath:/opt$ tar -x --lzma -f sage-5.0.1-linux-64bit-ubuntu_10.04.3_lts-x86_64-Linux.tar.lzma 
sage@sagemath:/opt$ ln -s sage-5.0.1-linux-64bit-ubuntu_10.04.3_lts-x86_64-Linux sage
sage@sagemath:~$ sage

Gurobi backend

cf http://www.sagemath.org/doc/thematic_tutorials/linear_programming.html
If no direct Internet connection is available:

$ ssh -R8008:apps.gurobi.com:8008 root@sagemath
root@sagemath:~# su -s /bin/bash - sage
sage@sagemath:~$ /opt/gurobi500/linux64/bin/grbgetkey --server=127.0.0.1 --verbose abcdefgh-1234-1234-1234-123456789abc
 => /home/sage/gurobi.lic
sage@sagemath:~$ ln -s /opt/gurobi500/linux64/include/gurobi_c.h /opt/sage/local/include
sage@sagemath:~$ ln -s /opt/gurobi500/linux64/lib/libgurobi.so.5.0.0  /opt/sage/local/lib/libgurobi.so
sage@sagemath:~$ sage -b

jsMath fonts

Client tuning

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

Server tuning

You can also install the fonts as images on the server so that clients without the TeX fonts will still see a proper result. It's not part of the standard Sage install by default because of its size (80Mb).

 sage$ sage -i jsmath-image-fonts-1.3

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.

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")