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Sage

2008-02-03T21:11:53Z

213.219.141.116: /* SAGE console via ssh with X11 forwarding */

===Installation===
Some notes on the installation of [http://www.sagemath.org/ Sage] 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:
<pre>
#! /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

:
</pre>
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

===Client tuning: jsMath fonts===
If you want to install the jsMath fonts locally on your client for a faster rendering:
 [http://www.math.union.edu/~dpvc/jsMath/download/jsMath-fonts.html Download TEX fonts] and install them either in ~/.fonts/ or C:\Windows\Fonts

===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
sage -i gnuplotpy-1.7.p3
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
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'"

===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")

Sage

2008-02-03T21:09:36Z

213.219.141.116:

===Installation===
Some notes on the installation of [http://www.sagemath.org/ Sage] 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:
<pre>
#! /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

:
</pre>
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

===Client tuning: jsMath fonts===
If you want to install the jsMath fonts locally on your client for a faster rendering:
 [http://www.math.union.edu/~dpvc/jsMath/download/jsMath-fonts.html Download TEX fonts] and install them either in ~/.fonts/ or C:\Windows\Fonts

===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.conf
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
sage -i gnuplotpy-1.7.p3
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
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'"

===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")