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.
Installing development Python packages
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")