Cluster: Sage Chroot

In order to chroot the Sage notebook, I used a mix of steps from the following guides:

• MSRI SAGE Installation Guide: Running the SAGE Notebook Securely
• [sage-support] Re: How to run the notebook in the background
• [sage-support] chroot jail -- unable to mount image file
• [sage-devel] Re: SAGE in chroot - This one is for RedHat

Chroot

The image itself is at /mounts/bobsced/sage_chroot.image (aka /cluster/bobscednew/sage_chroot.image). It gets mounted in the same directory as sage_chroot (it's an ext3 filesystem). The chroot needs to have /dev and /proc, so here's a copy of the relevant parts of /etc/fstab:

/mounts/bobsced/sage_chroot.image /mounts/bobsced/sage_chroot ext3 loop 0 0
/dev            /mounts/bobsced/sage_chroot/dev devpts  defaults        0 0
/proc           /mounts/bobsced/sage_chroot/proc proc   defaults        0 0

In order to get yum to install there, I had to edit /etc/yum.repos.d/CentOS-Base.repo and hard code $releasever to 3.5. I also commented out all the repositories except the top one. Then I was able to run:

yum --installroot=/mounts/bobsced/sage_chroot install bash fileutils sed which make gcc gcc-c++ m4 tar gzip bzip2 flex bison findutils yum rpm passwd perl diffutils sudo

to set up the base install of the OS for the chroot. It also needs a copy of /etc/hosts for the localhost entry.

Sage Install

I downloaded the tar ball normally and then moved it into the chroot from the base filesystem. I untarred it from the base filesystem, too, and put it in the directory /home/sage in the chroot, then ran (as the sage user in the chroot, which has id 5000, which isn't used in the main filesystem)

make

make test

Make sure to run ./sage once inside the chroot so it sets up its variables and everything.

Sage Setup on the Base Filesystem

I followed the post above for Red Hat. On the filesystem outside the chroot, I populated /etc/sysconfig/sage-config:

SAGE_SERVER=/mounts/bobsced/sage_image
ADDRESS=159.28.234.200
PORT=8000
USER=5000

And /usr/local/bin/sage-notebook:

#!/bin/bash
. /etc/sysconfig/sage-config
COMMAND="notebook(address='$ADDRESS', port=$PORT, accounts=True, open_viewer=false, secure=true)"

nohup /usr/sbin/chroot $SAGE_SERVER su - sage -c "sage -c \"$COMMAND\" " &

And /usr/local/bin/sage-killer:

#!/bin/bash
. /etc/sysconfig/sage-config

kill -9 `ps -u $USER -o "pid="` > /dev/null 2>/dev/null

And finally, /etc/rc.d/init.d/sage-notebook:

#!/bin/sh
#
# This script starts up a sage notebook in a chroot environment.
# Copied from http://www.mail-archive.com/sage-devel@googlegroups.com/msg03545.html
#
# chkconfig: 2345 35 98
# description: Run a notebook in chroot environment
#

. /etc/rc.d/init.d/functions

start()
{
        echo -n $"Starting sage "
        if [ ! -f  /var/lock/subsys/sage ]; then
                nohup /usr/local/bin/sage-notebook 2/dev/null
/dev/null &
        fi
        touch /var/lock/subsys/sage
        success
        echo
        return 0
}

stop()
{
        echo -n $"Stopping sage "
        /usr/local/bin/sage-killer
        rm -f  /var/lock/subsys/sage
        success
        echo
        return 0
}

status () {
    if [ ! -f /var/lock/subsys/sage ]; then
        echo $"Sage is not currently running"
        return 1
    else
        echo $"Sage is running"
        return 0
    fi

}
# See how we were called.
case "$1" in
  start)
        start
        ;;
  stop)
        stop
        ;;
  status)
        status
        ;;
  restart)
        stop
        start
        ;;
  *)
        echo $"Usage: $0 {start|stop|restart|status}"
        exit 1
esac

exit 0