In the meantime for the impatient, here is the guts of the text
version that I have had for sometime. Note that in the new FSL there
are 4 default queues used so I will have to add something for this!
(short.q, veryshort.q, long.q, verylong.q)
-------------
================================
SGE and Ubuntu howto
Andrew Janke - [log in to unmask]
================================
This is a quick walkthrough to get SGE going on Ubuntu and/or debian for those
who would like to use it for something like FSL
There are two things that you need to setup before you even begin to download
things, SGE runs as an admin user and needs two services. Note that I presume
you already have unified logins and NFS for data directories setup.
All the below must be done as root so either 'su -' or use 'sudo -s'
SGE generally consists of one master and a number of exec hosts, note that the
master machine can also be an exec host but more on that later.
First we add a username to all the machines we plan to use, in this case I use
the UID 536 for no other reason than that is what I decided to use.
# useradd --home-dir /usr/sge --system --uid 536 --gid 4 sgeadmin
Now we add a few lines to /etc/services to tell SGE which port numbers to use.
Note that on Gutsy and lenny this is already in /etc/services so you can skip
this bit. Add the following lines to the end of /etc/services
sge_qmaster 6444/tcp # qmaster port for SGE
sge_qmaster 6444/udp # qmaster port for SGE
sge_execd 6445/tcp # execd port for SGE
sge_execd 6445/udp # execd port for SGE
Now it is time to install SGE itself, first get the approriate files from here.
You will have to click through the license
http://gridengine.sunsource.net/downloads/61/download.html
In my case I get both the "Grid Engine comming files" and the
"Linux - AMD64, kernel 2.4, 2.6, glibc >= 2.3.2" given that I run an amd64
kernel.
Now we make a directory to put them all in on our master host:
# mkdir /usr/sge
# cd /usr/sge
untar the files
# tar zxvf sge-6.1beta-common.tar.gz
# tar zxvf sge-6.1-bin-lx24-amd64.tar.gz
Set an environment variable and then install the qmaster as such:
# export SGE_ROOT=/usr/sge
# ./install_qmaster
Now go through the interactive install process:
* accept the licence
* press enter at the into screen
* press "y" and then specify sgeadmin as the user id
* leave the install dir as /usr/sge
* accept the sge_qmaster info
* accept the sge_execd info
* leave the cell name as "default"
* leave the spool dir as is
* press "n" for no windows hosts!
* press "n" and then "y" so that the permissions are set correctly
* press "y" for all hosts in one domain
* press enter to accept the setup
* enter "classic" for classic spooling
* enter "20000-20100" as the GID range
* accept the default spool dir
* enter your admin email address
* accept a few more defaults, this will install the startup scripts
* press "n" for a list of hosts
* enter the names of your hosts who will be running jobs
* skip shadow hosts for now (press "n")
* choose "1" for normal configuration
* accept a few more defaults
Now that we are back to a shell (finally) we need to add a few things to our
root .bashrc so that we can access the SGE binaries. Add the following lines to
/root/.bashrc
# SGE settings
export SGE_ROOT=/usr/sge
if [ -e $SGE_ROOT/$SGE_CELL ]
then
. $SGE_ROOT/$SGE_CELL/common/settings.sh
fi
And then be sure to re-source your .bashrc
# . /root/.bashrc
Now we can add our own username as an admin so that we can mess with things
without becoming root. (My username is rotor so here is what I write)
# qconf -am rotor
Now we can add an execution host. For now I will presume you want to run jobs on
your master, if not skip this step.
# cd /usr/sge
# ./install_execd
If everything has been setup correctly you can just press enter about 20 times
with all the defaults as these are read from the master.
Now we can configure our default queue (all.q) do this as such, and given that
you have added your own username as an admin you can do this in your own account
$ qconf -mq all.q
Change the following settings:
priority => 20 (this is the lowest priority)
shell => /bin/sh
shell_start_mode => unix_behavior
Note that the above is not strictly required but are things that I have used to
make things work nice.
Now check that your install has worked with qstat:
$ qstat -f
You should get some output regarding all.q
-------------
On 11/9/07, David Gutman <[log in to unmask]> wrote:
> Fabulous--- I appreciate your hard work-- hopefully it's saving me some!
>
> If possible, focus on the "dummies" part in the wiki-- of course wikies are
> great, we can also edit it and "dummify" it ourselves
>
> :-)
>
> Thanks again!
>
> DAG
>
> On Nov 8, 2007 10:03 PM, Matt Glasser <[log in to unmask]> wrote:
> >
> >
> >
> >
> > Yes, this would be very nice. I have also been waiting for this.
> >
> >
> >
> > Peace,
> >
> >
> >
> > Matt.
> >
> >
> >
> > ________________________________
>
> >
> > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of David Gutman
> > Sent: Thursday, November 08, 2007 10:01 PM
> > To: [log in to unmask]
> > Subject: [FSL] SGE for Dummies?.... (on ubuntu/debian?)
> >
> >
> >
> >
> >
> >
> >
> > Does anyone know of a walkthrough or easy installation guide for SGE on a
> debian/ubuntu distribution. I've been reluctant to spend the time figuring
> out how to install it on my own and would like to use SGE/FSL--- just would
> rather piggy back on someone else's expertise. Also if there's an FAQ on
> integrating SGE with FSL that would also obviously be useful. I know it's
> been in the works, just haven't seen anything on the web site.
> >
> > DG
> >
> > --
> > David A Gutman, M.D. Ph.D.
> > Department of Psychiatry & Behavioral Sciences
> > Emory University School of Medicine
>
>
>
> --
> David A Gutman, M.D. Ph.D.
> Department of Psychiatry & Behavioral Sciences
> Emory University School of Medicine
--
Andrew Janke ([log in to unmask] || http://a.janke.googlepages.com/)
Canberra->Australia +61 (402) 700 883
|
