188. Notes: virtualbox and /etc/init.d/vboxdrv

If you install virtualbox and get ready to fire up the installation of a new virtual machine, but immediately get an error about having to do '/etc/init.d/vboxdrv setup' -- but find that there's no such executable in /etc/init.d in spite of having installed the virtualbox-dkms package, then

sudo apt-get install linux-headers-`uname -r`
sudo dpkg-reconfigure virtualbox-dkms

158. Setting up ecce with qsub at An Australian University computational cluster

EDIT: this works for G09 on that particular cluster. Come back in a week or two for a more general solution (end of May 2012/beginning of June 2012).

I don't feel comfortable revealing where I work. But imagine that you end up working at an Australian University in, say, Melbourne. I do recognise that I will be giving enough information here to make it possible to identify  who I am (and there are many reasons not to want to be identifiable -- partly because students can be mean and petty, and partly because I suffer from the delusion that IT rules apply to Other People, and not me -- and have described ways of doing things you're not supposed to be doing in this blog)

Anyway.

My old write-ups of ecce are pretty bad, if not outright inaccurate. Anyway, I presume that in spite of that you've managed to set up ECCE well enough to run stuff on nodes of your local cluster.

Now it's time for the next level -- on a remote site using SGE/qsub

So far I've only tried this out with G09 -- they are currently looking to set up nwchem on the university cluster. Not sure what the best approach to the "#$ -pe g03_smp2 2" switch is for nwchem.

--START HERE --

EVERYTHING I DESCRIBE IS DONE ON YOUR DESKTOP, NOT ON THE REMOTE SYSTEM. Sorry for shouting, but don't got a-messing with the remote computational cluster -- we only want to teach ecce how to submit jobs remotely. The remote cluster should be unaffected.

1. Creating the Machine
To set up a site with a queue manager, start
ecce -admin

Do something along the lines of what's shown in the figure above.

If you're not sure whether your qsub belongs to PBS or SGE, type qstat -help and look at the first line returned, e.g. SGE 6.2u2_1.

2. Configure the site
Now, edit your ecce-6.3/apps/siteconfig/CONFIG.msgln4  (local nodes go into ~/.ECCE  but remote SITES go in apps/siteconfig --  and that's what we're working with here).

   NWChem: /usr/local/bin/NWCHEM
   Gaussian-03: /usr/local/bin/G09
   perlPath: /usr/bin/perl
   qmgrPath: /usr/bin/qsub
 
   SGE {
   #$ -S /bin/csh
   #$ -cwd
   #$ -l h_rt=$wallTime
   #$ -l h_vmem=4G
   #$ -j y
   #$ -pe g03_smp2 2

   module load gaussian/g09
    }

A word of advice -- open the file in vim (save using :wq!) or do a chmod +w on it first since it will be set to read-only by default.

3. Queue limits
The same goes for the next file, which controls various job limits, ecce-6.3/apps/siteconfig/msgln4.Q:

# Queue details for msgln4
Queues:    squ8

squ8|minProcessors:       2
squ8|maxProcessors:       6
squ8|runLimit:       4320
squ8|memLimit:       4000
squ8|scratchLimit:       0

4. Connect
In the ecce launcher-mathingy click on Machine Browser, and Set Up Remote Access for the remote cluster. Basically, type in your user name and password.

Click on machine status to make sure that it's connecting

5.Test it out!
If all is well you should be good to go