349. SGE: removed node while jobs were queued

The Problem
There's a cluster (running ROCKS with Sun Grid Engine) which I manage remotely and which I did not set up. Instead it was the IT people at that uni who first configured it. For some reason they named the nodes

compute-0-0.local
compute-0-1.local
compute-0-2.local
compute-0-3.local
compute-0-6.local
compute-0-7.local

Recently a few extra disks were added to the system, so all jobs were suspended. However, while installing the disks the local IT peep decided to change the node names without consulting us. Now the nodes were called

compute-0-0.local
compute-0-1.local
compute-0-2.local
compute-0-3.local
compute-0-4.local
compute-0-5.local

instead. Suddenly there were two node-queues with jobs in them, but with no corresponding nodes.Trying to delete the jobs in those queues only lead to:

all.q@compute-0-5.local        BIP   0/8/8          9.12     lx26-amd64    
   5142 0.55500 submit__v3 me         r     02/27/2013 15:02:11     8        
---------------------------------------------------------------------------------
all.q@compute-0-6.local        BIP   0/8/8          -NA-     lx26-amd64    auo
   5074 0.55500 submit__nb me         dr    02/02/2013 21:53:59     8      

The Solution
It wasn't immediately obvious how to fix this, but it turned out to be simple:

qconf -cq all.q@compute-0-6.local

That clears and deletes the queue. That's all.

348. Using the official firefox 19 binary on debian testing/wheezy

UPDATE 20/3/2013: installing a system from scratch I'm having issues with xulrunner-10.0:i386, since it pulls in libstartup-notification0:i386 which causes all sorts of headaches (uninstalls xulrunner-10.0 and everything it depends on)

This post made me realise that installing the pre-built firefox binary isn't as straight-forward as one might like. A small nuisance is that the getfirefox.com versoin is only 32 bit, but that's life.

Here we go.

Download the standard binary version of firefox from here:
http://www.mozilla.org/en-US/firefox/new/?from=getfirefox

You can install it wherever you want, but I'm going for a local installation. Put the firefox-19.0.tar.bz2 in your home folder and untar it:

tar xvf firefox-19.0.tar.bz2
cd ~/firefox/
./firefox

If you get

bash: ./firefox: No such file or directory

then you are missing 32 bit compatibility libraries:

sudo dpkg --add-architecture i386
sudo apt-get update
sudo apt-get install ia32-libs
sudo apt-get install xulrunner-10.0:i386

To get flash set up you'll need the 32 bit version. Download the 32 bit version from http://get.adobe.com/flashplayer/?no_redirect

mkdir ~/.mozilla/plugins -p
mv ~/Downloads/install_flash_player_11_linux.i386.tar.gz ~/firefox
cd ~/firefox/
tar xvf install_flash_player_11_linux.i386.tar.gz
cp libflashplayer.so ~/.mozilla/plugins/libflashplayer.so

And that should leave you with a working firefox versions. Note that running 'firefox' as a command will invoke iceweasel if installed. To get around that you can e.g. do

echo "alias ffox='$HOME/firefox/./firefox'" >> ~/.bashrc
source ~/.bashrc

after which you can launch firefox by running ffox form the terminal. A standard installation would be to put everything in /opt and set up a .desktop file -- but there's plenty of guides to how to do that.

347. Minor ECCE oddity when pasting basis sets from BSE: lines longer than 254 chars wreak havoc

Using lines longer than 254 chars when editing nwchem input in ECCE leads to the rest of the input being dropped.

I discovered this when pasting basis sets from bse.pnl.gov. If you paste something which has a line longer than 254 chars, such as the one starting with # H He and ending with valence below (345 chars), everything that comes after that line will be dropped.

#  Def2-SVP  EMSL  Basis Set Exchange Library  2/27/13 8:08 PM
# Elements                             References
# --------                             ----------
# H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn : F. Weigend and R. Ahlrichs, Phys. Chem. Chem. Phys., Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence
# quality for H to Rn: Design and assessment of accuracy 7, 3297 (2005).
# 



BASIS "ao basis" PRINT
#BASIS SET: (4s,1p) -> [2s,1p]
H    S
     13.0107010              0.19682158E-01   
      1.9622572              0.13796524       
      0.44453796             0.47831935       
H    S
      0.12194962             1.0000000        
H    P
      0.8000000              1.0000000        
#BASIS SET: (7s,4p,1d) -> [3s,2p,1d]
O    S
   2266.1767785             -0.53431809926E-02      
    340.87010191            -0.39890039230E-01      
     77.363135167           -0.17853911985    
     21.479644940           -0.46427684959    
      6.6589433124          -0.44309745172    
O    S
      0.80975975668          1.0000000        
O    S
      0.25530772234          1.0000000
[..]

To reproduce, set up a calculation. In the editor, click on 'Final Edit'. Now paste your basis set. Save and exit (it's vi/m, so that means using :wq). 

Everything seems to be fine

Now, either select the job and hit Ctrl+I to see the input, or open the editor and click on 'Final Edit' again.

Nothing below the line immediately preceding the long line will be saved. It's not a visualisation issue either -- if you launch the job and do ctrl+o to see what NWChem received as input, it mirrors what you see as input.

Pasting anything other than that overly long line works fine.

A more artificial example would be to try to save this

a
b
abcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyz1234
d
e

which works, vs this:

a
b
abcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyzabcdefghijklmnopqrstuvxyz12345
d
e

which doesn't. There's a difference of one character.