609. NBO6 on a debian cluster (/w g09)

Curse blogspot and the lack of revision control and backups! I lost my post when it was almost finished.

So here's a briefer version. I have bought NBO6 and I want to integrate it with gaussian G09 rev. D (you can't use it directly with earlier binary versions)

My 'instructions' are basically copy/pasted from the NBO6 installation instructions -- this is a tl;dr version.

sudo cp nbo6.0-bin-linux-x86_64.tar.gz /opt/
cd /opt/
sudo tar xvf nbo6.0-bin-linux-x86_64.tar.gz 
sudo chown $USER:$USER nbo6 -R
vim nbo6/bin/gaunbo6

Edit:

3 set INT    = i8
  4 set BINDIR = /opt/nbo6/bin

In your queue file add

set path = ( /opt/nbo6/bin $path )

In my case, as I use ECCE I edited my apps/siteconfig/CONFIG.node files:

Gaussian-03Command{
set path = ( /opt/nbo6/bin $path )
setenv GAUSS_SCRDIR /home/me/scratch
setenv GAUSS_EXEDIR /opt/gaussian/g09d/g09/bsd:/opt/gaussian/g09d/g09/local:/opt/gaussian/g09d/g09/extras:/opt/gaussian/g09d/g09
/opt/gaussian/g09d/g09/g09< $infile > $outfile 
echo 0
}

I then tested it by running a basic gaussian calculation:

%Chk=H2O_631g.chk
#P rOPBE/6-31G 6D 10F SCRF=(PCM,Solvent=water)  Punch=(MO) pop=(nbo6)

H2O 6-31G

 0 1 ! charge and multiplicity
 O     0.00000     0.00000     0.118491
 H     0.00000     0.754898     -0.473964
 H     0.00000     -0.754898     -0.473964

and got

...
411          fchk file        "/home/me/scratch/Gau-24659.EFC"
412          mat. el file     "/home/me/scratch/Gau-24659.EUF"
413 
414  Writing Wrt12E file "/home/me/scratch/Gau-24659.EUF"
415  Gaussian matrix elements                                         Version   1 NLab= 7 Len12L=8 Len4L=8
416  Write GAUSSIAN SCALARS               from file   501 offset           0 to matrix element file.
..
429  Write ALPHA FOCK MATRIX              from file 10536 offset           0 to matrix element file.
430  No 2e integrals to process.
431  Perform NBO analysis...
432 
433  *********************************** NBO 6.0 ***********************************
434              N A T U R A L   A T O M I C   O R B I T A L   A N D
435           N A T U R A L   B O N D   O R B I T A L   A N A L Y S I S
436  ********************* Me *********************
..
447  Filename set to /home/me/scratch/Gau-24659
..
620           -------------------------------
621                  Total Lewis    9.99612  ( 99.9612%)
622            Valence non-Lewis    0.00029  (  0.0029%)
623            Rydberg non-Lewis    0.00358  (  0.0358%)
624           -------------------------------
625                Total unit  1   10.00000  (100.0000%)
626               Charge unit  1    0.00000
627 
628  $CHOOSE
629    LONE 1 2 END
630    BOND S 1 2 S 1 3 END
631  $END
632 
633  Maximum scratch memory used by NBO was 62605 words
634  Maximum scratch memory used by G09NBO was 9032 words
...

608. Bruker Topspin on Debian Jessie

Here's a more extensive description of how to install Bruker Topspin (student version):

Very briefly:

$ wget http://bruker.telemaxx.net/student/linux-topspin.sh
$ sudo dpkg --add-architecture i386
$ sudo apt-get update
$ sudo apt-get install libxft2:i386 libxtst6:i386 perl-tk libcups2:i386 openjdk-7-jdk
$ su -
# xauth merge /home/user/.Xauthority 
# exit
$ sh linux-topspin.sh
$ ~/carbon/topspin$ sh linux-topspin.sh 
Verifying archive integrity... All good.
Uncompressing TopSpin 3.2..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
NOTE: no display found - trying localhost:11.0
Using TCL_LIBRARY=/tmp/selfgz29293/linux/tcl-8.5.11/lib/tcl8.5
Using TK_LIBRARY=/tmp/selfgz29293/linux/tk-8.5.11/lib/tk8.5
Please enter root password if prompted for it.
Password: 
Starting /tmp/selfgz29293/linux/tk-8.5.11/bin/wish8.5 -f /tmp/selfgz29293/xwinstall.d/swim/lib/xwinstall.tcl --
Using log file: /tmp/install.log
Error while displaying /tmp/selfgz29293/rellet.pdf with /tmp/swim-29462/prog/bin/xpdf : 
/tmp/swim-29462/prog/bin/xpdf: error while loading shared libraries: libSM.so.6: cannot open shared object file: No such file or directory

Using log file: /opt/topspin3.2/install.log
Error: Cannot create user account flexlm: useradd flexlm: useradd: group flexlm exists - if you want to add this user to that group, use -g.
Errors occurred during installation:
Error: Cannot create user account flexlm: useradd flexlm: useradd: group flexlm exists - if you want to add this user to that group, use -g.

[I was doing this while logged in via ssh -XC to the student's computer, and without a pdf reader installed. If a pdf opens, close it to continue the installation. Don't worry about the errors.]

Here are screenshots from the installation process:

The only thing that remained was to install the license.dat file that Bruker had issued to my student:

sudo mv /usr/local/flexlm/Bruker/licenses/license.dat /usr/local/flexlm/Bruker/licenses/license.bak
sudo cp ~/carbon/topspin/license.dat /usr/local/flexlm/Bruker/licenses/license.dat

And then we were able to start topspin:

 And finally:

607. Ping...Topspin and ADF work on debian jessie

My blog post productivity has been getting increasingly poor over the past year and a half, with a precipitous dip occurring at the beginning of this year. The dip is due to teaching and research, and the slow but steady decline preceding it is due to parenthood (the older the little one gets, the less time -- and inclination! -- I have to do extra work. Toddlers can be so much fun.).

I've got a few posts that need a bit of polishing before I publish ('how to set up your own DNS server' and 'how to set up your own mail server' are two examples), but until then, I'll seed your google search results with the following information about something completely different:

* Bruker Topspin 3.2 (https://www.bruker.com/products/mr/nmr/nmr-software/software/topspin/overview.html) -- the NMR program, not the table tennis game -- installs fine on Debian Jessie 64 bit (the only version we tried). Note that:
** you'll need java
** you'll need the 32 bit package with libXtst.so.6, not the 64 bit package. It can be installed via apt-get install libxtst6:i386
** you'll need to enable the root account if you haven't already (the easiest way to do that is to do sudo passwd root, set a password and you're good to go)

* The trial version of the Amsterdam Density Functional package (ADF; http://www.scm.com/Downloads/2014) installs and runs fine* on one of my Debian Jessie 64 bit nodes. I did not install the intel mpi libraries, but then adf seems to be working according to a shared memory model.

Installation was quick and painless. I downloaded the package using the instructions in the email, copied the .tgz file to my node, ssh:d with X enabled (ssh -XC) to allow for interactive activation/registration, and to be able to use adfjobs (to draw molecules and set up jobs), and to be able to use adfview.

I untared the adf file:
tar xvf adf2014.07.pc64_linux.intelmpi.tgz

I then moved the folder to /opt and took ownership of it:
sudo mv adf2014.07 /opt/
sudo chown $USER:$USER /opt/adf2014.07 -R

I edited /opt/adf2014.07/adfrc.sh to read:

ADFHOME=/opt/adf2014.07

And then sourced it and ran adfjobs:
source adfrc.sh
bin/adfjobs

I was then asked to provide the username and password from my email, and from that point on it was just a matter of using the program (which has it's own quirks ).

*by default only six cores on a hex core i7-4930k are used. To force 12 cores (hyperthreading) you need to explicitly tell ADF to do so. The manual says not to, however. I haven't done any performance tests, BUT without specifying 12 cores the node is only running at half load.