282. Mesa 9.0.1 (64 bit) on debian wheezy

This post is intended as a step towards building wine with libOSmesa. Apparently any version of libOSmesa lower than 9 is no good, and debian wheezy currently have version 8.

Unfortunately building the 32 bit version turns out to be more complex than just requesting it via --enable-32-bit, so I'll be making a post on a chrooted build of the missing wine libraries later. I've also noticed that libOSMesa is just a small part of Mesa -- this build overlaps a lot with mesa-common-dev as well.

Finally, I don't really have a good grasp over graphics on linux -- which means that I'm still confused by OpenGl, CL, Mesa etc.

UPDATE (10th Jan 2013): See here for Wine 1.5.21 using the multiarch approach: http://verahill.blogspot.com.au/2013/01/308-compiling-wine-1521-on-debian.html

As usual: I have a lot of packages installed on my standard compile node, so there are probably a lot of packages which are needed which I didn't notice. But here we go:

---

First you need to build e.g. libdrm 2.4.40 since wheezy and sid currently have v2.4.33 and you need 2.4.39 or newer.

sudo apt-get install libpciaccess-dev checkinstall
wget http://cgit.freedesktop.org/mesa/drm/snapshot/libdrm-2.4.40.tar.gz
tar xvf libdrm-2.4.40.tar.gz
cd libdrm-2.4.40/
./autogen 
make
sudo checkinstall

When you're asked for a description, type 'libdrm 2.4.40' and it should get the version number right.
(you could also build with --prefix and install it somewhere else but that makes things trickier later)

Make sure it installed correctly:

aptitude show libdrm
Package: libdrm                          
New: yes
State: installed
Automatically installed: no
Version: 2.4.40-1
Priority: extra
Section: checkinstall
Maintainer: root@beryllium
Architecture: amd64
Uncompressed Size: 733 k
Description: libdrm 2.4.40

---

Build OS mesa v.9.0.1.

sudo apt-get install flex bison libdrm-dev xutils-dev x11proto-gl-dev x11proto-dri2-dev libx11-xcb-dev libxcb-glx0-dev libxcb-dri2-0-dev libxcb-xfixes0-dev llvm automake
cd ~/tmp
wget ftp://ftp.freedesktop.org/pub/mesa/9.0.1/MesaLib-9.0.1.tar.gz
tar xvf MesaLib-9.0.1.tar.gz
cd Mesa-9.0.1/
./autogen.sh --enable-osmesa
make
sudo checkinstall

This package will be built according to these values: 

0 -  Maintainer: [ root@beryllium ]
1 -  Summary: [ Mesa 9.0.1 64 bit]
2 -  Name:    [ mesa ]
3 -  Version: [ 9.0.1 ]
4 -  Release: [ 1 ]
5 -  License: [ GPL ]
6 -  Group:   [ checkinstall ]
7 -  Architecture: [ amd64 ]
8 -  Source location: [ Mesa-9.0.1 ]
9 -  Alternate source location: [  ]
10 - Requires: [  ]
11 - Provides: [ mesa ]
12 - Conflicts: [  ]
13 - Replaces: [  ]

Some notes:
xutils-dev contains makedepend; x11proto-gl-dev is GLPROTO, x11proto-dri2-dev is DRI2PROTO
LLVM is needed for one step in the build process (gallium). I'm sure you can get around it, but I'm not too bothered.



Links to this post:
http://forums.linuxmint.com/viewtopic.php?f=190&p=696973

281. Visualising NWChem output with GabEdit

Update: please read Karol's comment below. I will put a link here once I've written up a post on how to modify nwchem.

Update 2: Here's the post: http://verahill.blogspot.com.au/2013/02/3xx-modifying-nwchem-611-to-work-with.html .The conclusion is that you MUST edit nwchem. Luckily, it's easy.

Original post:
I've never liked Gabedit much (looks a bit dated, tries to do 'too much') -- until today. Suddenly I have a newfound respect for the developer(s) behind it. It actually doesn't try to do 'too much' -- it simply does A LOT, and actually does it in a pretty transparent way.

Long story short -- you can do things with gabedit which you can't do (easily) with ECCE, and as such it has become an important ally. Besides, it's always nice to have alternatives.

GabEdit is in the Debian repos.

Running your calculations
There are some restrictions"
1. NOTE: you must run your nwchem job with explicit basis sets (i.e. entered as text) -- to do that in ECCE tick the box as shown in the figure below. If you're running 'pure' nwchem, you (probably) have to cut and paste from the basis set directory -- see e.g. section 7.2 here. It's a minor convenience for gaining access to what GabEdit has to offer.

2. You can only open Single point/Energy calculations i.e. Optimizations won't work. So do a single point calculation on your optimized structure.

3. Also, you need to rename/copy your output file so that it ends with .out.

gabedit won't read it otherwise

GabEdit
It's fairly straightforward -- just point and click. One thing which you will want to play with are the iso-surface settings. The defaults are rarely good.

Anyway, I'll let the screenshots do the talking:

Go straight to the Output viewer -- Geometry/Orbital/Density

Click on the M, or right-click anywhere in the window, and load your renamed nwchem output file.

Here's triplet oxygen. The alpha, beta orbitals are listed in the right window

You can do electron localisation

Look at spin density (the unpaired electrons are in the anti-bonding  pi orbitals)

Contour plots are neat -- here showing spin density

Electrostatic potential. 

There's a lot to explore. GabEdit can obviously also prepare and submit jobs, but I'm happy with ECCE in this respect, and content with using GabEdit for post-processing.

280. gOpenMol on Debian Wheezy

This is a quick description of how to install gOpenMol (software for visualising output from various comp. chem. packages) on debian:

wget http://www.csc.fi/english/pages/g0penMol/Downloads/gopenmol-3.00-linux.tar.gz
gopenmol-3.00-linux.tar.gz
tar xvf gopenmol-3.00-linux.tar.gz
sudo mv gOpenMol-3.00 /opt/
/opt/gOpenMol-3.00/./install
echo 'export PATH=$PATH:/opt/gOpenMol-3.00/bin' >> ~/.bashrc
source ~/.bashrc
rungOpenMol

I'm having issues with a transparent background in the main window on my nvidia box. Not sure what it's like  on other machines.