PC GAMESS benchmarks

Alex Granovsky presented the results of the PC GAMESS (version of Gamess US designed to work better on x86 architecture) benchmarks on new AMD Opteron and Intel Core2 processors. You can find them here.

The most important observations are:

• Intel CPUs are much faster,
• but AMDs scale better with number of cores.

BTW. You can find other interesting benchmark in the Performance section of the PC GAMESS website.

Tips for starting MacOSX apps

1. If you want to start a MacOSX applications from a terminal (or a shell script) you have to use the open command, i.e.: open /Application/Firefox.app (based on xahlee.org)
2. If you need to write a wrapper starting a binary file (which is inside of a MacOSX app) with some options you can use following construction: HERE=`dirname $0`; $HERE/name.x -options The same construction is useful if you need to set some environment variables.
3. Sometimes is it necessary to have a location of an app, but apps can be place in a very strange places. MacOSX binaries are located third level deep inside of an app, so the following command save location of an app in the TOPDIR variable: TOPDIR=`cd $HERE/../../../; pwd`

3D in Linux

There is a very interesting overview of present state (Nov 2007) of 3D graphic card drivers on Mitch Meyran's blog.

Two chemical links

This time two links to websites related to chemistry.

• The Supercomputing Institute from University of Minnesota prepared kit of Tutorials for Computational Chemistry and Physics Sciences.
• Vitalii Vanovschi created the website with many important chemical informations.

OpenGL and Windows

I'm starting to me more interesting in 3D graphic. Looking for some information about OpenGL on Windows I found Lucian Wischik old webpage. Maybe information collected on it isn't the latest news, but at least one thing is quite interesting. There is a register key which keep information about which library provided OpenGL functionality on your computer. HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\OpenGLDrivers. The another interesting finding is OpenGL Extension Viewer provided by RealTech-Vr. It works on Windows, MacOSX and under Wine.

Getting the Molcas CASPT2 exciation energy

This is the short bash/awk script printing an energy of excitation to a first excited stated obtain by CASPT2 method in Molcas6:

for i in *.log
do echo $i
grep "Total energy:" $i| gawk ' BEGIN {l=1} {if (l==1) {a=$3} else if (l==2) \
{b=$3; print 27.2097*(b-a)} l++} '
done

LaTeX font catalog

If you need nice, non-standard fonts for LaTeX visit Palle Jørgensen LaTeX Font Catalogue.

I Gited my PhD

From the beginning of writing my PhD thesis I've been using RCS to store revision of my tex files. I even add settings to my GVIM that Ctrl+S make a new revision. Recently, when I started to finishing Phd ;), I found lack information about files other than main tex files (tabels, figures etc). I also wanted to be sure that change prepered on one machines can be easily reach from other ones. I decided to use something more complex than RCS and chose git. It is very easy to send commits to my academic server (git push ssh://user@server/~/PhD) and getting the latest version from it (git pull ssh://user@server/~/PhD). However, I found that it isn't so easy to edit files on my server. Directory doesn't change after pushing it from remote repository. My first work around was on the server first committing changes - it means reverting files to state before pushing, and latter reverting to previous version -it means last version committed from remote machine. Does it sound complicated? Yes! So I was trying find the other way. Today I found it. On remote machine I do: git add filename(if needed) git commit -a git push ssh://user@server/~/PhD Later on server: git reset --hard HEAD And now I has the same files at server and any remote machines. Nice. And I need only ssh to do it.

Nekochan.Net

If you like IRIX and other old UNIX systems, Nekochan.Net is a place for you. There are a lot of software for IRIX, very interesting forum (not only about IRIX) and nice screenshots, like this one:

Comparing two list of files

I had to compare list of files, which was stored in two files. I wrote a small shell script.

for i in `cat ~buildman/WhiteList`
do
        grep $i ~buildman/BlackList
done

But beware it is taking each line of WhiteList as a substring. So if you have aaa in WhiteList that aaaaa from BlackList will be printed out.

Find

Unix find command is powerful tool. Recently, I learn how to use it to fix wrong permission of a whole directory tree (hundres of files). If you will be in similar situation try to use: find -nouser - looking for files (directories) not belongs to user. find -type f -not -perm 644 - looking for files with permision other that 644 find -type d -not -perm 755 - looking for directories with permision other that 755

10 nice shell command

Here you can find 10 nice, but not very other using shell command. Personally, I was using bc and lsof.

Solaris vs. Linux for Application Developers

At Sun Developer Network there is quite the article examines similarities and differences in the development environments between Linux and Solaris operating systems.

Another interesting blog about HPC

John West, the Director of the DoD Major Shared Resource Center at ERDC in Vicksburg, MS has created a blog where he discusses new developments in HPC. Check it out - very interesting info.

Geometries from Gaussian Scan

Reading geometries from Gaussian file storing information about Potential Energy Scan (PES) isn't easy. I was sure that there were some tools to do this, but I cannot find any yesterday, so I prepared my own. It is writing in python, of course ;). Right now have very basic features. It reads input file and created output xyz files (as many as stationary points was found). You are using it simply writing in command line:

scaner-0.1.py inputfile

Greping excitation energy from Gaussian output

I've already written about CIS energies, but my suggestion is more general. You can use that command also for TDDFT calculations. But if you need energies from perturbative correction of CIS method (CIS(D) method) you have to use this:

 grep "CIS(D) Exc\. E" *.log

'Symmetry' font in LaTeX

If you need nice font for symmetry group names use mathrsfs package and next (example for C2 group) $\mathscr{C}_2$ in the text. Of course you can use it for many other purpose.

Hack a Rox

I like Rox, but it has some annoying small problems. One of them is that the program which open the file is running from home directory. Now I write short script which fix it for gvim and I'm thinking how to do global...

#!/bin/sh
cd `dirname "$@"`
gvim `basename "$@"`

Vim's colorscheme

I've found nice site with sample of Vim's colorschemse. I miss only python samples.

XymTeX: example

I'm using XymTeX to creating chemical structures in PhD thesis. I'm not fully satisfe, but it create structures' counter , which can be use for numbering and refering to structures. Recently I created Reichardt Betaine subtituted by eter crown. The command which create this picture is below. Is nice, isn't it ;) \begin{XyMcompd}(800,2000)(,-1400){zw:korona}{}
\sixheterov[ace]{4==\upnobond{N}{$\oplus$}} %
{1==Ph;3==Ph;5==Ph; %
4==\cyclohexanev[ace %
{c\sixfusev[ %
{c\sixfusev[ %
{d\sixfusev{2==O;5==\null}{}{A}[ef]} %
]{1==\null;4==\null}{}{F}[de]} %
]{3==O}{}{F}[cde]} %
{d\sixfusev[ %
{d\sixfusev[ %
{c\sixfusev{3==O;6==O}{}{F}[ab]} %
]{1==\null;4==\null}{}{A}[bc]} %
]{5==O}{}{A}[bcd]} %
] %
{4D=={\hspace*{-1.5mm}$| \underline{\mathrm{O}}|^{\ominus}$};1==(yl)}}
\end{XyMcompd}
If you don't like XymTeX you can try konwerter very nice program by Piotr Wawrzyniak.