GLUE - Emergent Wiki

BMC GLUE

Bryn Mawr College Group of Linux and Unix Enthusiasts

These pages contain notes and links of the BMC GLUE. Please help us by adding and editing these pages. Feel free to put useful information here.

Schedule

The new new time for meetings is Tuesday 12 -1.

As we will not meet every week, please check this page for updates

12 noon Tuesday, Dec 7th, 2004

I will not be there (mrice) but please meet without me if you can.

12 noon Tuesday, Nov 30, 2004

12 noon Tuesday, Nov 23, 2004

We will have an update on the progress of getting Gaussian and Grid Mathematica running on the Beowulf cluster. (From Matt, Doug, Swarna and Xianlong.)

Here are some references on the Gaussian program running on Beowulf cluster. The first impression is that there is no trouble for Guassian to run a Beowulf cluster.

1. From DHPC Technical Report DHPC-073, dated on Jan, 2000. It's a very long report. All kinds of deail issues were dicussed. Two ab inito computational chemistry packages were installed, Gaussian and Gamess-US. http://dhpc.adelaide.edu.au/reports/073/html/dhpc-073.html

2. The Edda Beowulf at Geman, an example of Gaussian98 running on Beowulf. Performance scaling results with node number on a specific gaussian job were reported. http://vanilla.ice.mpg.de/departments/ChemInf/edda.html

3. Paper from J Computational Chemistry. Vol. 19, p1053 Detail discussion on the parallellelization in Guassian which is based on Linda. http://www3.interscience.wiley.com/cgi-bin/fulltext/33941/PDFSTART

Starting gridMathematica:

(you will have to be root on the machine to do this)

assuming that many individually licensed copies of mathematica are suitable:

STEP 1)

mount -t nfs lyndoch.brynmawr.edu:/software <mount_point>

run the installer:

<mount_point>/mathematica_5s/Unix/Installer/MathInstaller

to install mathematica 5.0

(you can register in seconds over the web (as a single machine). Our license # is L2976-7106 )

(Type Mathematica to start mathematica)

(there is also a folder mathematica_5n on Lyndoch. I was given two disks, one for "single licenses" and one for "network licenses". I am not sure of the difference, as the mathematica_5s seems to have a "network" option. At the moment, we do not (to my knowledge) have a license server on campus though, so have never installed from mathematica_5n/ nor chosen the "network" license option.)

STEP 2)

Once you have Mathematica installed, you then need to install the PCT

run the installer

<mount_point>/mathematica_pct_1.0/Unix/Installer/AppInstaller

(I had trouble getting this to start. I tried switching shells and tried

sh <mount_point>/mathematica_pct_1.0/Unix/Installer/AppInstaller

one of these worked I cant remember which. I was in a bash shell on a debian box)

Install is very quick (as I think it just copies some .m files over to the Applications directory.)

I suppose that you have to do at least step 1 (if not both) on at least two computers to use the parallel functionality.)

This is really where I must turn it over to the users (apart from learning to install the license manager if it is needed, or makes the grid computing easier.) I started mathematica, and poked around.

typing

<<Parallel` (to load the package)

does not give any errors, but more than that I do not know. From my brief poking around, the package Parallel rewrites standard mathematica functions in a suitable form for parallel computing.

There is documentation in:

/usr/share/Mathematica/Applications/Parallel/Documentation/English

and I am sure you can find stuff on the web.

4pm Wednesday, Nov 10, 2004

Meeting in room 380 Collier.

Discussion topic: Swarna and Xianlong will give us a demo of Gaussian in action.

4pm Wednesday, Nov 3, 2004

Meeting rescheduled

1pm Thursday, Oct 28, 2004

Matt presented a HOWTO on VNC, Virtual Network Computer.

Links:

Here is Deepak's /home/dkumar/.vnc/xstartup file:

   #! /bin/sh
   exec /etc/X11/xinit/xinitrc

It would be useful to be able to cut and paste from the local to the remote host. A utility to do this is:

autocutsel

I have the binary in my bin on bubo, and will probably install it system wide on the cs lab machines.

One should add the line: autocutsel & before the window manager in your xstartup file, like so:

   #! /bin/sh
   autocutsel & 
   exec /etc/X11/xinit/xinitrc