Cluster Computing Group: Update - Josh H

June 20, 2004

Update - Josh H - June 20, 2004

Worked On/Working On

Weather Duck I updated the code to make it a bit more robust, and checked the sound. It seems to work exactly as it should, but I cannot verify the dB since I don't have anything that produces a given dB that I can measure with it. Some informal testing showed that it was working fine, but not nearly as sensitive as it once was.
GROMACS Port PVM: Version 0, 1, and 2 are finished. Version 3 should be finished Monday morning. Next to run is the MP-Lite port.
GROMACS Port MP-Lite: I am compiling the first version using the MPI bindings and default TCP window sizes. Once the PVM runs are finished then I can fully test my configure scripts, and make sure that I have everything wired up correctly.
Versions:
1. Version 0: (mp_iterface = MP-Lite) Use MPI Bindings and little to no changes in the GROMACS code.
2. Version 1: (mp_iterface = MP-Litev1) Use make tcp_sync to see how much of a performace gain we can set from the syncronous TCP version.
3. Version 2: (mp_iterface = MP-Litev2) Possible Convert GROMACS source from MPI to MP-Lite syntax to see if there is a performace benifit from using the native calls instead of the Wrappers. This is unlikely, but possible.
4. Version 3: (mp_iterface = MP-Litev3) Use the suggested rmem_max and wmem_max sizes in the MP-Lite/README
I am working on a tool to catalog informaiton about molecules. Specificaly Fail modes, and contributed information. I am currently working on the web interface to this tool. I have created 2 new tables in the databse, and thier schemas have been appended to the end of the db-objects.sql file.

To do

B-and-T-GROMACS Paper
F@C development
Port GROMACS to:
1. MPICH
2. MPICH2

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Cluster Computing Group

General Project

June 20, 2004

Update - Josh H - June 20, 2004