Amber 6.0 on Intel IA-64 Server

From: EPD-BLRSJP-PEG <Ramakrishna>
Date: Fri 9 Nov 2001 08:38:51 +0530

> Dear Sir,
> I am Ramakrishna (ramki) working in Wipro Infotech, Product Engineering
> Group, INDIA. I am working on the Server Range of Products for Wipro
> Infotech.
> Once of our Customer as asked for Amber 6.0 with MPICH + RedHat Linux for
> IA-64 on our IA-64 Server.
> As per the customer the customer is facing some issues in Compiling the
> Source (g77) of Amber on IA-64 Server. We have checked the MPICH and is
> working fine. Complier Options tried out are Intel Compile C/C++ for IA-64
> and Default Complier that comes with RedHat Linux for IA-64
> ( Customer is IIT-Delhi)
> 1. Requirement : 128 CPU Cluster running AMBER 6.0 (This requires
> G77complier for Linux)
> ( Customer is looking at 128 CPU IA-64 Cluster = 32 * 4 CPU Intel LION
> Servers in a Cluster!)
> ****************************Project Details ****************************
> Project title : Molecular dynamics Computer Simulations on
> Dihydrofolate Reductase
> (DHFR) to investigate Structure and Dynamics of the Enzyme
> paving the way
> eventually for Inhibitor/Drug Design.
> Project description:
> The system IIT intends to study consists of ~ 25000 atoms equivalent
> to 75000 degrees of freedom). Proposed to solve Newton's equations of
> motion for this system, i.e. numerically integrate 75000 coupled
> differential equations for each time step, which is equivalent to 1
> femtosecond (fs). The system has to be monitored for at least 10ns which
> amounts to a computational work of calculating 75000 forces, positions,
> velocities and other parameters and solving the 75000 coupled differential
> equations 10 million times. It is desirable that this process be completed
> in about 1 hour for efficient drug design. The molecular dynamics
> software package used is AMBER 6.0.
> Eventually a cluster, with sufficient number of nodes, has to be
> established at IIT to meet the above objectives.
> Progress made : We have established a Beowulf cluster and have tested with
> 4 node (IA-32 Platform) and checked out the functionality. The test was
> conducted and results not giving the Performance the customer requires and
> has request us for the same on IA-64 Platform and is facing the problem
> described above
> We would like to know the Machine file to be used for IA-64 Platform to
> compile the AMBER source. (We are presently using the Default MPICH
> machine file for compiling)
> We would appreciate if you could help us on this.
> Waiting for a speedy response.
> Regards,
> ramki.
> S.Ramakrishna
> Specialist - Product Engg. Group
> Wipro Infotech.
> Bangalore
> Email :
> website :
> Tel :091-80-8440329

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Received on Thu Nov 08 2001 - 19:08:51 PST
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