Difference: Applications (23 vs. 24)

Revision 242012-10-26 - DanieleCesini

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MPI-multicore: Applications

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 The NEMO 3.4 oofs2 multiscale simulation package has been ported in the Grid environment in order to run parallel calculations. The NEMO code has significant CPU and memory demand (from our calculations we estimated 1GB/core for a 8 cores simulation). The NEMO code can be used for production as well as for testing purposes by modifying the model (this means recompiling the source code) or varying the input parameters. The user community was interested in exploiting the Grid for the second use case (model testing and tuning) which implies that the package must be executed several times in a parameter sweeping approach. An additional benefit coming from this work is that scientist operating in the field of oceanographic who would be interested in the execution of the code, can share application and results using the Grid data management and sharing facilities.
Namd - Alessandro Venturini (CNR-BO)
Namd - Alessandro Venturini (ISOF-CNR-BO)
 NAMD is a powerful parallel Molecular Mechanics(MM)/Molecular Dynamics(MD) code particularly suited for the study of large biomolecules. However, it is also compatible with different force fields, making possible the simulation of systems of quite different characteristics. NAMD can be efficiently used on large multi-core platforms and clusters.

The NAMD use case was a simulation of a 36000 atoms lipid provided by a CNR-ISOF [21] group located in Bologna. To have a real-life use case the simulation had to be run for at least 25 nanoseconds of simulated time resulting on a wallclock time of about 40 days if run on a 8 cores machine.

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  • the length of the simulation implied many computation checkpoints given the time limits on the batch system queues of the sites matching the requirements. We decided to split the simulation in 50 steps each 500 ps of simulated time long, allowing to complete each step without reaching the queues time limits.
Gaussian - Stefano Ottani (ISOF-CNR-BO)
provides state-of-the-art capabilities for electronic structure modeling can run on single CPU systems and in parallel on shared-memory multiprocessor systems Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Uses a couston system to parallelize the code or linda.

The use case foresees an umbrella sampling calculation with many short parallel simulations whose output is statistically analysed.

Globo - (ISAC-CNR-BO)
RegCM - Stefano Cozzini (SISSA)

RegCM is the first limited area model developed for long term regional climate simulation currently being developed at the Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy. RegCM4 is a regional climate model based on the concept of one-way nesting, in which large scale meteorological fields from a Global Circulation Model (GCM) run provides initial and time-dependent meteorological boundary conditions for high resolution simulations on a specific region. The RegCM4 computational engine is CPU intensive using MPI parallel software.

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