Diapositiva 1

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ENEA Grid infrastructures 1
ENEA -12 research centers in Italy -A Central
Computer and Network Service (INFO) - 6
Computer Centres Casaccia, Frascati,
Bologna,Trisaia, Portici, Brindisi -
Multiplatform resources for serial parallel
computation and graphical post-processing. -
Others computer resources in ENEA
departments individuals
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Ingegneria dei Materiali e Grid 2009-04-03
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ENEA Grid infrastructures 2
Main features - Access from any kind of
connection - Sharing data in world wide areas
(geographical file system AFS) - Access to the
data from any kind of digital device client -
Running any kind of programs - Access to
National and International GRIDS
For each computational site, ENEA manages Local
Networks (LAN) whereas the computational centres
(WAN) are interconnected via Consortium GARR
Network
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ENEA Grid computatonal resources 4
O.S. CPU/Core Gflops where
AIX gt300 3000 Frascati(258), Bologna(24), Portici(18),Brindisi(2)
Linux x86 32/64 gt3000 25000 Frascati(140), Casaccia(54), Portici(2700),Trisaia(20), Brindisi(84)
Linux IA64 (Altix) 64 300 Casaccia
IRIX 26 40 Frascati(8), Casaccia(4), Portici(1),Trisaia(8), Brindisi(1), Bologna(5)
Solaris 8 10 Trisaia(4), Casaccia(2), Bologna(2)
Windows 32/64 46 100 Frascati(4), Portici(34),Trisaia(4), Brindisi(4)
Mac OS X 14 60 Frascati(1), Trisaia(13)
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ENEA Grid Architecture resources integration 3
A choice of mature components for reliability
and easiness of support and
maintenance Distributed File System AFS Job
and resources manager LSF Multicluster Unified
GUI access Java and Citrix Technologies Quality
monitoring system Patrol Licence Servers
Integration with department and individual
resources Distributed File System
AFS Licence pool sharing Possible
integration with other institutions
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CRESCO (Portici site) computatonal resources 5
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ENEA Grid / Cresco Capability for Material
Science codes

• Multicores Platforms (Cresco Linux, sp AIX)
  8, 16, 32, 48 smp nodes
• GPFS / Infiniband for high parallelism codes
• Hybrid Parallelism (Cresco smp nodes with IB
  interconnections)
• Distributed parallel Jobs across WAN or
  heterogeneous platforms
• (Parallel Jobs arrays (AFS sysname
  mechanism))
• Nvidia / Cell processor / FPGA accelerators
  (next)

Some Codes running in ENEA env. CPMD Gromacs
Pc Gamess Gaussian. . others Abinit, Amber,
etc
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Gromacs
GROMACS is a versatile package to perform
molecular dynamics, i.e. simulate the Newtonian
equations of motion for systems with hundreds to
millions of particles. It is primarily designed
for biochemical molecules like proteins and
lipids that have a lot of complicated bonded
interactions, but it can be used also for
research on non-biological systems, e.g. polymers.
Dimeric protein water ions 77000
atoms Timescale of simulation 5 ns Simulation
made on 16 cores on Cresco1, Time required 40
h.
Peptide water ions 2500 atoms Timescale of
simulation 40 ns Time required 24 h (on 8 cores
smp Intel Xeon)
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PC GAMESS / Firefly
PC GAMESS/Firefly computational Chemistry code
for ab initio and DFT calculations. Developed for
high performance calculation on Intel processors
(x86, AMD64, and EM64T). http//classic.chem.msu
.su/gran/gamess/index.html
Used on CRESCO for studying electronic
proprieties and absorption spectrum of molecules
in the photovoltaic field. On Cresco
Performances improvement of 370 (16 cores)
compared to runs on PC Desktop quad core.
modello TDDFT B3LYP/6-311G modello TDDFT B3LYP/6-311G
N. cores (MPI procs) Elapsed Time ( min.)
16 313.7
32 200.2
48 142.7
64 125.1
80 114.0
96 103.1
112 93.9
128 90.0
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Gaussian 03 electronic structure program.
Starting from the basic laws of quantum
mechanics, Gaussian is used to predicts the
energies, molecular structures, and vibrational
frequencies of molecular systems, along with
numerous molecular properties derived from these
basic computation types. It is used to study
molecules and reactions under a wide range of
conditions, including both stable species and
compounds which are difficult or impossible to
observe experimentally.

• On CRESCO is used to study proteins folding
• On shared memory
• Embarrassing parallel array of parallel jobs
• on 8 cores smp nodes.

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CPMD Car-Parrinello Molecular Dynamics
Extented tests in order to 1- Scaling
performances up to 1024 cores 2- Exploiting
Dual-level Parallelism 3- Outer loop
parallelization TASKSGROUPS
It is a plane wave/pseudopotential implementation
of Density Functional Theory, particularly
designed for ab-initio molecular dynamics.
Total tasks MPI Threads TASKS GROUPS Iterations / sec
1024 10241 8 0.0068
1024 10241 NO 0.0060
1024 5122 8 0.0244
1024 5122 NO 0.0089
1024 2564 8 0.0253
1024 2564 NO 0.0131
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Conclusions
Some Example Codes running in ENEA env. CPMD
Gromacs Pc Gamess Gaussian
References in ENEA
Some Example Codes running in ENEA env. CPMD
Gromacs Pc Gamess Gaussian
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