Biomedical Engineering Reference
In-Depth Information
dependent threads needing fast communications have to use the shared
memory within the same SM.
The latest generation of GP-GPU proposed by Nvidia, known as the Fermi
architecture, signifi cantly improves the memory bandwidth with a much larger
and reconfi gurable cache, ECC (error correction code) memory, and impres-
sive peak performances in standardized Institute of Electrical and Electronics
Engineers (IEEE) double precision with 512 CUDA cores compared to what
was obtained a few years before [34]. In order to deploy a large number of
GPUs in data centers, ECC memory was needed to detect and correct errors
introduced during storage or data transmission. In addition, the size of address-
able global memory has been considerably augmented, up to 1 terabyte for a
single GP-GPU board, to meet the needs of some supercomputing
applications.
Dealing with parallel stochastic simulations, there is a need of rigor in the
parallelization of random streams [35]. We have proposed a survey of the
current pseudo-random-number generators (PRNGs) available on GPU and
we have given a particular focus to the recent Mersenne Twister for Graphics
Processors (MTGP) that has just been released by Saito on Matsumoto's
homepage. We have empirically checked thousands of PRNGs with the most
stringent testing suite, TestU01 “ Big crush ” from [36] . The dedicated GP - GPU
generators have been created with the Dynamic Creator software designed to
propose independent MTGPs, 30% of them found to be weak according to
the current level of statistical tests. A current challenge is to prevent potential
bias introduced by the parallelization pseudo-random-number streams in grid
computing and particularly when using the latest Mersenne Twister generator
dedicated to GP - GPU.
15.6.3
New Challenge: System Radiobiology
Understanding the impact of radiation on living organisms is of crucial impor-
tance to both biology and health care. Living organisms, including humans, are
constantly exposed to ionizing particles through sunlight and radioactive
materials in the ground. Radiation exposure results in damage to the cellular
genome. This damage can kill the cell or result in mutations. Radiation expo-
sure is therefore an initiator for evolution and also one of the earliest identi-
fi ed causes of cancers. Radiation is also used to kill cancerous cells through
brachytherapy and radiotherapy treatment.
Radiobiology aims at reaching a deeper understanding of the interaction
of radiation with living organisms. Progress in acceleration and imaging tech-
niques as well as high-throughput sequencing opens new avenues for a quan-
titative assessment of the damage one ionizing particle can produce on the
genome of a model organism or a human cell.
These data are needed for the modeling of living organisms under radiation
exposure. Such modeling requires simulating the living organism, the interac-
tion of ionizing particles inside it, in particular the damage to its DNA, and
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