458 research outputs found
Scalable temporal order analysis for large scale debugging
We present a scalable temporal order analysis technique that sup-ports debugging of large scale applications by classifying MPI tasks based on their logical program execution order. Our approach combines static analysis techniques with dynamic analysis to de-termine this temporal order scalably. It uses scalable stack trace analysis techniques to guide selection of critical program execu-tion points in anomalous application runs. Our novel temporal or-dering engine then leverages this information along with the ap-plication’s static control structure to apply data flow analysis tech-niques to determine key application data such as loop control vari-ables. We then use lightweight techniques to gather the dynamic data that determines the temporal order of the MPI tasks. Our evaluation, which extends the Stack Trace Analysis Tool (STAT), demonstrates that this temporal order analysis technique can isolate bugs in benchmark codes with injected faults as well as a real world hang case with AMG2006
Double Field Theory
The zero modes of closed strings on a torus --the torus coordinates plus dual
coordinates conjugate to winding number-- parameterize a doubled torus. In
closed string field theory, the string field depends on all zero-modes and so
can be expanded to give an infinite set of fields on the doubled torus. We use
the string field theory to construct a theory of massless fields on the doubled
torus. Key to the consistency is a constraint on fields and gauge parameters
that arises from the L_0 - \bar L_0=0 condition in closed string theory. The
symmetry of this double field theory includes usual and 'dual diffeomorphisms',
together with a T-duality acting on fields that have explicit dependence on the
torus coordinates and the dual coordinates. We find that, along with gravity, a
Kalb-Ramond field and a dilaton must be added to support both usual and dual
diffeomorphisms. We construct a fully consistent and gauge invariant action on
the doubled torus to cubic order in the fields. We discuss the challenges
involved in the construction of the full nonlinear theory. We emphasize that
the doubled geometry is physical and the dual dimensions should not be viewed
as an auxiliary structure or a gauge artifact.Comment: 51 pages. v2: Corrected typo in eqn. (2.48) and very minor typos
elsewhere. Added ref. [9] to M. Van Raamsdon
Lessons learned at 208K: Towards debugging millions of cores
Petascale systems will present several new challenges to performance and correctness tools. Such machines may contain millions of cores, requiring that tools use scalable data structures and analysis algorithms to collect and to process application data. In addition, at such scales, each tool itself will become a large parallel application – already, debugging the full BlueGene/L (BG/L) installation at the Lawrence Livermore National Laboratory requires employing 1664 tool daemons. To scale to such counts and beyond, tools must employ a scalable communication infrastructure and manage their own tool processes efficiently. Some system resources, such as the file system, may also become a tool bottleneck. In this paper, we present challenges to petascale tool development, using the Stack Trace Analysis Tool (STAT) as a case study. STAT is a lightweight tool that gathers and merges stack traces from a parallel application to identify process equivalence classes. We use results gathered at thousands of tasks on an Infiniband cluster and results up to 208K processes on BG/L to identify current scalability issues as well as challenges that will be faced at the petas-cale. We then present solutions to these challenges that have been implemented and show the resulting performance improvements. We also discuss future plans to meet the debugging demands of petascale machines.
UBVRI Light Curves of 44 Type Ia Supernovae
We present UBVRI photometry of 44 type-Ia supernovae (SN Ia) observed from
1997 to 2001 as part of a continuing monitoring campaign at the Fred Lawrence
Whipple Observatory of the Harvard-Smithsonian Center for Astrophysics. The
data set comprises 2190 observations and is the largest homogeneously observed
and reduced sample of SN Ia to date, nearly doubling the number of
well-observed, nearby SN Ia with published multicolor CCD light curves. The
large sample of U-band photometry is a unique addition, with important
connections to SN Ia observed at high redshift. The decline rate of SN Ia
U-band light curves correlates well with the decline rate in other bands, as
does the U-B color at maximum light. However, the U-band peak magnitudes show
an increased dispersion relative to other bands even after accounting for
extinction and decline rate, amounting to an additional ~40% intrinsic scatter
compared to B-band.Comment: 84 authors, 71 pages, 51 tables, 10 figures. Accepted for publication
in the Astronomical Journal. Version with high-res figures and electronic
data at http://astron.berkeley.edu/~saurabh/cfa2snIa
Silent but Not Static: Accelerated Base-Pair Substitution in Silenced Chromatin of Budding Yeasts
Subtelomeric DNA in budding yeasts, like metazoan heterochromatin, is gene poor, repetitive, transiently silenced, and highly dynamic. The rapid evolution of subtelomeric regions is commonly thought to arise from transposon activity and increased recombination between repetitive elements. However, we found evidence of an additional factor in this diversification. We observed a surprising level of nucleotide divergence in transcriptionally silenced regions in inter-species comparisons of Saccharomyces yeasts. Likewise, intra-species analysis of polymorphisms also revealed increased SNP frequencies in both intergenic and synonymous coding positions of silenced DNA. This analysis suggested that silenced DNA in Saccharomyces cerevisiae and closely related species had increased single base-pair substitution that was likely due to the effects of the silencing machinery on DNA replication or repair
Upper limits on the strength of periodic gravitational waves from PSR J1939+2134
The first science run of the LIGO and GEO gravitational wave detectors
presented the opportunity to test methods of searching for gravitational waves
from known pulsars. Here we present new direct upper limits on the strength of
waves from the pulsar PSR J1939+2134 using two independent analysis methods,
one in the frequency domain using frequentist statistics and one in the time
domain using Bayesian inference. Both methods show that the strain amplitude at
Earth from this pulsar is less than a few times .Comment: 7 pages, 1 figure, to appear in the Proceedings of the 5th Edoardo
Amaldi Conference on Gravitational Waves, Tirrenia, Pisa, Italy, 6-11 July
200
Improving the sensitivity to gravitational-wave sources by modifying the input-output optics of advanced interferometers
We study frequency dependent (FD) input-output schemes for signal-recycling
interferometers, the baseline design of Advanced LIGO and the current
configuration of GEO 600. Complementary to a recent proposal by Harms et al. to
use FD input squeezing and ordinary homodyne detection, we explore a scheme
which uses ordinary squeezed vacuum, but FD readout. Both schemes, which are
sub-optimal among all possible input-output schemes, provide a global noise
suppression by the power squeeze factor, while being realizable by using
detuned Fabry-Perot cavities as input/output filters. At high frequencies, the
two schemes are shown to be equivalent, while at low frequencies our scheme
gives better performance than that of Harms et al., and is nearly fully
optimal. We then study the sensitivity improvement achievable by these schemes
in Advanced LIGO era (with 30-m filter cavities and current estimates of
filter-mirror losses and thermal noise), for neutron star binary inspirals, and
for narrowband GW sources such as low-mass X-ray binaries and known radio
pulsars. Optical losses are shown to be a major obstacle for the actual
implementation of these techniques in Advanced LIGO. On time scales of
third-generation interferometers, like EURO/LIGO-III (~2012), with
kilometer-scale filter cavities, a signal-recycling interferometer with the FD
readout scheme explored in this paper can have performances comparable to
existing proposals. [abridged]Comment: Figs. 9 and 12 corrected; Appendix added for narrowband data analysi
Using Combined Morphological, Allometric and Molecular Approaches to Identify Species of the Genus Raillietiella (Pentastomida)
Taxonomic studies of parasites can be severely compromised if the host species affects parasite morphology; an uncritical analysis might recognize multiple taxa simply because of phenotypically plastic responses of parasite morphology to host physiology. Pentastomids of the genus Raillietiella are endoparasitic crustaceans primarily infecting the respiratory system of carnivorous reptiles, but also recorded from bufonid anurans. The delineation of pentastomids at the generic level is clear, but the taxonomic status of many species is not. We collected raillietiellids from lungs of the invasive cane toad (Rhinella marina), the invasive Asian house gecko (Hemidactylus frenatus), and a native tree frog (Litoria caerulea) in tropical Australia, and employed a combination of genetic analyses, and traditional and novel morphological methods to clarify their identity. Conventional analyses of parasite morphology (which focus on raw values of morphological traits) revealed two discrete clusters in terms of pentastome hook size, implying two different species of pentastomes: one from toads and a tree frog (Raillietiella indica) and another from lizards (Raillietiella frenatus). However, these clusters disappeared in allometric analyses that took pentastome body size into account, suggesting that only a single pentastome taxon may be involved. Our molecular data revealed no genetic differences between parasites in toads versus lizards, confirming that there was only one species: R. frenatus. This pentastome (previously known only from lizards) clearly is also capable of maturing in anurans. Our analyses show that the morphological features used in pentastomid taxonomy change as the parasite transitions through developmental stages in the definitive host. To facilitate valid descriptions of new species of pentastomes, future taxonomic work should include both morphological measurements (incorporating quantitative measures of body size and hook bluntness) and molecular data
Quantum state preparation and macroscopic entanglement in gravitational-wave detectors
Long-baseline laser-interferometer gravitational-wave detectors are operating
at a factor of 10 (in amplitude) above the standard quantum limit (SQL) within
a broad frequency band. Such a low classical noise budget has already allowed
the creation of a controlled 2.7 kg macroscopic oscillator with an effective
eigenfrequency of 150 Hz and an occupation number of 200. This result, along
with the prospect for further improvements, heralds the new possibility of
experimentally probing macroscopic quantum mechanics (MQM) - quantum mechanical
behavior of objects in the realm of everyday experience - using
gravitational-wave detectors. In this paper, we provide the mathematical
foundation for the first step of a MQM experiment: the preparation of a
macroscopic test mass into a nearly minimum-Heisenberg-limited Gaussian quantum
state, which is possible if the interferometer's classical noise beats the SQL
in a broad frequency band. Our formalism, based on Wiener filtering, allows a
straightforward conversion from the classical noise budget of a laser
interferometer, in terms of noise spectra, into the strategy for quantum state
preparation, and the quality of the prepared state. Using this formalism, we
consider how Gaussian entanglement can be built among two macroscopic test
masses, and the performance of the planned Advanced LIGO interferometers in
quantum-state preparation
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