IPP Annual Report 2007 - Max-Planck-Institut für Plasmaphysik ...

ATLAS is one particular detector, which will provide huge
amounts of data from 2008 on, and many institutes all over
the world consider working with these data. In order to make
this feasible, a hierarchical network of so-called Tier centres
has been established, by which the data is shared and replicated
in a reasonable fashion and the workload is distributed
to the centres.
In Munich, a Tier2 centre was set up by the MPP, the Physics
department of the LMU and the associated computing centres
LRZ and RZG. The tasks of a Tier2 centre are to provide a
certain amount of compute and memory resources, which are
placed at the disposal of all sites taking part in the WLCG
(world-wide LHC Computing Grid) community, and to establish
sufficient memory bandwidth and services for the data
exchange with the associated Tier1 centre. Furthermore, the
Tier2 centre has to provide and support a so-called Gridmiddleware
system, which enables all partners in the WLCG
to access and use the mutual resources.
Bioinformatics/Computational Biology
Within an interdisciplinary consortium joined by several
Max Planck Institutes, the RZG has established a soft and
hardware infrastructure for computational-biology applications
called MIGenAS (Max Planck Integrated Gene Analysis
System). Generally speaking, this environment allows integrated
access to all relevant software tools and biological
data which are required for comprehensive analyses of biological
systems and mediates transparent access to the underlying
computing resources operated by the RZG. With the
help of two scientific positions provided by the Max Planck
Society, the RZG hosts various bioinformatics services for
project-internal and public use, offers application support
for bioinformatics projects of the Max Planck Society, contributes
original software development and also participates
in various research projects.
Currently we are, for example, involved in a number of computationally
challenging analyses which are emerging from
so-called metagenomics projects: Thanks to the latest generation
of high-throughput sequencing technology, huge amounts
of DNA sequence data can nowadays efficiently be recovered
from all kinds of environmental samples. Comparing
such DNA sequence data with large databases of annotated
sequences allows one to assign species information to the
unknown sequences and thus gain insights into the biodiversity
of the corresponding habitat. Given the amount of
sequence data to be processed and the size of the relevant
databases to compare with, thorough optimizations of the
corresponding computations have become indispensable. To
this end, a systematic survey of existing algorithms and their
implementation in software was conducted in the context of
a Diploma thesis (H. Zimmerer) supervised jointly with
Prof. D. Huson (University of Tübingen).
Computer Center Garching
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Concerning bioinformatics software development work has
been focused on the reimplementation and functional extension
of HaloLex, which is a software system for the central
management, integration, curation, and web-based visualization
of genomic and other related “omics” experimental
data (e.g. proteomics) for micro-organisms. The reimplementation
of HaloLex is based on modern software technology
and is being performed in close collaboration with the
original authors (Dept. Oesterhelt, MPI of Biochemistry).
Meanwhile, the system is capable of efficiently handling
data for any given micro-organism and the new web portal
(www.halolex.mpg.de) is already being used by different collaborations
in production for data curation of various genomes.
Videoconferencing (VC)
The VC infrastructure load surpassed the 2006 level. The
total conference time increased to 7152 h, that is about 30 %
plus compared to 2006. The Gatekeeper worked without
breakdowns, with some scheduled shut-downs due to power
supply work. The number of registered endpoints increased
to 350, a plus of 40 %. Conferences with presentation sharing
have become standard. The new Codian MCUs of the
DFNVC Service delivered a very reliable and high-quality
performance; about 30 % of all calls are multi-point. The
new booking system covering 28 rooms (8 VC rooms in
Garching, 6 in Greifswald, 14 non VC meeting rooms) has
been accepted throughout both sites. In 2006 there have
been 2123 bookings (the system was implemented in July
2006), in 2007 the number was 10767 equivalent to an average
1.5 bookings/room/working day. Several test and beta
installations have been done, including a new web-based
calendar and Microsoft’s Office Communicator and its coupling
to the VC standard H.323 via an MCU.
Data Networking
IPP’s data network infrastructure was planned with a
cabling structure in mind that can easily be adapted to future
technologies. The network realized is therefore based on the
concept of a “collapsed backbone”, consisting of high-level
switches at a few central locations which directly connect to
all endpoints via links based on copper or fibre – eliminating
the need of limiting switches at workgroup or story level.
With this structure we greatly improved overall network
performance (uplinks up to 10 Gigabit/s) and security and
integrity of data, because eavesdropping is almost impossible.
For logical security based on the functionality of the internet
protocol suite TCP/IP a packet filter firewall combined with
stateful inspection at the access point to the internet (a Cisco
6509 router with hardware-based firewall module) is implemented,
where all the incoming/outgoing packets are
checked against a set of blocking or granting rules.