Provozní změny infrastruktur MetaCentra a CERIT-SC: uzly s Debian 7 + nový SW

Počínaje tímto kalendářním měsícem se Vás pokusíme pravidelně 1x měsíčně informovat o nejdůležitějších provozních změnách (zahrnujících mj. i nově instalovaný SW) provedených na infrastrukturách MetaCentra a CERIT-SC.

Nejdůležitější provozní novinky:
1. Testovací uzly s OS Debian 7 brzy do produkčního provozu

rádi bychom Vás informovali, že jsme připravili testovací sadu uzlů s OS Debian 7, na které již nyní můžete testovat své aplikace
uzly budou od zítřejšího dne (aktuálně probíhá upgrade BIOSu) přístupné po zadání vlastnosti "debian7".
případné problémy s během aplikací na těchto uzlech nám, prosíme, neprodleně hlašte.

2. Nově instalovaný/pořízený SW: (vzhledem k této první novince budeme výjimečně sumarizovat SW za posledních 5 kalendářních měsíců)

Pozn.: Bližší informace o instalovaných aplikacích jsou k dispozici na stránce aplikací: https://wiki.metacentrum.cz/wiki/Kategorie:Aplikace

KOMERČNÍ PROGRAMY (dostupné všem registrovaným uživatelům):

ANSYS Academic Research CFD (Fluent + CFX)
- SW for modelling flow, turbulence, heat transfers, etc. (Fluent) and a high-performance, general purpose fluid dynamics SW for solving wide-range of fluid flow problems (CFX)
- ver. 14.5.7, 25 licenses purchased by MetaCentrum
ANSYS Academic Research Mechanical
- a suite of tools allowing the structural and thermodynamic simulations
- ver. 14.5.7, 5 licenses purchased by CERIT-SC
ANSYS Academic Research HPC
- enhances the performance of Ansys products by enabling the computations to run on multiple processors/cores
- ver. 14.5.7, 60 licenses purchased by MetaCentrum
Gaussian 09
- a program for predicting the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous derived properties
- upgrade to rev. D.01 (previously purchased by MetaCentrum)
Matlab
- an integrated system covering tools for symbolic and numeric computations, analyses and data visualizations, modeling and simulations of real processes, etc.
- upgrade to ver. 8.2, new 100 licenses (450 in total) purchased by MetaCentrum
Wolfram Mathematica
- computer algebra system
- ver. 9, 10 licenses purchased by CERIT-SC (+ upgrades for FZU, JCU and UK)
Wolfram GridMathematica
- an integrated extension system for increasing the power of (your) Mathematica licenses
- upgrade to ver. 9, 15 licenses (=>240 cores) purchased by MetaCentrum
Intel C++ Composer XE
- a set of tools for development of parallel as well as serial programs programmed in C, C++ (without FORTRAN), including Intel MKL libraries
- upgrade to ver. 13, 2 licenses (previously purchased by MetaCentrum)
PGI Accelerator CDK
- a collection of tools for development parallel and serial programs in C, Fortran, etc.
- upgrade to ver. 12.4, 2 licenses (previously purchased by CERIT-SC)
Allinea DDT
- a debugging tool designed for parallel/distributed programs using OpenMP/MPI libraries
- upgrade to ver. 4.1, licensed for debugging 32 running processes (previously purchased by CERIT-SC)
TotalView
- a GUI-based debugger (includes ReplayEngine, CUDA-Debugging, Memory Scape, Remote Display and Script Debugging)
- upgrade to ver. 8.12, licensed for debugging 64 running processes (previously purchased by CERIT-SC)

VOLNĚ DOSTUPNÉ PROGRAMY:
* argus (ver. 3.0.6) - a tool for developing network activity audit strategies and prototype technology to support network operations, performance and security management
* bedtools (ver. 2.17) - bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks
* bfast (ver. 0.7.0) - a tool for fast and accurate mapping of short reads to reference sequences
* bioperl (ver. 1.6.1) - a toolkit of perl modules useful in building bioinformatics solutions in Perl
* blast (ver. 2.2.26) - a program that compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches
* blast+ (ver. 2.2.26 + 2.2.27) - a program that compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches
* boost (ver. 1.49) - a boost library
* bowtie (ver. 1.0.0) - an ultrafast, memory-efficient short read aligner of short DNA sequences
* bwa (ver. 0.7.5a) - a fast lightweight tool that aligns relatively short sequences to a sequence database
* clumpp (ver. 1.1.2) - a program that deals with label switching and multimodality problems in population-genetic cluster analyses
* cp2k (ver. 2.3 + 2.4) - a program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems
* dendroscope (ver. 3.2.8) - an interactive viewer for rooted phylogenetic trees and networks
* echo (ver. 1.12) - Short-read Error Correction
* erne (ver. 1.2) - a short string alignment package providing an all-inclusive set of tools to handle short (NGS-like) reads
* fpc (ver. 9.4) - a tool that takes a set of clones and their restriction fragments as an input and assembles the clones into contigs
* gcc (ver. 4.7.0 + 4.8.1) - a compiler collection, which includes front ends for C, C++, Objective-C, Fortran, Java, Ada and libraries for these languages
* gromacs (ver. 4.6.1) - a program package enabling to define minimalization of energy of system and dynamic behaviour of molecular systems
* ltrdigest (ver. 1.3.3 + 1.5.1) - a collection of bioinformatics tools (in the realm of genome informatics)
* minia (ver. 1.5418) - a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day
* mosaik (ver. 1.1 + 2.1) - a reference-guided assembler
* mpich2 - an implementation of MPI
* mpich3 - an implementation of MPI
* mrbayes (ver. 3.2.2) - a program for the Bayesian estimation of phylogeny
* multidis - a package for numerical simulations of mixed classical nuclear and quantum electronic dynamics of atomic complexes with many electronic states and transitions between them involved
* mvapich (ver. 3.0.3) - MPI implementation supporting Infiniband
* ncl (ver. 6.1.2) - an interpreted language designed specifically for scientific data analysis and visualization
* nco (ver. 4.2.5-gcc) - a tool that manipulates data stored in netCDF format
* numpy (ver. 1.7.1-py2.7) - a Python language extension defining the numerical array and matrix type and basic operations over them (compiled with Intel MKL libraries support for faster performance)
* open3dqsar - a software aimed at high-throughput chemometric analysis of molecular interaction fields
* openmpi (ver. 1.6) - an implementation of MPI
* parallel (ver. 2013) - a shell tool for executing jobs in parallel using one or more computers
* phycas - an application for carrying out phylogenetic analyses; it's also a C++ and Python library that can be used to create new applications or to extend the current functionality
* phyml (ver. 3.0) - estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences
* pyfits (ver. 3.1.2-py2.7) - a Python library providing access to FITS files (used within astronomy community to store images and tables)
* python (ver. 2.7.5) - a general-purpose high-level programming language
* qiime (ver. 1.7.0) - a software package for comparison and analysis of microbial communities
* raxml (ver. 7.3.0) - fast implementation of maximum-likelihood (ML) phylogeny estimation that operates on both nucleotide and protein sequence alignments
* R (ver. 3.0.1) - a software environment for statistical computing and graphics
* samtools (ver. 0.1.18 + 0.1.19) - utilities for manipulating alignments in the SAM format
* scipy (ver. 0.12.0-py2.7) - a language extension that uses numpy to do advanced math, signal processing, optimization, statistics and much more (compiled with Intel MKL libraries support for faster performance)
* sklearn (ver. 0.14.1-py2.7) - a Python language extension that uses Numpy and Scipy to provide simple and efficient tools for data mining and data analysis
* snapp (ver. 1.1.1) - a package for inferring species trees and species demographics from independent biallelic markers
* sox (ver. 14.4.1) - a command line utility that can convert various formats of audio files and apply to them various sound effects
* sparsehash (ver. 2.0.2) - an extremely memory-efficient hash_map implementation
* sratools (ver. 2.3.2) - a collection of tools storing and manipulating raw sequencing data from the next generation sequencing platforms (using the NCBI-defined interchange format)
* stacks (ver. 1.02) - a software pipeline for building loci from short-read sequences
* symos97 (ver. 6.0) - an application for developing of dispersion sutudies for evaulating quality of atmosphere according to SYMOS'97 methodics (just for VSB-TU users)
* wrf (ver. 3.4.1) - a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs
* xcrysden (ver. 1.5) - a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contour
* xmipp (ver. 3.0.1) - a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy

S pozdravem Tomáš Rebok,
MetaCentrum + CERIT-SC.

Tom Rebok, Wed Nov 13 22:00:00 CET 2013