Operational news of the MetaCentrum & CERIT-SC infrastructures: extended scheduler capabilities + new SW

Operational news of the MetaCentrum & CERIT-SC infrastructures: extended scheduler capabilities + new SW

As we've announced, we're providing another regular information about operational news of the MetaCentrum & CERIT-SC infrastructures:

1. Extended scheduler capabilities -- new possibilities for specifying the expected jobs run time:

• now, it is possible to submit the jobs *without queue specification* (if you do not use a specialized one) in the same way as previously available at CERIT-SC. Then, the expected job runtime could be specified via the "-l walltime=..." parameter.
• the walltime specification format has been adapted so that more human-friendly specification is possible (i.e., "-l walltime=10d", "-l walltime=3d30m", ...) -- available both in MetaCentrum and CERIT-SC
• submitting the jobs using this new specification (no queue & with walltime) is *highly recommended* -- the jobs submitted this way are queued into multiple internal queues, which may lead to shorter time required for jobs startup (e.g., the job with "-l walltime=12d" may be started before a job submitted to the "long" queue)
• the previously available queues "short", "normal", "long" remain available (submissions to them are supported, even though not recommended)
• see more information at https://wiki.metacentrum.cz/wiki/Running_jobs_in_scheduler#Brief_summary_of_job_scheduling

2. Newly installed/purchased SW:

Note: More pieces of information about the installed applications are available on the applications' web page: https://wiki.metacentrum.cz/wiki/Kategorie:Applications

COMMERCIAL APPLICATIONS (available for all the registered users):

• Intel Cluster Studio XE (intelcdk-14)
  • a set of tools for development of parallel as well as serial programs programmed in C, C++, FORTRAN 77, Fortran 95 and High Performance Fortran
  • version 2013, 2 licenses purchased by Cesnet
• PGI Accelerator CDK (pgicdk-13.10)
  • a collection of tools for development parallel and serial programs in C, Fortran, etc.
  • version 13.10, 2 licenses purchased by Cesnet
• Ansys CFD (Fluent + CFX) and Ansys Mechanical
  • SW for modelling flow, turbulence, heat transfers, etc. (Fluent) + a high-performance, general purpose fluid dynamics SW for solving wide-range of fluid flow problems (CFX) + a suite of tools allowing the structural and thermodynamic simulations
  • upgrade to version 15.0.1
• Allinea DDT
  • a debugging tool designed for parallel/distributed programs using OpenMP/MPI libraries
  • upgrade to version 4.2

OPEN-SOURCE/FREE APPLICATIONS:

* atomsk (ver. b0.7.2)  - a command-line program intended to read many types of atomic position files, and convert them to many other formats
* clview (ver. 2010)  - graphical, interactive tool for inspecting the ACE format assembly files generated by CAP3 or phrap
* cthyb   - The TRIQS-based hybridization-expansion matrix solver allows to solve the generic problem of a quantum impurity embedded in a conduction bath
* erlang (ver. r16)  - programming language used to build massively scalable soft real-time systems with requirements on high availability
* erne (ver. 1.4, gcc+intel)  - a short string alignment package providing an all-inclusive set of tools to handle short (NGS-like) reads
* repeatexplorer   - RepeatExplorer is a computational pipeline for discovery and characterization of repetitive sequences in eukaryotic genomes.

With best regards,
Tomáš Rebok, MetaCentrum + CERIT-SC