Scalable Software Services for Life Science

Development Tools

 
 
 
 
 
 

The partner computing centers in ScalaLife provide the necessary tools for software development, along with the core simulation packages. The tools include version control systems, build environemnts, compilers, debuggers, performance tools and special libraries. Analysis and visualization software is also provided.

Some of the provided tools require special or paid licenses. Users will need to obtain those licenses themselves, except for the cases where the centres provide system wide licensing scheme. Please contact support for more information.

Access to the tools (and pre-compiled applications)

Some of the centers use module systems to manage access to the tools. See below for details.

PDC at the Royal Institute of Technology (KTH)

Precompiled versions of the tools are provided through the Tcl modules systems on all clusters at PDC. Information about their usage through the module system can be found on the PDC website.

LRZ

LRZ uses the modules approach to manage the user environment for different software versions. This is the standard method available for user environment management on all Linux-based LRZ HPC platforms. More information can be found on the LRZ website.

BSC

BSC uses the module tools to manage the user environment to support  different software stack versions. More information about software and tools can be found at BSC website

OeRC

Tools such as the GNU build system and compilers which are part of the standard Linux distributions are available by default. The other tools can be added as modules. More information is available on the OeRC website.

Documentation

Links to documentation about the usage of the tools can be found in the performance section.

Provision of tools

The availability of the tools on the different platforms is presented in the table below. More details are available in the support tools matrix.

 

Tools Description Availability
Analysis tools
Gromacs analysis tools a large collecion of tools for analysis of molecular structures and trjectories. Comes bundled with the Gromacs package KTH: Povel, Lindgren

LRZ: all
BSC: MareNostrum, bscsmp
OeRC: Hal, Sal, Skynet, RedQueen, Queeg
R free software environment for statistical computing and graphics KTH: Povel, Lindgren

LRZ: all

BSC: MareNostrum, bscsmp
OeRC: Hal, Sal, RedQueen, Queeg
Build environments
Autotools GNU build system tools KTH: all

LRZ: all

BSC: all

OeRC: all
CMake cross-platform build system KTH: all

LRZ: all

BSC: all

OeRC: all
Compilers

GNU Compiler Collection
(g++/gcc/gfortran)

Integrated distribution of compilers for several programming languages. KTH: all

LRZ: all

BSC: all

OeRC: all (4.1.0)
IBM Compilers
(XL c/c++, fortran)
Compilers optimized for the IBM POWER systems BSC: MareNostrum, MariCel, tamariu
Intel Compilers
(icc/ifort)
Highly optimized compilers for Intel and Intel-compatible processors. KTH: all

LRZ: all

BSC: bscsmp, GPU clusters

OeRC: all (11.1)
Debuggers
DDD GNU DDD is a graphical front-end for command-line debuggers such as GDB LRZ: all

BSC: MareNostrum

OeRC: RedQueen, Queeg
GDB GNU Project debugger KTH: all

LRZ: all

BSC: all

OeRC: all
Intel Debugger
(IDB)
Part of the Intel suite of programming tools. It can be used also in a GDB interface mode. KTH: all

LRZ: all

BSC: bscsmp

OeRC: Hal, Sal, Skynet, RedQueen, Queeg (11.1)
Totalview powerful parallel debugger with multi-process/multi-threading support KTH: all

LRZ: all

BSC: MareNostrum, MariCel, bscsmp

OeRC: none
DDT  powerful parallel debugger with multi-process/multi-threading support KTH: all

LRZ: all
BSC: MareNostrum
OeRC: all
Valgrind memory debuggin and profiling framework KTH: all

LRZ: all

BSC: all

OeRC: Hal, Sal, Skynet, RedQueen, Queeg
Performance tools
Paraver flexible performance visualization and analysis tool KTH: all

LRZ: none

BSC: all

OeRC: none
Scalasca software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior KTH: Povel

LRZ: all

BSC: MareNostrum

OeRC: none
Tau portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, Java, Python KTH: Povel

LRZ: all

BSC: MareNostrum

OeRC: Hal, Sal
VTune performance analyzer from Intel KTH: none

LRZ: SGI Altix 4700

BSC: none

OeRC: none
Vampir analysis framework for performance optimization KTH: none

LRZ: all

BSC: MareNostrum

OeRC: none
gprof GNU profiler KTH: all

LRZ: all

BSC: all

OeRC: all
Programming models and libraries
COMPSs Programming model for automatic parallelization KTH: none

LRZ: none

BSC: MareNostrum

OeRC: none
FFTW library for calculating discrete Fourier transforms KTH: all

LRZ: all

BSC: MareNostrum, bscsmb, taimaru, GPU cluster

OeRC: all (2.1.5, 3.1.2)
MKL Optimized math libraries from Intel KTH: all

LRZ: all

BSC: bscsmp

OeRC: all (11.1)
MPI message-passing interface for a distribute programming model KTH: all

LRZ: all
BSC: all

OeRC: all
CUDA/OpenCL compilers, libraries and development tools for accelerated calculations on NVIDIA GPGPUs KTH: all

LRZ: GVS cluster

BSC: GPU cluster

OeRC: Skynet
Version Control Systems
Git powerful  distributed control system KTH: all

LRZ: all

BSC: none

OeRC: all
SVN modern version of the classic CVS system KTH: Povel

LRZ: all

BSC: MareNostrum, bscsmp

OeRC: all
Visualization tools
Maestro unified interface for all modecular modeling software from Schrödinger KTH: none

LRZ: gvs

BSC: none

OeRC: none
Molden package for displaying Molecular Density KTH: all

LRZ: hlrb2

BSC: MareNostrum

OeRC: Hal, Sal
PyMol molecular visualization system KTH: all

LRZ: gvs

BSC: MareNostrum, bscsmp

OeRC: none
VMD molecular visualization program for displaying, animating, and analyzing KTH: none

LRZ: gvs

BSC: MareNostrum, bscsmp
OeRC: none