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 |
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 |


