LSC Computing
Available software
The group's computers all run Ubuntu Linux (version 20.04 - Focal). This is a long-term support (LTS) release of Ubuntu, with support until April 2025.
We use only LTS releases, and upgrade all LSC systems whenever a new LTS release occurs. The next upgrade, to Ubuntu 24.04, is scheduled for Summer 2024.
Software versions
For some scientific software, we may need more up-to-date versions than are installed by default within Ubuntu Bionic.
Below we list the default versions available, as well as any extra versions compiled especially for the CSC network.
More up-to-date versions are found within /lsc/opt.
| Package | Description | Default version | Other version(s) | Directory |
| gcc | C/C++/Fortran compiler | 9.4.0 | 10.2 | /lsc/opt/gcc-11 |
| CUDA | NVIDIA CUDA compiler and toolkit | 11.4 | /lsc/opt/cuda-11.4 | |
| Boost libraries | C++ helper libraries | 1.75 | /lsc/opt/modules/boost-1.75.0 | |
| gdb | C/C++/Fortran debugger | 9.2.0 | ||
| clang | C/C++ compiler | 10.0 | ||
| OpenMPI | MPI implementation | 4.0.3 | ||
| valgrind | Application Profiler | 3.13 | 3.19 | /lsc/opt/valgrind-3.19.0 |
| HDF libraries | HDF libraries | 1.10.7 | /lsc/opt/modules/hdf5-1.10.7 | |
| Doxygen | Code documentation tool | 1.8.17 | /lsc/opt/doxygen-1.8.17 | |
| VisIt | Visualisation software | 3.2.2 (*) | /lsc/opt/visit | |
| ParaView | Visualisation software | 5.9.0 | /lsc/opt/Paraview-5.9 | |
| R | Statistical programming environment(CRAN packages) | Not installed | ||
| TexLive | Text publishing packages | 2019 | 2022 | /lsc/opt/texlive/2022/bin |
| gnuplot | Basic plotting tool | 5.2.8 | ||
| emacs | Text editor | 26.3 | ||
| armadillo | C++ linear algebra library | 9.800.4 | ||
| CMake | Compilation tool | 3.16.3 | ||
| Python | Python interpreter | |||
| Numpy | Large array support for Python | See below | ||
| mpi4py | MPI support for Python | See below | ||
| scipy | Scientific tools for Python | See below | ||
| six | Python 2/3 compatibility layer | See below | ||
| scikit-learn | Machine Learning in Python | See below | ||
| Theano | Efficient multi-D array expressions in Python | See below | ||
| Fenics | Finite element solver with Python and C++ bindings | 2018.1.0 | /lsc/opt/modules/dolfin-2018.1.0 |
(*) VisIt 3.2.2 can be used as a client to connect to CSD3, using the built-in Host Profile.
Software installed in /lsc/opt/modules/ is
compiled against gcc-9.2 which is the default compiler on
Ubuntu Focal.
In order to use any non-standard-versions of these packages, you need to add the appropriate directory to your PATH. For example, to use the latest version of gcc:
export PATH=/lsc/opt/gcc-11.2/bin/:$PATH
You may wish to add the preceding command to your ~/.bashrc to make it available for all new terminals.
In order to import the later versions of Python packages listed above:
export PYTHONPATH=/lsc/opt/modules/lib/python3.8/site-packages/:$PYTHONPATH
or
export PYTHONPATH=/lsc/opt/modules/gcc-7.3.0/lib/lib/python3.6/site-packages/:$PYTHONPATH
It may be possible to persuade a sysadmin to install other packages or later versions of those already installed. This is usually easier if the particular software is needed by many members of the group.
LSC-AMR
Under the directory /lsc/opt/modules/ there is a complete set of libraries as required
to compile and run the group's LSC_AMR code, when compiling
using the default gcc, with C++11 support (-std=c++11).