Commit 9606be77 authored by Lukáš Krupčík's avatar Lukáš Krupčík

fix links

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# Environment and Modules
## Environment Customization
After logging in, you may want to configure the environment. Write your preferred path definitions, aliases, functions and module loads in the .bashrc file
```console
# ./bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# User specific aliases and functions
alias qs='qstat -a'
module load intel/2015b
# Display information to standard output - only in interactive ssh session
if [ -n "$SSH_TTY" ]
then
module list # Display loaded modules
fi
```
!!! note
Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental functionality (SCP, PBS) of your account! Take care for SSH session interactivity for such commands as stated in the previous example.
### Application Modules
In order to configure your shell for running particular application on Salomon we use Module package interface.
Application modules on Salomon cluster are built using [EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). The modules are divided into the following structure:
```console
base: Default module class
bio: Bioinformatics, biology and biomedical
cae: Computer Aided Engineering (incl. CFD)
chem: Chemistry, Computational Chemistry and Quantum Chemistry
compiler: Compilers
data: Data management & processing tools
debugger: Debuggers
devel: Development tools
geo: Earth Sciences
ide: Integrated Development Environments (e.g. editors)
lang: Languages and programming aids
lib: General purpose libraries
math: High-level mathematical software
mpi: MPI stacks
numlib: Numerical Libraries
perf: Performance tools
phys: Physics and physical systems simulations
system: System utilities (e.g. highly depending on system OS and hardware)
toolchain: EasyBuild toolchains
tools: General purpose tools
vis: Visualization, plotting, documentation and typesetting
```
!!! note
The modules set up the application paths, library paths and environment variables for running particular application.
The modules may be loaded, unloaded and switched, according to momentary needs.
To check available modules use
```console
$ ml av
```
To load a module, for example the Open MPI module use
```console
$ ml OpenMPI
```
loading the Open MPI module will set up paths and environment variables of your active shell such that you are ready to run the Open MPI software
To check loaded modules use
```console
$ ml
```
To unload a module, for example the Open MPI module use
```console
$ ml -OpenMPI
```
Learn more on modules by reading the module man page
```console
$ man module
```
### EasyBuild Toolchains
As we wrote earlier, we are using EasyBuild for automatized software installation and module creation.
EasyBuild employs so-called **compiler toolchains** or, simply toolchains for short, which are a major concept in handling the build and installation processes.
A typical toolchain consists of one or more compilers, usually put together with some libraries for specific functionality, e.g., for using an MPI stack for distributed computing, or which provide optimized routines for commonly used math operations, e.g., the well-known BLAS/LAPACK APIs for linear algebra routines.
For each software package being built, the toolchain to be used must be specified in some way.
The EasyBuild framework prepares the build environment for the different toolchain components, by loading their respective modules and defining environment variables to specify compiler commands (e.g., via `$F90`), compiler and linker options (e.g., via `$CFLAGS` and `$LDFLAGS`), the list of library names to supply to the linker (via `$LIBS`), etc. This enables making easyblocks largely toolchain-agnostic since they can simply rely on these environment variables; that is, unless they need to be aware of, for example, the particular compiler being used to determine the build configuration options.
Recent releases of EasyBuild include out-of-the-box toolchain support for:
* various compilers, including GCC, Intel, Clang, CUDA
* common MPI libraries, such as Intel MPI, MPICH, MVAPICH2, Open MPI
* various numerical libraries, including ATLAS, Intel MKL, OpenBLAS, ScaLAPACK, FFTW
On Salomon, we have currently following toolchains installed:
| Toolchain | Module(s) |
| --------- | ---------------------------------------------- |
| GCC | GCC |
| ictce | icc, ifort, imkl, impi |
| intel | GCC, icc, ifort, imkl, impi |
| gompi | GCC, OpenMPI |
| goolf | BLACS, FFTW, GCC, OpenBLAS, OpenMPI, ScaLAPACK |
| iompi | OpenMPI, icc, ifort |
| iccifort | icc, ifort |
......@@ -161,7 +161,7 @@ After successful obtainment of login credentials for the local IT4Innovations ac
## File Transfers
PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see [the section in the general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/hell-and-data-access/).
PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see [the section in the general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
......
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