User environment

User workspace

The default login shell for your user account is bash. To determine your current login shell :

$ echo $SHELL

By default, the login shell change directory to $HOME folder.

Each user has 2 folders ($HOME and $WORK) organized as follows:

Directory	Environment variable	File system	Backup	Quota
/users/<login>	$HOME	NFS	Protected	20 Gio
/work/mesobfc/<login>	$WORK	BeeGFS	No	8 Tio

directories

• $WORK is used as working directory: all simulation data must be copied in this folder.
• $HOME is read-only in computing nodes (batch).

To display your quota usage for $HOME and $WORK, you can use the command show-disk-quota.

Using modules to manage your environment

Installed applications are organized using module command according to the architecture of the node (Intel, AMD).
The module command supports the following subcommands:

Command	Description
module display <module>	Display what a module does
module list	List loaded modules
module avail	List all the modules which are available to be loaded
module load <mod1> [mod2...]	Load a module
module unload <module>	Unload a module
module purge	Unload all modules (purge)

For example on the login node, one can view all installed/available package software:

$ module avail -t
/soft/spack/share/spack/modules/linux-rocky8-x86_64:
miniconda3-22.11.1/gcc-13.1.0

/soft/spack/share/spack/modules/linux-rocky8-skylake_avx512:
cp2k-2023.2/openmpi-4.1.5/gcc-13.1.0-openblas
gromacs-2023.1/double/openmpi-4.1.5/gcc-13.1.0-openblas
octopus-12.2/gcc-13.1.0-openblas
openmpi-4.1.5/gcc-13.1.0
openmx-3.9/gcc-13.1.0-openblas
quantum-espresso-7.1/gcc-13.1.0-openblas
wps-4.3.1/gcc-13.1.0-ccub_no_leap
wps-4.3.1/gcc-13.1.0-ccub_no_leap-serial_NO_GRIB2
wps-4.3.1/gcc-13.1.0-serial_NO_GRIB2
wrf-4.3.3/gcc-13.1.0-ccub_fcoptim
wrf-4.3.3/gcc-13.1.0-ccub_fcoptim-ccub_no_leap

/soft/spack/share/spack/modules/linux-rocky8-icelake:
cp2k-2023.2/openmpi-4.1.5/gcc-13.1.0-openblas
gromacs-2023.1/double/openmpi-4.1.5/gcc-13.1.0-openblas
hpl-2.3/gcc-13.1.0-openblas
namd-2.14/gcc-13.1.0
octopus-12.2/gcc-13.1.0-openblas
openmpi-4.1.5/gcc-13.1.0
openmx-3.9/gcc-13.1.0-openblas
osu-micro-benchmarks-7.1-1/gcc-13.1.0
siesta-4.0.2/gcc-13.1.0-openblas
wps-4.3.1/gcc-13.1.0-ccub_no_leap
wps-4.3.1/gcc-13.1.0-ccub_no_leap-serial_NO_GRIB2
wrf-4.3.3/gcc-13.1.0-ccub_fcoptim-ccub_no_leap

modules

• The management of modules according to the node architecture is provided by Spack software.
• Module name is generated according to the software version, compiler version and even MPI version if enabled.

For example to load and use openmx-3.9/openmpi-4.1.5/gcc-13.1.0-openblas (OpenMX version 3.9 compiled with GCC-13.1.0 and OpenMPI 4.1.5 and openblas lib)

$ module load openmx-3.9/openmpi-4.1.5/gcc-13.1.0-openblas

Transfer data from/to MesoBFC

Using SSH command line

caution

These commands must be executed on your local machine !

• To copy files from your localhost to MesoBFC:

$ scp file1 file2 login@login-1.mesobfc.fr:WORK

This command will copy file1 and file2 to directory WORK on MesoBFC.

• To copy files from MesoBFC to your localhost:

$ scp login@login-1.mesobfc.fr:WORK/files.tgz .

This command will copy files.tgz from directory WORK on MesoBFC to your current directory on localhost.

Using graphical tools

FileZilla is a good Graphical User Interface (GUI) to SFTP protocol (based on SSH).
Use the same credentials as with ssh/scp and use port 22 to use SFTP protocol.

Once connected, you can simply transfer files by drag & drop operations or by right-clicking in the file(s) you wish to transfer.

Citizenship on MesoBFC

Be always aware that you are working on a shared system where your behavior could have a negative impact on the workflow of other users.