Tools & scripts for running scaffold models on Piz Daint
Clone this repository into your home folder:
cd ~
git clone https://github.com/dbbs-lab/bsb-daint
Add the following to ~/.bashrc:
export PROJECT="my_project"
export ACCOUNT="my_account"
source ~/bsb-daint/shell.sh
Note: Replace PROJECT and ACCOUNT with the correct information.
Install the scaffold stack into your shared project directory:
source ~/bsb-daint/install.sh
You can also opt to install it elsewhere, like in your user directory:
source ~/bsb-daint/install.sh $HOME
In your SLURM job script use the load helper script:
#!/bin/bash -l
#SBATCH --job-name="hello_world"
# ...
source ~/bsb-daint/load.sh
srun bsb simulate my_simulation --hdf5=my_network_file.hdf5
Note: Always prepend srun to the BSB commands for correct initialisation of MPI and
parallelisation of the scaffold. E.g. srun bsb simulate poc --hdf5=netw.hdf5.
Note: Do not use bsb compile on multiple nodes as it cannot run in parallel and will
just duplicate the process n times.
If you followed the installation instruction for the shell shortcuts you'll have access to the following commands:
Updates the bsb-daint to the latest version and performs an installation of the
BSB, its dependencies and compiles your mod files.
Executes bsb reconfigure $1 $2 as a job.
Runs whatever follows debug as a job in debug mode. For example debug python -c "print('Hello, world!')".
Checks your job queue
Checks which modules are available and contain the search term
$> maa python
adept-utils/606ebad-CrayGNU-20.08-python3
dyninst/10.2.0-CrayGNU-20.08-python3
gprof2dot/2019.11.30-python3(default)
pudb/2019.2-CrayGNU-20.08-python3(default)
scorep_binding_python/3.0-CrayGNU-20.08-python3(default)
termgraph/0.4.2-python3(default)
Boost/1.70.0-CrayGNU-20.08-python3(default)
ParaView/5.8.1-CrayGNU-20.08-OSMesa-python3(default)
ParaView/5.9.0-CrayGNU-20.08-OSMesa-python3
PyExtensions/python3-CrayGNU-20.08
cftime/1.0.2.1-CrayGNU-20.08-python3
dask/2.2.0-CrayGNU-20.08-python3(default)
h5py/2.10.0-CrayGNU-20.08-python3-parallel(default)
h5py/2.10.0-CrayGNU-20.08-python3-serial
netcdf-python/1.4.1-CrayGNU-20.08-python3
netcdf-python/1.5.4-CrayGNU-20.08-python3(default)
python_virtualenv/15.0.3
cray-python/3.8.2.1(default)