Some of configuration parameters can be changed via command line parameters, which are described in Command line arguments.
STEMsalabim supports both threaded (shared memory) and MPI (distributed memory) parallelization. For most efficient resource usage we recommend a hybrid approach, where one MPI task is run per node that spawns a bunch of threads to parallelize the work within the node. (See Hybrid Parallelization model for more information on how STEMsalabim can be parallelized.)
You can execute STEMsalabim on a single multi-core computer as follows:
$ stemsalabim --params=./my_config_file.cfg --num-threads=32
This will run the simulation configured in
my_config_file.cfg on 32 cores, of which 31 are used as workers.
MPI only parallelization¶
For pure MPI parallelization without spawning additional threads, STEMsalabim must be called via
mpiexec, depending on the MPI implementation available on your machine:
$ mpirun -n 32 stemsalabim --params=./my_config_file.cfg --num-threads=1 --package-size=10
This command will run the simulation in parallel on 32 MPI processors without spawning additional threads.
We chose a work package size ten times the number of threads on each MPI processor (which is 1 here). This is so that each thread calculates (on average) ten pixels until results are communicated via the network. This reduces management overhead but increases the amount of data sent via the network.
Hybrid parallelization is the recommended mode to run STEMsalabim.
For hybrid parallelization, make sure that on each node only a single MPI process is spawned and that there is no CPU pinning active, i.e., STEMsalabim needs to be able to spawn threads on different cores.
For example, if we wanted to run a simulation in parallel on 32 machines using OpenMPI and on each machine use 16 cores, we would run
$ mpirun -n 32 --bind-to none --map-by ppr:1:node:pe=16 \ stemsalabim \ --params=./my_config_file.cfg \ --num-threads=16 \ --package-size=160
--bind-to none --map-by ppr:1:node:pe=16 tell OpenMPI not to bind the process to anything and to reserve
16 threads for each instance. Please refer to the manual of your MPI implementation to figure out how start a hybrid
parallelization run. On computing clusters, node and/or socket topology may affect performance, so it is wise to consult
your cluster admin team.
Si 001 example¶
In the source code archive you find an
examples/Si_001 folder that contains a simple example that you can
execute to get started. The file
Si_001.xyz describes a 2x2x36 unit cell Si sample. Please see
Crystal file format for the format description.
In the file
Si_001.cfg we find the simulation configuration / parameters. The file contains
all available parameters, regardless of whether they are set to their default value. We recommend to always
specify a complete set of simulation parameters in the configuration files.
You can now run the simulation:
$ /path/to/stemsalabim --params Si_001.cfg --num-threads=8
After the simulation finished (about 3 hours on an Intel i7 CPU with 8 cores) you can analyze the
results found in
Si_001.nc. Please see the next page (Visualization of crystals and results) for details.
ssb-mkin and ssb-run¶
Along with the main
stemsalabim binary, the
ssb-run tools are also compiled and put into
ssb-run can be used to start a STEMsalabim simulation from an existing NetCDF file. Results in the file are discarded
and all required parameters are read from the file. Most importantly, the generated atomic displacements for all the
frozen phonon configurations are read from the file, so that starting from an NetCDF file
ssb-run should always produce
the exact same results.
ssb-mkin is the complementary tool to
ssb-run, generating an input NetCDF file from a parameter file
(see Parameter files) and a crystal file (see Crystal file format). The output of
ssb-mkin is identical to
the output of
stemsalabim, except that it doesn’t contain any results.
$ /path/to/ssb-mkin --params Si_001.cfg --output-file Si_001.nc $ /path/to/ssb-run --params Si_001.nc --num-threads=8
The above two commands are identical to the example in Si 001 example.
Si_001.nc file is small (as it contains no results) and contains everything required to start
a simulation. It is therefore well-suited for backing up or sending around. In addition, the
parameter can be used.
ssb-run accept the
--stored-potentials command line parameter. When it is specified,
the scattering Coulomb potentials are calculated already while running
ssb-mkin and written to the NetCDF file in
ssb-run then reads the potentials from the file and starts the multi-slice simulation
without recalculating the potentials.
This is useful for inspecting and modifying potentials prior to the simulation.
STEMsalabim writes its results and a bunch of information about the simulation to in NetCDF binary format. NetCDF is a hierarchical storage format for storing multi-dimensional data. It is (most of the times) based on HDF5.
Please see Output file format for more information how to read / write NetCDF files.