Auto3DEM is a semi-automated image reconstruction system that provides all the tools to process raw micrographs acquired at an electron microscope and generate a three-dimensional reconstruction. The most intensive computational procedure like orientation search and reconstruction can be executed either in serial or in parallel on a computer cluster.
- HPC_AUTO3DEM_DIR - installation directory
- Parallel Auto3dem is an MPI application. To submit successful jobs make sure to specify a valid MPI SLURM job layout in the job script and to match the requested CPU cores to the number passed to auto3dem. For example:
#SBATCH --nodes=1 #SBATCH --ntasks=4 #SBATCH --cpus-per-task=1 #SBATCH --memory-per-cpu=1gb
can be matched with the default setup_rmc configuration, which requests '-ncpu 4' for auto3dem e.g.
setup_rmc -nmodels 10 -nimages 100 -ncpu 4 ./RMC_run