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auto3dem website  

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.

Required Modules

Parallel (MPI)

  • intel/2016
  • openmpi
  • auto3dem

System Variables

  • HPC_AUTO3DEM_DIR - installation directory

Additional Information

  • 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