Difference between revisions of "Auto3DEM"

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|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 
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{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
  
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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;Note:
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:* 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:
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#SBATCH --nodes=1
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#SBATCH --ntasks=4
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#SBATCH --cpus-per-task=1
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#SBATCH --memory-per-cpu=1gb
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 +
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
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./RMC_run
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Revision as of 22:15, 11 August 2016

Description

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/2013
  • openmpi
  • auto3dem

System Variables

  • HPC_{{#uppercase:auto3dem}}_DIR - installation directory

Additional Information

Note
  • 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