Difference between revisions of "Auto3DEM"

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(Created page with "Category:SoftwareCategory:Image Reconstruction {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|auto3dem}} |{{#vardefine:url|http://cryoem.ucsd.edu/wikis/software/st...")
 
 
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[[Category:Software]][[Category:Image Reconstruction]]
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[[Category:Software]][[Category:Image Processing]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|auto3dem}}
 
|{{#vardefine:app|auto3dem}}
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
 
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
 
|{{#vardefine:policy|}}        <!--POLICY-->
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<!--Modules-->
 
<!--Modules-->
 
==Required Modules==
 
==Required Modules==
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<!--
 
<!--
 
===Serial===
 
===Serial===
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* intel
 
* intel
 
* {{#var:app}}
 
* {{#var:app}}
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-->
 
===Parallel (MPI)===
 
===Parallel (MPI)===
* intel
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* intel/2016
 
* openmpi
 
* openmpi
 
* {{#var:app}}
 
* {{#var:app}}
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<!--
 
-->
 
-->
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
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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:
 +
#SBATCH --nodes=1
 +
#SBATCH --ntasks=4
 +
#SBATCH --cpus-per-task=1
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#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
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|}}
 
|}}

Latest revision as of 15:24, 12 August 2022

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/2016
  • openmpi
  • auto3dem

System Variables

  • HPC_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