Difference between revisions of "Auto3DEM"
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|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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 | ||
| + | |||
|}} | |}} | ||
Revision as of 22:15, 11 August 2016
Description
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