Difference between revisions of "Auto3DEM"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:Image Reconstruction {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|auto3dem}} |{{#vardefine:url|http://cryoem.ucsd.edu/wikis/software/st...") |
|||
| (7 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category:Image | + | [[Category:Software]][[Category:Image Processing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|auto3dem}} | |{{#vardefine:app|auto3dem}} | ||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#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--> | ||
| Line 22: | Line 22: | ||
<!--Modules--> | <!--Modules--> | ||
==Required Modules== | ==Required Modules== | ||
| + | |||
<!-- | <!-- | ||
===Serial=== | ===Serial=== | ||
| Line 28: | Line 29: | ||
* intel | * intel | ||
* {{#var:app}} | * {{#var:app}} | ||
| + | --> | ||
===Parallel (MPI)=== | ===Parallel (MPI)=== | ||
| − | * intel | + | * intel/2016 |
* openmpi | * openmpi | ||
* {{#var:app}} | * {{#var:app}} | ||
| + | <!-- | ||
--> | --> | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 42: | Line 45: | ||
{{#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 | ||
| + | |||
|}} | |}} | ||
Latest revision as of 15:24, 12 August 2022
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/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