Auto3DEM: Difference between revisions

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

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Image Reconstruction]]
+[[Category:Software]][[Category:Image Processing]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|auto3dem}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 31: / Line 31: @@
 -->
 ===Parallel (MPI)===
-* intel/2013
+* intel/2016
 * openmpi
 * {{#var:app}}
@@ Line 37: / Line 37: @@
 -->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 45: / Line 45: @@
 {{#if: {{#var: exe}}|==Additional Information==
-WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+;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
 |}}