Fully automatic acccurate, convenient and extremely fast particle picking for EM

References:

• http://www.mrc-lmb.cam.ac.uk/kzhang/Gautomatch

• Gautomatch Main Site

• Module Name: gautomatch (see the modules page for more information)
• GPU app
• Example files in /usr/local/apps/gautomatch/TEST_DATA/

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --gres=gpu:k80:1 --mem=20g -c14
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ cp /usr/local/apps/gautomatch/TEST_DATA/ice_carbon_aggregation_low-contrast/* .

[user@cn3144 ~]$ module load gautomatch
[+] Loading gautomatch 0.56 on cn4178
[+] Loading CUDA Toolkit 8.0.44 ...

[user@cn3144 ~]$ gautomatch --apixM 1.34 --diameter 400 --T templates_lp40_3.2A.mrcs --apixT 3.2 --lave_D 100 --lave_min -0.8 --lsigma_cutoff 1.2  --cc_cutoff 0.25 test?.mrc
***************************************************************************************************
User input parameters:
       --apixM              1.340
       --diameter           400.00
       --T                  templates_lp40_3.2A.mrcs
       --apixT              3.200
       --lave_D             100.000
       --lave_min           -0.800
       --lsigma_cutoff      1.200
       --cc_cutoff          0.250
[...]
File test2.mrc finished.
>>>>>>TIME<<<<<<                         PICKING: 1.049951s
#################################################################################################################################
All 2 files finished successfully:
>>>>>>TIME<<<<<<                           TOTAL: 4.786598s
#################################################################################################################################
[...]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. gautomatch.sh). For example:

#!/bin/bash
set -e
module load gautomatch
gautomatch --apixM 1.34 --diameter 400 --T templates_lp40_3.2A.mrcs --apixT 3.2 --lave_D 100 --lave_min -0.8 --lsigma_cutoff 1.2  --cc_cutoff 0.25 test?.mrc

Submit this job using the Slurm sbatch command.

sbatch --partition=gpu --gres=gpu:k80:1 --cpus-per-task=14 --mem=20g gautomatch.sh

Create a swarmfile (e.g. gautomatch.swarm). For example:

gautomatch [...] test1_?.mrc
gautomatch [...] test2_?.mrc
gautomatch [...] test3_?.mrc

Submit this job using the swarm command.

swarm -f gautomatch.swarm -g 20 -t 14 --module gautomatch