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Distribution of protein simulations on machines Sridhar, Dept of Biochemistry Example commandline of one simula1on job nohup

  1. Distribution of protein simulations on machines ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ ¡ Sridhar, Dept of Biochemistry Example ¡commandline ¡of ¡one ¡simula1on ¡job ¡ nohup /work/sridhar/rosetta/rosetta_source/bin/match.linuxiccrelease @/gpfs/DS3524-1/WORK/sridhar/scripts/ myscripts/test_jobdistribution/general_match.flags -match:geometric_constraint_file /gpfs/DS3524-1/WORK/ sridhar/scripts/myscripts/test_jobdistribution/Orgpho_S_H_DE_oxya_FP1_match.cst -s /lab/shared/scaffolds/pb/ 1pbp/1pbp_nohet_1_relax.pdb -match:scaffold_active_site_residues /lab/shared/scaffolds/pb/1pbp/ 1pbp_nohet_1.pdb_0.pos > log & Input file: pb/1pbp/1pbp_nohet_1.pdb_0.pos ¡ 1pbp 2gbp 1abe 2uvh …. …. ….. Submi5ng ¡10 ¡jobs ¡manually ¡would ¡be ¡easier ¡ But ¡submi5ng ¡1000 ¡jobs ¡is ¡painful ¡to ¡do ¡manually. ¡ A ¡python ¡script ¡to ¡automate ¡distribu1on ¡of ¡jobs ¡and ¡have ¡check ¡on ¡them ¡ would ¡be ¡ideal ¡

  2. Inputs : 1.Protein Name 2. specification 1. Process input, Internal 2. Check in database Database 3. generate commandline 4. Communicate with machines 5. Distribute jobs and wait 7 dig21 ¡ 12 14 dig4 ¡ dig8 ¡ 4 18 17 20 dig17 ¡ Machines

  4. Before execution Execution After execution

  5. from Job_Distribution import * hostlist = get_hostlist(4,27) onlinedigs = online_digs(hostlist) killalldigs(onlinedigs)

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