tgenerate-consolidation-scripts-comet.py - sphere - GPU-based 3D discrete element method algorithm with optional fluid coupling
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       tgenerate-consolidation-scripts-comet.py (3349B)
       ---
            1 #!/usr/bin/env python
            2 
            3 # Account and cluster information
            4 # https://portal.xsede.org/sdsc-comet
            5 # https://www.sdsc.edu/support/user_guides/comet.html
            6 account = 'csd492'  # from `show_accounts`
            7 jobname_prefix = 'cons-1e4-'
            8 walltime = '2-0'   # hours:minutes:seconds or days-hours
            9 partition = 'gpu-shared'
           10 no_gpus = 1
           11 no_nodes = 1
           12 ntasks_per_node = 1
           13 folder = '~/code/sphere/python'
           14 
           15 
           16 # Simulation parameter values
           17 effective_stresses = [10e3, 20e3, 100e3, 200e3, 1000e3, 2000e3]
           18 
           19 
           20 # Script generating functions
           21 
           22 def generate_slurm_script(jobname):
           23 
           24     script = '''#!/bin/bash
           25 #SBATCH -A {account}
           26 #SBATCH --job-name="{jobname}"
           27 #SBATCH --output="{jobname}.%j.%N.out"
           28 #SBATCH --time={walltime}
           29 #SBATCH --partition={partition}
           30 #SBATCH --gres=gpu:{no_gpus}
           31 #SBATCH --nodes={no_nodes}
           32 #SBATCH --ntasks-per-node={ntasks_per_node}
           33 #SBATCH --export=ALL
           34 
           35 echo Job start `whoami`@`hostname`, `date`
           36 module load cmake
           37 module load cuda/7.0
           38 module load python
           39 module load scipy
           40 
           41 cd {folder}
           42 python ./{jobname}.py
           43 
           44 echo Job end `whoami`@`hostname`, `date`
           45 '''.format(account=account,
           46            jobname=jobname,
           47            walltime=walltime,
           48            partition=partition,
           49            no_gpus=no_gpus,
           50            no_nodes=no_nodes,
           51            ntasks_per_node=ntasks_per_node,
           52            folder=folder)
           53     with open(jobname + '.sh', 'w') as file:
           54         file.write(script)
           55 
           56 
           57 def generate_slurm_continue_script(jobname):
           58 
           59     script = '''#!/bin/bash
           60 #SBATCH -A {account}
           61 #SBATCH --job-name="{jobname}"
           62 #SBATCH --output="{jobname}.%j.%N.out"
           63 #SBATCH --time={walltime}
           64 #SBATCH --partition={partition}
           65 #SBATCH --gres=gpu:{no_gpus}
           66 #SBATCH --nodes={no_nodes}
           67 #SBATCH --ntasks-per-node={ntasks_per_node}
           68 #SBATCH --export=ALL
           69 
           70 echo Job start `whoami`@`hostname`, `date`
           71 module load cmake
           72 module load cuda/7.0
           73 module load python
           74 module load scipy
           75 
           76 cd {folder}
           77 python ./continue_sim.py {jobname} 0
           78 
           79 echo Job end `whoami`@`hostname`, `date`
           80 '''.format(account=account,
           81            jobname=jobname,
           82            walltime=walltime,
           83            partition=partition,
           84            no_gpus=no_gpus,
           85            no_nodes=no_nodes,
           86            ntasks_per_node=ntasks_per_node,
           87            folder=folder)
           88     with open(jobname + '-cont.sh', 'w') as file:
           89         file.write(script)
           90 
           91 
           92 # Generate scripts for sphere
           93 def generate_simulation_script(jobname, effective_stress):
           94 
           95     script = '''#!/usr/bin/env python
           96 import sphere
           97 
           98 cons = sphere.sim('init-1e4')
           99 cons.readlast()
          100 cons.id('{jobname}')
          101 
          102 cons.periodicBoundariesXY()
          103 
          104 cons.setStiffnessNormal(1.16e7)
          105 cons.setStiffnessTangential(1.16e7)
          106 cons.setStaticFriction(0.5)
          107 cons.setDynamicFriction(0.5)
          108 cons.setDampingNormal(0.0)
          109 cons.setDampingTangential(0.0)
          110 
          111 cons.consolidate(normal_stress={effective_stress})
          112 cons.initTemporal(total=3.0, epsilon=0.07)
          113 
          114 cons.run(dry=True)
          115 cons.run(device=0)
          116 
          117 cons.visualize('energy')
          118 cons.visualize('walls')
          119 '''.format(jobname=jobname,
          120            effective_stress=effective_stress)
          121 
          122     with open(jobname + '.py', 'w') as file:
          123         file.write(script)
          124 
          125 
          126 # Generate scripts
          127 for effective_stress in effective_stresses:
          128 
          129     jobname = jobname_prefix + '{}Pa'.format(effective_stress)
          130 
          131     print(jobname)
          132 
          133     # Generate scripts for slurm, submit with `sbatch <script>`
          134     generate_slurm_script(jobname)
          135 
          136     generate_slurm_continue_script(jobname)
          137 
          138     generate_simulation_script(jobname, effective_stress)