clusterfunc.py

# Lisa Cohen
# commonly-used functions
# to use, "import clusterfunc"

import os
import subprocess
from subprocess import Popen, PIPE

def check_dir(dirname):
    if os.path.isdir(dirname)==False:
        os.mkdir(dirname)
        print "Directory created:",dirname

def get_qsub_filename(basedir,process_name,filename):
    qsub_dir=basedir+"qsub_files/"
    check_dir(qsub_dir)
    qsub_filename=qsub_dir+process_name+"_"+filename+".qsub"
    return qsub_dir,qsub_filename

def get_module_load_list(module_name_list):
    module_list=[]
    for module in module_name_list:
        module_load="module load "+module
        module_list.append(module_load)
    return module_list

def qsub_file(basedir,process_name,module_name_list,filename,process_string):
    working_dir=os.getcwd()
    qsub_dir,qsub_filename=get_qsub_filename(basedir,process_name,filename)
    os.chdir(qsub_dir)
    module_load=get_module_load_list(module_name_list)
    f="""#!/bin/bash
#PBS -l walltime=02:00:00,nodes=1:ppn=8
#PBS -l mem=32gb
#PBS -l feature=intel16
#PBS -j oe
#PBS -A ged
#PBS -M ljcohen@msu.edu
#PBS -m ae
#PBS -W umask=027
cd ${{PBS_O_WORKDIR}}
export MKL_NUM_THREADS=8
export OMP_NUM_THREADS=8
""".format()
    with open(qsub_filename,"w") as qsub:
	 qsub.write(f)
         for module_string in module_load:
             qsub.write(module_string+"\n")
             #print module_string
         for string in process_string:
             qsub.write(string+"\n")
             print string
	 qsub.write("qstat -f ${PBS_JOBID}\n")
	 qsub.write("cat ${PBS_NODEFILE} # Output Contents of the PBS NODEFILE\n")
         qsub.write("env | grep PBS # Print out values of the current jobs PBS environment variables\n")
    qsub_string='qsub -V '+qsub_filename
    print qsub_string
    s=subprocess.Popen(qsub_string,shell=True)
    s.wait()
    os.chdir(working_dir)