qmcpack/labs/misc/jobrun_vesta

#! /usr/bin/env python

import os
import sys

#=======#
# usage # 
#=======#
#  jobrun_vesta exe_name exe_inputs/options


#=============#
# global data #
#=============#
# the account to charge time to 
account = 'QMCPACK-training' # participant account!
#account = 'QMCPACK'  # instructor account!

# executables jobrun_vesta knows how to handle
exe_name_list = 'ppconvert rungms convert4qmc pw.x pw2qmcpack.x qmcpack qmcpack_comp'.split()
exe_names = set(exe_name_list)

# protect user against errors and print pedagogical error messages
guard = True
#guard = False

# examples displayed to user if no arguments are provided
examples = '''
jobrun_vesta ppconvert --gamess_pot O.BFD.gamess --s_ref "1s(2)2p(4)" --p_ref "1s(2)2p(4)" --d_ref "1s(2)2p(4)" --log_grid --upf O.BFD.upf

jobrun_vesta rungms H2O.PBE

jobrun_vesta convert4qmc -gamessAscii H2O.CISD.orbs.output -ci H2O.CISD.orbs.output -threshold 0.01 -readInitialGuess 60  -add3BodyJ

jobrun_vesta pw.x scf.in

jobrun_vesta pw2qmcpack.x p2q.in

jobrun_vesta qmcpack opt.in.xml
'''

# portions of template qsub script
cobalt_header = '''#!/bin/bash
#COBALT -q qmcpack
#COBALT -A {0}
#COBALT -n {1}
#COBALT -t {2}
#COBALT -O {3}
'''
#cobalt_header = '''#!/bin/bash
##COBALT -q default
##COBALT -A {0}
##COBALT -n {1}
##COBALT -t {2}
##COBALT -O {3}
#'''


cobalt_shape = '''LOCARGS="--block $COBALT_PARTNAME ${COBALT_CORNER:+--corner} $COBALT_CORNER ${COBALT_SHAPE:+--shape} $COBALT_SHAPE"
echo "Cobalt location args: $LOCARGS" >&2
'''
runjob='runjob --np {0} -p {1} $LOCARGS --verbose=INFO --envs OMP_NUM_THREADS={2} : {3}{4}'


#==================#
# global functions #
#==================#
def error(msg):
    print 'jobrun error:\n  '+msg.replace('\n','\n  ')
    print 'exiting'
    sys.exit()
#end def error

def join_args(args):
    s = ''
    for a in args:
        s+=' '+a
    #end for
    return s.lstrip()
#end def join_args


#==================#
# actual execution #
#==================#
# get the tokens provided by the user
args = sys.argv[1:]

# require at least one argument, the exe name
if len(args)==0:
    error('no arguments provided to jobrun_vesta\nfirst argument to jobrun_vesta must be the exe name\nvalid options are: {0}\nan example for each executable is shown below\n{1}'.format(exe_name_list,examples))
#end if

# get the exe name and any arguments for the exe itself
exe_name = args[0]
exe_arg_list = args[1:]

# exe must be known
if exe_name not in exe_names:
    error('invalid exe name: {0}\nvalid options are: {1}'.format(exe_name,exe_name_list))
#end if

# generate submission command based on target executable
script = False
runstr = None
command = ''
if exe_name=='ppconvert':
    #===========#
    # ppconvert #
    #===========#
    for n in range(len(exe_arg_list)-1): # put " back on arguments
        arg1 = exe_arg_list[n]
        arg2 = exe_arg_list[n+1]
        if arg1.startswith('--') and arg1.endswith('ref'):
            if not arg2.startswith('"'):
                arg2 = '"'+arg2
            #end if
            if not arg2.endswith('"'):
                arg2 = arg2+'"'
            #end if
            exe_arg_list[n+1] = arg2
        #end if
    #end for
    script  = True
    #exe     = '/soft/applications/qmcpack/Binaries/ppconvert'
    exe     = '/home/yeluo/qmcdev/trunk/src/QMCTools/ppconvert/build/ppconvert'
    prefix  = 'ppconv'
    nodes   = 1
    procs   = 1
    threads = 1
    time    = 60
    argstr  = ' '+join_args(exe_arg_list)+'\n'
    runstr  = exe+argstr
    
elif exe_name=='rungms':
    #========#
    # GAMESS #
    #========#
    if len(exe_arg_list)!=1:
        error('must provide a single argument to rungms, the input file prefix\narguments provided: {0}'.format(exe_arg_list))
    #end if
    infile_prefix = exe_arg_list[0]
    if guard:
        if infile_prefix.endswith('.inp'):
            infile = infile_prefix
            infile_prefix = infile_prefix.rsplit('.',1)[0]
            error('rungms expects the input file prefix, not the file itself\nfile provided: {0}\nprefix expected: {1}'.format(infile,infile_prefix))
        else:
            infile = infile_prefix+'.inp'
        #end if
        if not os.path.exists(infile):
            error('gamess input file does not exist: {0}'.format(infile))
        #end if
    #end if
    #gms   = '/soft/applications/qmcpack/Binaries/gmsbgq'
    gms   = '/home/yeluo/qmcdev/DFT_Binaries/gmsbgq.old' # 1 May 2012 (R2) 
    nodes = 32
    time  = 20
    mode  = 'c1'
    # rungms prefix nodes time mode account prefix
    command = '{0} {1} {2} {3} {4} {5} {1}'.format(gms,infile_prefix,nodes,time,mode,account,infile_prefix)
elif exe_name=='convert4qmc':
    #=============#
    # convert4qmc #
    #=============#
    prefix   = 'c4q'
    for n in range(len(exe_arg_list)):
        if exe_arg_list[n]=='-prefix' and n+1<len(exe_arg_list):
            prefix = exe_arg_list[n+1]
        #end if
    #end for
    script  = True
    exe     = '/soft/applications/qmcpack/Binaries/convert4qmc'
    nodes   = 1
    procs   = 1
    threads = 1
    time    = 10
    argstr  = ' '+join_args(exe_arg_list)+'\n'

elif exe_name=='pw.x':
    #======#
    # pw.x #
    #======#
    if len(exe_arg_list)!=1:
        error('must provide a single argument to pw.x, the input file\narguments provided: {0}\n(pw.x can accept other inputs outside the training environment)'.format(exe_arg_list))
    #end if
    infile = exe_arg_list[0]
    if guard:
        if not os.path.exists(infile):
            error('pw.x input file does not exist: {0}'.format(infile))
        #end if
    #end if
    if '.' in infile:
        prefix = infile.rsplit('.',1)[0]
    else:
        prefix = infile
    #end if
    script  = True
    exe     = '/soft/applications/qmcpack/Binaries/pw.x'
    nodes   = 32
    procs   = 16
    threads = 1
    time    = 60
    argstr  =  ' -input '''+infile+'\n'

elif exe_name=='pw2qmcpack.x':
    #==============#
    # pw2qmcpack.x #
    #==============#
    if len(exe_arg_list)!=1:
        error('must provide a single argument to pw2qmcpack.x, the input file\narguments provided: {0}\n(pw2qmcpack.x can accept other inputs outside the training environment)'.format(exe_arg_list))
    #end if
    infile = exe_arg_list[0]
    if guard:
        if not os.path.exists(infile):
            error('pw2qmcpack.x input file does not exist: {0}'.format(infile))
        #end if
    #end if
    if '.' in infile:
        prefix = infile.rsplit('.',1)[0]
    else:
        prefix = infile
    #end if
    script  = True
    exe     = '/soft/applications/qmcpack/Binaries/pw2qmcpack.x'
    nodes   = 1
    procs   = 1
    threads = 1
    time    = 60
    argstr  = '<'+infile+'\n'

elif exe_name=='qmcpack' or exe_name=='qmcpack_comp':
    #=========#
    # QMCPACK #
    #=========#
    if len(exe_arg_list)!=1:
        error('must provide a single argument to qmcpack, the input file\narguments provided: {0}\n(qmcpack can accept other inputs outside the training environment)'.format(exe_arg_list))
    #end if
    infile = exe_arg_list[0]
    if guard:
        if not os.path.exists(infile):
            error('qmcpack input file does not exist: {0}'.format(infile))
        #end if
    #end if
    if '.' in infile:
        if infile.endswith('.in.xml'):
            prefix = infile.rsplit('.',2)[0]
        else:
            prefix = infile.rsplit('.',1)[0]
        #end if
    else:
        prefix = infile
    #end if
    script  = True
    exe     = '/soft/applications/qmcpack/Binaries/'+exe_name
    nodes   = 32
    procs   = 1
    threads = 16
    #threads = 64
    time    = 60
    argstr  = ' '+infile+'\n'
#end if

if script:
    script_text = cobalt_header.format(account,nodes,time,prefix)
    script_text += cobalt_shape
    if runstr is None:
        script_text += runjob.format(nodes*procs,procs,threads,exe,argstr)
    else:
        script_text += runstr+'\n'
    #end if
    script_file = prefix+'.qsub.in'
    open(script_file,'w').write(script_text)
    os.system('chmod +x '+script_file)
    command = 'qsub --mode script --env BG_SHAREDMEMSIZE=32 {0}'.format(script_file)
#end if

# execute the submission command
print command
os.system(command)