def main():
alljobs = []
for coordfile in glob('*.d.cor'):
coordfileroot = coordfile[:-6]
#Generates coordinate file without Drude particles
nonpolcoordfile = coordfileroot +'.cor'
if not os.path.exists(nonpolcoordfile):
dedrude(coordfile, nonpolcoordfile)
if True or not os.path.exists(coordfileroot):
print 'Preparing', coordfileroot
if not os.path.exists(coordfileroot): os.mkdir(coordfileroot)
os.chdir(coordfileroot)
#Copy runpack
copywild('/home/cjh/rmt/runpack/*', '.')
#Copy coordinate files
#NB Due to a limitation of CHARMM's environment variable
# parsing mechanism, the coordinate filenames
# must be in upper case.
if not os.path.exists(coordfile.upper()):
os.symlink(os.path.join('..', coordfile), coordfile.upper())
if not os.path.exists(nonpolcoordfile.upper()):
os.symlink(os.path.join('..', nonpolcoordfile), \
nonpolcoordfile.upper())
#makejobs(coordfileroot)
os.chdir('..')
alljobs += iteratejobs(coordfileroot)
#exit()
f = open('sgearraytasklist.txt', 'w')
for i, j in enumerate(alljobs):
f.write(str(i+1)+' \t')
f.write(' '.join(j) + '\n')
f.close()
numjobs = len(alljobs)
print 'Indexed', numjobs, 'jobs'
#Now create SGE array job and submit self as an array job
import SGE
import sys
x = SGE.qsubOptions()
x.args.N = 'h2pc-qmmm-rmt'
x.args.t = '1-'+str(numjobs)
x.args.o = '$JOB_NAME.$JOB_ID.$TASK_ID.stdout.log'.replace('$', '\$')
x.args.command = sys.argv[0]
print '#To submit the array job, run this command:'
x.execute(mode = 'echo')
def PrepareJobs(runpack = '/home/cjh/rmt/runpack/*',
joblist = 'sgearraytasklist.txt', sge_jobname = 'h2pc-qmmm-rmt',
DoOverwrite = False, h5filename = 'h2pc-data.h5'):
"""
Prepares jobs to be executed in a term:`SGE` array job environment.
This does the following:
1. Scans all files in the current directory for files matching
@c \*.d.cor, which will be assumed to be :term:`CHARMM card file` s
containing coordinates for the molecular system, and also Drude
particles. For each such file, it will generate the corresponding
:term:`CHARMM card file` s without Drude particles using dedrude().
1. Copies files specified by runpack using linkwild() to a
directory named after the root of the :term:`CHARMM card file` name.
If this directory does not exist, it will be created.
1. Creates a symlink to the :term:`CHARMM card file`. If necessary, the
filename will be converted into upper case due to a limitation of
CHARMM.
1. Writes data needed by :py:func:`domyjob` to a file named in joblist.
1. Generates the command line needed to submit the array job to a Sun
Grid Engine environment.
This function requires the homebrew :py:mod:`SGE` module.
.. versionadded:: 0.1
"""
logger = logging.getLogger('SGEInterface.PrepareJobs')
if os.path.exists(joblist) and not DoOverwrite:
logger.info('Skipping population of %s', joblist)
#count numjobs
numjobs = 0
for line in open(joblist):
len_line = len(line.split())
if len_line == 4:
numjobs += 1
elif len_line != 0:
raise ValueError, 'Invalid format of line:' + line
else:
alljobs = []
#Collect all data into HDF5 file
h5data = tables.openFile(h5filename, 'a')
#############################
# Load in residues to do QM #
#############################
MolList = OpenHDF5Table(h5data, '/Model', 'MolList',
ResidList, 'List of molecule ids for which QM data exist',
DoOverwrite)
if MolList is not None:
if os.path.exists('../mol.list'):
MolListFileName = '../mol.list'
elif os.path.exists('mol.list'):
MolListFileName = 'mol.list'
else:
raise ValueError, "Could not find list of molecule IDs"
for res_id in open(MolListFileName):
logger.info('Adding mol.list')
try:
data = MolList.row
data['ResID'] = int(res_id)
data.append()
except ValueError:
pass
MolList.flush()
###############################################
# Load in atomic charges from CHARMM topology #
###############################################
for CHARMM_RTFile in glob(runpack+'.rtf'):
RTF = OpenHDF5Table(h5data, '/Model', 'CHARMM_RTF',
CHARMM_RTF_Short, 'CHARMM Topology File', DoOverwrite, DoAppend = True)
if RTF is not None:
for line in open(CHARMM_RTFile):
logger.info('Adding CHARMM RTF: %s', CHARMM_RTFile)
t = line.split()
try:
data = RTF.row
data['Type'] = t[1]
data['Charge'] = float(t[3])
data.append()
except (ValueError, IndexError):
pass
RTF.flush()
#####################################
# Load coordinates from CHARMM CARD #
#####################################
for coordfile in glob('*.cor'):
logger.info('Adding CHARMM CARD: %s', coordfile)
coordfileroot = coordfile.split('.')[0]
Coords = OpenHDF5Table(h5data, '/'+coordfileroot, 'CHARMM_CARD',
CHARMM_CARD, 'CHARMM CARD File', DoOverwrite)
if Coords is not None:
LoadCHARMM_CARD(Coords, coordfile)
alljobs += iteratejobs(coordfileroot)
with open(joblist, 'w') as f:
for i, j in enumerate(alljobs):
f.write(str(i+1)+' \t')
f.write(' '.join(j) + '\n')
numjobs = len(alljobs)
logger.info('Indexed %d jobs', numjobs)
#Now create SGE array job and submit self as an array job
x = SGE.qsubOptions()
x.args.N = sge_jobname
x.args.t = '1-'+str(numjobs)
x.args.p = '-500'
x.args.o = '$JOB_NAME.$JOB_ID.$TASK_ID.stdout.log'.replace('$', '\$')
FullPathToJobHandler = os.path.dirname(sys.argv[0])+os.sep+'JobHandler.py'
x.args.command = 'python '+FullPathToJobHandler+' --taskfile '+joblist
x.args.b = 'y'
print '#To submit the array job, run this command:'
x.execute(mode = 'echo')