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WH_Res_QSUB_bioRxiv0.py
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WH_Res_QSUB_bioRxiv0.py
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#!/imaging/local/software/anaconda/latest/x86_64/bin/python
"""
==========================================
Submit qsub jobs for WH Resolution analysis
allow dependencies between jobs
==========================================
OH July 2018
"""
print(__doc__)
import subprocess
from os import path as op
# indices of subjects to process
subjs = range(0,16)
job_list = \
[
# #####
# # COMPUTING and MORPHING Sensitivity Maps
# #####
# {'N': 'R_SMap', # job name
# 'Py': 'WH_Res_SensitivityMaps', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': subjs, # subject indices
# 'mem': '1GB', # memory for qsub process
# 'dep': '',
# 'var': '"RMS"'}, # variable string for python script (e.g. for filenames)}, # name of preceeding process (optional)
# {'N': 'R_MphSM', # job name
# 'Py': 'WH_Res_MorphSTC_SMap', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': subjs, # subject indices
# 'mem': '1GB', # memory for qsub process
# 'dep': 'R_SMap',
# 'var': '"RMS"'}, # additional variables for python script (optional)
# #####
# # AVERAGING Sensitivity Maps
# #####
# ### The following depends on completion of previous jobs for ALL subjects
# {'N': 'R_AvgMphSMap', # job name
# 'Py': 'WH_Res_AvgSTCs_SMaps', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': [''], # subject indices, '' if across all subjects
# 'mem': '2GB', # memory for qsub process
# 'dep': '',
# 'var': '"SensitivityMaps RMS"'},
#####
# COMPUTING Resolution Metrics
#####
{'N': 'R_LocErrPeak', # job name
'Py': 'WH_Res_ResolutionMetrics', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': subjs, # subject indices
'mem': '1GB', # memory for qsub process
'var': '"locerr peak"',
'dep': ''},
{'N': 'R_LocErrCOG', # job name
'Py': 'WH_Res_ResolutionMetrics', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': subjs, # subject indices
'mem': '1GB', # memory for qsub process
'var': '"locerr cog"',
'dep': ''},
{'N': 'R_WidthSD', # job name
'Py': 'WH_Res_ResolutionMetrics', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': subjs, # subject indices
'mem': '1GB', # memory for qsub process
'var': '"width sd"',
'dep': ''},
{'N': 'R_WidthMR', # job name
'Py': 'WH_Res_ResolutionMetrics', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': subjs, # subject indices
'mem': '1GB', # memory for qsub process
'var': '"width maxrad"',
'dep': ''},
{'N': 'R_AmpSum', # job name
'Py': 'WH_Res_ResolutionMetrics', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': subjs, # subject indices
'mem': '1GB', # memory for qsub process
'var': '"amplitude sum"',
'dep': ''},
{'N': 'R_AmpPeak', # job name
'Py': 'WH_Res_ResolutionMetrics', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': subjs, # subject indices
'mem': '1GB', # memory for qsub process
'var': '"amplitude peak"',
'dep': ''},
# #####
# # MORPHING Resolution Metrics
# #####
# {'N': 'R_MphLocErrPeak', # job name
# 'Py': 'WH_Res_MorphSTC', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': subjs, # subject indices
# 'mem': '2GB', # memory for qsub process
# 'dep': 'R_LocErrPeak',
# 'var': '"ResolutionMetrics locerr_peak"'},
# {'N': 'R_MphLocErrCOG', # job name
# 'Py': 'WH_Res_MorphSTC', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': subjs, # subject indices
# 'mem': '2GB', # memory for qsub process
# 'dep': 'R_LocErrCOG',
# 'var': '"ResolutionMetrics locerr_cog"'},
# {'N': 'R_MphWidthSD', # job name
# 'Py': 'WH_Res_MorphSTC', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': subjs, # subject indices
# 'mem': '2GB', # memory for qsub process
# 'dep': 'R_WidthSD',
# 'var': '"ResolutionMetrics width_sd"'},
# {'N': 'R_MphWidthMR', # job name
# 'Py': 'WH_Res_MorphSTC', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': subjs, # subject indices
# 'mem': '2GB', # memory for qsub process
# 'dep': 'R_WidthMR',
# 'var': '"ResolutionMetrics width_maxrad"'},
# {'N': 'R_MphAmpSum', # job name
# 'Py': 'WH_Res_MorphSTC', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': subjs, # subject indices
# 'mem': '2GB', # memory for qsub process
# 'dep': 'R_AmpSum',
# 'var': '"ResolutionMetrics amplitude_sum"'},
# {'N': 'R_MphAmpPeak', # job name
# 'Py': 'WH_Res_MorphSTC', # Python script
# 'Cf': 'WH_Res_config', # configuration script
# 'Ss': subjs, # subject indices
# 'mem': '2GB', # memory for qsub process
# 'dep': 'R_AmpPeak',
# 'var': '"ResolutionMetrics amplitude_peak"'}
#####
# AVERAGING Resolution Metrics
#####
### NOTE: The following depend on completion of previous jobs for ALL subjects
{'N': 'R_AMLocErrPeak', # job name
'Py': 'WH_Res_AvgSTCs', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': [''], # subject indices, '' if across all subjects
'mem': '1GB', # memory for qsub process
'var': '"ResolutionMetrics locerr_peak"'},
{'N': 'R_AMLocErrCog', # job name
'Py': 'WH_Res_AvgSTCs', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': [''], # subject indices, '' if across all subjects
'mem': '1GB', # memory for qsub process
'var': '"ResolutionMetrics locerr_cog"'},
{'N': 'R_AMWidthSD', # job name
'Py': 'WH_Res_AvgSTCs', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': [''], # subject indices, '' if across all subjects
'mem': '1GB', # memory for qsub process
'var': '"ResolutionMetrics width_sd"'},
{'N': 'R_AMWidthMR', # job name
'Py': 'WH_Res_AvgSTCs', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': [''], # subject indices, '' if across all subjects
'mem': '1GB', # memory for qsub process
'var': '"ResolutionMetrics width_maxrad"'},
{'N': 'R_AMAmpSum', # job name
'Py': 'WH_Res_AvgSTCs', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': [''], # subject indices, '' if across all subjects
'mem': '1GB', # memory for qsub process
'var': '"ResolutionMetrics amplitude_sum"'},
{'N': 'R_AMAmpPeak', # job name
'Py': 'WH_Res_AvgSTCs', # Python script
'Cf': 'WH_Res_config', # configuration script
'Ss': [''], # subject indices, '' if across all subjects
'mem': '1GB', # memory for qsub process
'var': '"ResolutionMetrics amplitude_peak"'}
]
# directory where python scripts are
dir_py = op.join('/', 'home', 'olaf', 'MEG', 'WakemanHensonEMEG', 'ScriptsResolution')
# directory for qsub output
dir_qsub = op.join('/', 'home', 'olaf', 'MEG', 'WakemanHensonEMEG', 'ScriptsResolution', 'qsub_out')
# wrapper to run python script via qsub
fname_wrap = op.join('/', 'home', 'olaf', 'MEG', 'WakemanHensonEMEG', 'wrapper_qsub_python_v015.sh')
# keep track of qsub Job IDs
Job_IDs = {}
for job in job_list:
for Ss in job['Ss']:
Ss = str(Ss) # turn into string for filenames etc.
N = job['N']
Py = op.join(dir_py, job['Py'])
Cf = job['Cf']
mem = job['mem']
# files for qsub output
file_out = op.join(dir_qsub, job['N'] + '_' + Cf + '-%s.out' % str(Ss))
file_err = op.join(dir_qsub, job['N'] + '_' + Cf + '-%s.err' % str(Ss))
# if job dependent of previous job, get Job ID and produce command
if 'dep' in job: # if dependency on previous job specified
if job['dep']=='':
dep_str = ''
else:
job_id = Job_IDs[job['dep'], Ss]
dep_str = '-W depend=afterok:%s' % (job_id)
else:
dep_str = ''
if 'node' in job: # if node constraint present (e.g. Maxfilter)
node_str = job['node']
else:
node_str = ''
if 'var' in job: # if variables for python script specified
var_str = job['var']
else:
var_str = ''
# use wrapper to submit python script
qsub_cmd = 'qsub %s \
-N %s%s \
-l walltime=24:00:00,mem=%s \
-o %s \
-e %s \
-v pycmd="%s.py %s",subj_idx=%s,var=%s \
%s \
%s' \
% (fname_wrap, N, Ss, mem, file_out, file_err, Py, Cf, Ss, var_str, dep_str, node_str)
# format string for display
print_str = qsub_cmd.replace(' ' * 25, ' ')
print('\n%s\n' % print_str)
# execute qsub command
proc = subprocess.Popen(qsub_cmd, stdout=subprocess.PIPE, shell=True)
# get linux output
(out, err) = proc.communicate()
# keep track of Job IDs from qsub
Job_IDs[N, Ss] = out.split('.')[0]
# Done