def qsub_cmd_gen(template, job_name, i, sid, fODF, im, data_path,
cmd_file_path=cmd_file_path, python_path=python_path,
bashcmd=bashcmd, mem=25):
reload(template)
template = sge.getsourcelines(template)[0]
# Name the job and generate the parameters for each job
if job_name[0:2] != "im":
params_dict = dict(i=i, sid=sid, fODF=fODF, im=im,
data_path=data_path)
name = '%s_%s_%s%s'%(job_name,fODF,shorthand_im,i)
else:
params_dict = dict(i=i, sid=sid, im=im,
data_path=data_path)
name = '%s_%s%s'%(job_name,shorthand_im,i)
code = sge.add_params(template,params_dict)
cmd_file = os.path.join(cmd_file_path, '%s.py'%name)
print("Generating: %s"%cmd_file)
sge.py_cmd(ssh,
code,
file_name=cmd_file,
python=python_path)
cmd_file = os.path.join(cmd_file_path, '%s.py'%name)
batch_sge.append(sge.qsub_cmd(
'%s %s'%(bashcmd, cmd_file), name, mem_usage=mem))
import os
import nibabel as ni
import numpy as np
import osmosis.io as oio
from osmosis.parallel import sge
import osmosis.parallel.kfold_xval_precision_template as mb_template
reload(mb_template)
template = sge.getsourcelines(mb_template)[0]
ssh = sge.SSH(hostname='proclus.stanford.edu', username='******', port=22)
batch_sge = []
for i in np.arange(65):
params_dict = dict(i=i)
code = sge.add_params(template, params_dict)
name = 'kfold_xval_sph_cc_m%s' % (i)
cmd_file = '/home/klchan13/pycmd/%s.py' % name
print("Generating: %s" % cmd_file)
sge.py_cmd(ssh,
code,
file_name=cmd_file,
python='/home/klchan13/anaconda/bin/python')
cmd_file = '/home/klchan13/pycmd/%s.py' % name
batch_sge.append(
sge.qsub_cmd('/home/klchan13/bashcmd.sh %s' % cmd_file,
name,
email='*****@*****.**'))
import nibabel as ni
import numpy as np
import osmosis.io as oio
from osmosis.parallel import sge
import osmosis.parallel.mb_predict_template_smm as mb_template
reload(mb_template)
template = sge.getsourcelines(mb_template)[0]
ssh = sge.SSH(hostname='proclus.stanford.edu',username='******', port=22)
batch_sge = []
for i in range(65):
params_dict = dict(i=i)
code = sge.add_params(template,params_dict)
name = 'multi_bi_exp_rs%s'%(i)
cmd_file = '/home/klchan13/pycmd/%s.py'%name
print("Generating: %s"%cmd_file)
sge.py_cmd(ssh,
code,
file_name=cmd_file,
python='/home/klchan13/anaconda/bin/python')
cmd_file = '/home/klchan13/pycmd/%s.py'%name
batch_sge.append(sge.qsub_cmd(
'/home/klchan13/bashcmd.sh %s'%cmd_file,name))
# Add some header stuff:
batch_sge = ['#!/bin/bash'] + batch_sge
