Python qsub_cmd Beispiele

Beispiel #1

Datei: all_brain_analyses_wrapper.py Projekt: zhangerjun/osmosis

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))

Beispiel #2

Datei: kfold_xval_sph_cc_wrapper.py Projekt: zhangerjun/osmosis

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='*****@*****.**'))

# Add some header stuff:
batch_sge = ['#!/bin/bash'] + batch_sge
sge.write_file_ssh(ssh, batch_sge, '/home/klchan13/batch_sge.sh')

Beispiel #3

Datei: ssd_wrapper.py Projekt: zhangerjun/osmosis

                                           params_file=params_file)

                        code = sge.add_params(template, params_dict)
                        name = 'ssd_%s_b%s_data%s_l1ratio%s_alpha%s_%03d' % (
                            subject, b, data_i + 1, l1_ratio, alpha, i)
                        cmd_file = '/home/arokem/pycmd/%s.py' % name
                        print("Generating: %s" % cmd_file)

                        sge.py_cmd(ssh,
                                   code,
                                   file_name=cmd_file,
                                   python='/home/arokem/anaconda/bin/python')

                        cmd_file = '/home/arokem/pycmd/%s.py' % name
                        batch_sge.append(
                            sge.qsub_cmd(
                                '/home/arokem/bashcmd.sh %s' % cmd_file, name))

# Add some header stuff:
#batch_sge = ['export PATH=$PATH:/hsgs/software/oge2011.11p1/bin/linux-x64/'] + batch_sge
#batch_sge = ['export SGE_ROOT=/hsgs/software/oge2011.11p1'] + batch_sge
batch_sge = ['#!/bin/bash'] + batch_sge
sge.write_file_ssh(ssh, batch_sge, '/home/arokem/batch_sge.sh')

#stat = os.system('scp -c blowfish -C tmp/* %s:~/pycmd/.'%ssh.hostname)
#if stat != 0:
#    print "what what!"

#ssh.exec_command('./batch_sge.sh')
#ssh.disconnect()

Beispiel #4

Datei: mb_predict_wrapper.py Projekt: JuergenNeubauer/osmosis

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
sge.write_file_ssh(ssh, batch_sge, '/home/klchan13/batch_sge.sh')

Beispiel #5

Datei: ssd_wrapper.py Projekt: JuergenNeubauer/osmosis

                            wm_file=wm_file,
                            params_file = params_file)
                                    
                        code = sge.add_params(template,params_dict)
                        name = 'ssd_%s_b%s_data%s_l1ratio%s_alpha%s_%03d'%(
                            subject, b, data_i+1, l1_ratio, alpha, i)
                        cmd_file = '/home/arokem/pycmd/%s.py'%name
                        print("Generating: %s"%cmd_file)
                        
                        sge.py_cmd(ssh,
                                   code,
                                   file_name=cmd_file,
                                   python='/home/arokem/anaconda/bin/python')

                        cmd_file = '/home/arokem/pycmd/%s.py'%name
                        batch_sge.append(sge.qsub_cmd(
                            '/home/arokem/bashcmd.sh %s'%cmd_file,name))

# Add some header stuff:
#batch_sge = ['export PATH=$PATH:/hsgs/software/oge2011.11p1/bin/linux-x64/'] + batch_sge
#batch_sge = ['export SGE_ROOT=/hsgs/software/oge2011.11p1'] + batch_sge
batch_sge = ['#!/bin/bash'] + batch_sge
sge.write_file_ssh(ssh, batch_sge, '/home/arokem/batch_sge.sh')


#stat = os.system('scp -c blowfish -C tmp/* %s:~/pycmd/.'%ssh.hostname)
#if stat != 0:
#    print "what what!"

#ssh.exec_command('./batch_sge.sh')
#ssh.disconnect()

Beispiel #6

from osmosis.parallel import sge

import osmosis.parallel.multib_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 range(1): 
    #params_dict = dict(i=i)
    #code = sge.add_params(template,params_dict)
name = 'mb_model_params'
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
sge.write_file_ssh(ssh, batch_sge, '/home/klchan13/batch_sge.sh')

Beispiel #7

Datei: mb_model_params_wrapper.py Projekt: zhangerjun/osmosis

import numpy as np
import osmosis.io as oio
from osmosis.parallel import sge

import osmosis.parallel.mb_multi_model_params_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 range(65):
    params_dict = dict(i=i)
    code = sge.add_params(template, params_dict)
    name = 'mp_multi_se%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
sge.write_file_ssh(ssh, batch_sge, '/home/klchan13/batch_sge.sh')

Beispiel #8

Datei: kfold_xval_sph_cc_wrapper.py Projekt: JuergenNeubauer/osmosis

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 = '*****@*****.**'))

# Add some header stuff:
batch_sge = ['#!/bin/bash'] + batch_sge
sge.write_file_ssh(ssh, batch_sge, '/home/klchan13/batch_sge.sh')