1 | #!/usr/bin/env python |
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2 | # |
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3 | # Author: Dennis Stam |
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4 | # Date: 30 September 2014 |
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5 | # Description: This is a very simple jobscript parser to fetch all #PBS arguments |
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6 | # and convert them to a attropl list which can be used for submission |
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7 | # |
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8 | |
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9 | import re |
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10 | import sys |
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11 | import argparse |
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12 | import time |
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13 | import pbs |
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14 | |
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15 | class JobParser(object): |
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16 | '''A simple simple jobscript parser to fetch all #PBS arguments from the header''' |
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17 | |
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18 | job_script = None |
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19 | matcher = re.compile(r'\#PBS\s(?P<args>.+)') |
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20 | |
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21 | ## These are the arguments that exist in Torque |
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22 | pbs_attrs = { |
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23 | 'a' : { |
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24 | 'func': 'pbs_datetime', |
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25 | 'args_opts': { |
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26 | 'type': str, |
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27 | }, |
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28 | }, |
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29 | 'A' : { |
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30 | 'args_opts': { |
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31 | 'type': str, |
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32 | }, |
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33 | }, |
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34 | # Checkpoint is not yet implemented |
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35 | #'c' : { |
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36 | # 'args_opts': { |
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37 | # 'type': str, |
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38 | # 'action': 'append', |
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39 | # }, |
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40 | #}, |
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41 | 'e' : { |
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42 | 'args_opts': { |
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43 | 'type': str, |
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44 | }, |
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45 | }, |
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46 | 'F' : { |
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47 | 'args_opts': { |
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48 | 'type': str, |
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49 | }, |
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50 | }, |
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51 | 'f' : { |
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52 | 'args_opts': { |
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53 | 'action' : 'store_true', |
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54 | }, |
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55 | }, |
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56 | 'h' : { |
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57 | 'args_opts': { |
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58 | 'action' : 'store_true', |
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59 | }, |
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60 | }, |
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61 | 'I' : { |
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62 | 'args_opts': { |
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63 | 'action' : 'store_true', |
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64 | }, |
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65 | }, |
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66 | 'j' : { |
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67 | 'args_opts': { |
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68 | 'type': str, |
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69 | 'choices': ['eo','oe','n'], |
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70 | }, |
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71 | }, |
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72 | 'k' : { |
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73 | 'args_opts': { |
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74 | 'type': str, |
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75 | 'choices' : ['e','o','eo','oe','n'], |
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76 | }, |
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77 | }, |
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78 | 'l' : { |
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79 | 'args_opts': { |
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80 | 'type': str, |
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81 | 'action': 'append', |
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82 | }, |
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83 | }, |
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84 | 'm' : { |
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85 | 'args_opts': { |
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86 | 'type': str, |
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87 | 'choices': ['a','b','e','n'], |
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88 | }, |
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89 | }, |
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90 | 'M' : { |
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91 | 'args_opts': { |
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92 | 'type': str, |
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93 | 'action': 'append', |
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94 | }, |
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95 | }, |
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96 | 'N' : { |
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97 | 'args_opts': { |
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98 | 'type': str, |
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99 | }, |
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100 | }, |
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101 | 'o' : { |
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102 | 'args_opts': { |
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103 | 'type': str, |
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104 | }, |
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105 | }, |
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106 | 'p' : { |
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107 | 'args_opts': { |
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108 | 'type': int, |
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109 | }, |
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110 | }, |
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111 | 'P' : { |
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112 | 'args_opts': { |
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113 | 'type': str, |
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114 | }, |
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115 | }, |
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116 | 'q' : { |
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117 | 'args_opts': { |
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118 | 'type': str, |
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119 | }, |
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120 | }, |
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121 | 'r' : { |
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122 | 'args_opts': { |
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123 | 'action' : 'store_true', |
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124 | }, |
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125 | }, |
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126 | 'S' : { |
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127 | 'args_opts': { |
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128 | 'type': str, |
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129 | 'action' : 'append', |
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130 | }, |
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131 | }, |
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132 | 't' : { |
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133 | 'args_opts': { |
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134 | 'type': str, |
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135 | }, |
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136 | }, |
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137 | 'u' : { |
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138 | 'args_opts': { |
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139 | 'type': str, |
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140 | 'action' : 'append', |
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141 | }, |
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142 | }, |
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143 | 'W' : { |
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144 | 'args_opts': { |
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145 | 'type': str, |
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146 | 'action' : 'append', |
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147 | }, |
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148 | }, |
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149 | } |
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150 | |
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151 | def __init__(self, job_script=None): |
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152 | if hasattr(job_script, 'readlines'): |
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153 | self.job_script = job_script.readlines() |
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154 | |
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155 | def read(self, filename): |
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156 | try: |
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157 | with open(filename, 'r') as fi: |
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158 | self.job_script = fi.readlines() |
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159 | except IOError: |
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160 | error_str = "Jobscript filename does not exists: %s" %(filename) |
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161 | raise Exception(error_str) |
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162 | |
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163 | def __get_pbs_args(self): |
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164 | if not self.job_script: |
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165 | raise Exception("User function read to read from file") |
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166 | |
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167 | args = list() |
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168 | for line in self.job_script: |
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169 | if self.matcher.search(line.strip()): |
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170 | args.append(self.matcher.findall(line.strip())[0]) |
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171 | return args |
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172 | |
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173 | def pbs_datetime(self, input): |
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174 | |
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175 | current_time, current_seconds = tuple(time.strftime('%Y%m%d%H%M.%S').split('.')) |
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176 | |
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177 | if len(input.strip()) == 12: |
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178 | return input.strip() |
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179 | elif len(input.strip()) == 10: |
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180 | return current_time[0:2] + input.strip() |
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181 | elif len(input.strip()) == 8: |
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182 | return current_time[0:4] + input.strip() |
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183 | elif len(input.strip()) == 6: |
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184 | return current_time[0:6] + input.strip() |
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185 | elif len(input.strip()) == 4: |
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186 | return current_time[0:8] + input.strip() |
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187 | |
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188 | return current_time |
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189 | |
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190 | def parse_pbs(self): |
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191 | '''Parse the arguments and check if they are using the correct format''' |
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192 | |
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193 | ## First create an arguments parser |
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194 | parser = argparse.ArgumentParser(add_help=False) |
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195 | for arg, options in self.pbs_attrs.items(): |
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196 | parser.add_argument('-'+arg, **options['args_opts']) |
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197 | |
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198 | ## Parse the arguments that have been found in the jobscript |
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199 | args = parser.parse_args(self.__get_pbs_args()) |
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200 | |
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201 | ## Create an dict with items we wan't to set, skip evrything which is None, empty of False |
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202 | process_args = dict() |
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203 | for k,v in args.__dict__.items(): |
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204 | if v: |
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205 | if self.pbs_attrs.has_key(k) and self.pbs_attrs[k].has_key('func'): |
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206 | try: |
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207 | process_args[k] = getattr(self, self.pbs_attrs[k]['func'])(v) |
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208 | except AttributeError as err: |
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209 | raise Exception('Could not locate function') |
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210 | else: |
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211 | if type(v) is type(list()): |
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212 | value = list() |
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213 | for x in v: |
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214 | value.extend(x.strip().split(',')) |
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215 | process_args[k] = ",".join(value) |
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216 | else: |
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217 | process_args[k] = v.strip() |
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218 | return process_args |
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219 | |
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220 | def get_attropl(self): |
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221 | data = self.parse_pbs() |
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222 | |
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223 | ### First al the keys, except for --resource-list/-l |
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224 | ## and perhaps more later |
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225 | length = len([ x for x in data.keys() if x not in ['l']]) |
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226 | if data.has_key('l'): |
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227 | length += len(data['l'].split(',')) |
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228 | |
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229 | attropl = pbs.new_attropl(length) |
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230 | index = 0 |
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231 | |
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232 | for attr, value in data.items(): |
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233 | if attr in ['l']: |
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234 | for v in value.split(','): |
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235 | parts = v.split('=') |
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236 | resource, value = parts[0], "=".join(parts[1:]) |
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237 | attropl[index].name = getattr(pbs, 'ATTR_'+attr) |
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238 | attropl[index].resource = resource |
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239 | attropl[index].value = value |
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240 | index += 1 |
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241 | else: |
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242 | attropl[index].name = getattr(pbs, 'ATTR_'+attr) |
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243 | attropl[index].value = value |
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244 | index += 1 |
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245 | return attropl |
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246 | |
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247 | if __name__ == '__main__': |
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248 | jp = JobParser() |
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249 | |
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250 | try: |
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251 | jp.read(sys.argv[1]) |
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252 | except IndexError: |
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253 | print("Usage: %s <jobscript>" %(sys.argv[0])) |
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254 | sys.exit(1) |
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255 | |
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256 | |
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257 | server_name = pbs.pbs_default() |
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258 | con = pbs.pbs_connect(server_name) |
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259 | job_id = pbs.pbs_submit(con, jp.get_attropl(), sys.argv[1], 'batch', 'NULL') |
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260 | |
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261 | e, e_txt = pbs.error() |
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262 | if e: |
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263 | print(e, e_txt) |
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264 | else: |
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265 | print(job_id) |
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