| commit | author | age | ||
| 8ab985 | 1 | import configobj |
| SP | 2 | import xml.etree.ElementTree as ET |
| 3 | import base64 | |
| 4 | import zlib | |
| 5 | import sys,io | |
| 6 | import os | |
| 7 | from itertools import islice | |
| 8 | import mmap | |
| 9 | import shlex | |
| 10 | import psutil | |
| 11 | import time | |
| 12 | import datetime | |
| 13 | import subprocess | |
| 14 | import shutil | |
| 15 | ||
| 16 | # Process status | |
| 17 | TS_NOLOCK=0 # lock file does not exist | |
| 18 | TS_NONEXISTANT=0 # process is not in the list of processes | |
| 19 | TS_STOPPED=1 # the process is listed, but is in stopped state | |
| 20 | TS_RUNNING=2 # process is running | |
| 21 | TS_COMPLETED=3 #simulation is completed | |
| 22 | ||
| c1504d | 23 | #namespace variable. Seems the best place to put the variable in :) |
| SP | 24 | _analysis_list={} |
| 25 | ||
| 8ab985 | 26 | class FileContent: |
| SP | 27 | ''' |
| 28 | Class is helpful for reading and writting the specific files. | |
| 29 | ''' | |
| 30 | def __init__(self,filename): | |
| 31 | ''' The instance is done by calling constructor FileContent(filename) | |
| 32 | ||
| 33 | The object then reads filename if it exists, otherwise the data is empty string. | |
| 34 | User may force to reread file by calling the readline() method of the class. | |
| 35 | ||
| 36 | Filename is stored in local variable for future file operations. | |
| 37 | ''' | |
| 38 | ||
| 39 | self.filename=filename | |
| 40 | self.readfile() | |
| 41 | ||
| 42 | def readfile(self): | |
| 43 | '''Force reread of the file and setting the data''' | |
| 44 | self.data="" | |
| 45 | try: | |
| 46 | with open (self.filename, "r") as myfile: | |
| 47 | self.data=myfile.read().replace('\n', '') #read the file and remove newline from the text | |
| 48 | except: | |
| 49 | pass # does nothing if error occurs | |
| 50 | ||
| 51 | ||
| 52 | def writefile(self, data, mode='w'): | |
| 53 | '''File may be updated by completely rewritting the file contents or appending the data to the end of the file. | |
| 54 | this is achieved by calling writefile(data, mode) method, where data is the string data to be written and | |
| 55 | mode can be 'a' for append and 'w' for writting the file anew. | |
| 56 | ''' | |
| 57 | with open (self.filename, mode) as myfile: | |
| 58 | myfile.write(data) | |
| 59 | ||
| 60 | def getText(self): | |
| 61 | ''' | |
| 62 | Method getText() or calling the object itself returns string of data | |
| 63 | ''' | |
| 64 | return self.data | |
| 65 | ||
| 66 | def __str__(self): | |
| 67 | ''' | |
| 68 | Method getText() or calling the object itself returns string of data | |
| 69 | ''' | |
| 70 | return self.getText() | |
| 71 | ||
| 72 | class Tape: | |
| 73 | ''' | |
| 74 | Special class that manages configuration of trisurf (commonly named tape). It can read and parse configuration from disk or parse it from string. | |
| 75 | ''' | |
| 76 | ||
| 77 | def __init__(self): | |
| 78 | '''The object is instatiated by calling Tape() constructor without parameters''' | |
| 79 | return | |
| 80 | ||
| 81 | def readTape(self, tape='tape'): | |
| 82 | ''' | |
| 83 | Tape is read and parsed by calling the readTape() method with optional tape parameter, which is full path to filename where the configuration is stored. | |
| 84 | If the tape cannot be read, it prints error and exits. | |
| 85 | ''' | |
| 86 | try: | |
| 87 | self.config=configobj.ConfigObj(tape) | |
| 88 | with open (tape, "r") as myfile: | |
| 89 | self.rawText=myfile.read() #read the file | |
| 90 | ||
| 91 | except: | |
| 92 | print("Error reading or parsing tape file!\n") | |
| 93 | exit(1) | |
| 94 | ||
| 95 | def setTape(self, string): | |
| 96 | '''Method setTape(string) parses the string in memory that hold the tape contents.''' | |
| 97 | self.config=configobj.ConfigObj(io.StringIO(string)) | |
| 98 | self.rawText=string | |
| 99 | return | |
| 100 | ||
| 101 | def getValue(self,key): | |
| 102 | '''Method getValue(key) returns value of a single parsed setting named "key".''' | |
| 103 | ||
| 104 | return self.config[key] | |
| 105 | ||
| 106 | def __str__(self): | |
| 107 | '''Calling the object itself, it recreates the tape contents from parsed values in form of key=value.''' | |
| 108 | retval="" | |
| 109 | for key,val in self.config.iteritems(): | |
| 110 | retval=retval+str(key)+" = "+str(val)+"\n" | |
| 111 | return retval | |
| 112 | ||
| 113 | ||
| 114 | ||
| 115 | class Directory: | |
| 116 | ''' | |
| 117 | Class deals with the paths where the simulation is run and data is stored. | |
| 118 | ''' | |
| 119 | def __init__(self, maindir=".", simdir=""): | |
| 120 | '''Initialization Directory() takes two optional parameters, namely maindir and simdir. Defaults to current directory. It sets local variables maindir and simdir accordingly.''' | |
| 121 | self.maindir=maindir | |
| 122 | self.simdir=simdir | |
| 123 | return | |
| 124 | ||
| 125 | def fullpath(self): | |
| 126 | ''' | |
| 127 | Method returns string of path where the data is stored. It combines values of maindir and simdir as maindir/simdir on Unix. | |
| 128 | ''' | |
| 129 | return os.path.join(self.maindir,self.simdir) | |
| 130 | ||
| 131 | def exists(self): | |
| 132 | ''' Method checks whether the directory specified by fullpath() exists. It return True/False on completion.''' | |
| 133 | path=self.fullpath() | |
| 134 | if(os.path.exists(path)): | |
| 135 | return True | |
| 136 | else: | |
| 137 | return False | |
| 138 | ||
| 139 | def make(self): | |
| 140 | ''' Method make() creates directory. If it fails it exits the program with error message.''' | |
| 141 | try: | |
| 142 | os.makedirs(self.fullpath()) | |
| 143 | except: | |
| 144 | print("Cannot make directory "+self.fullpath()+"\n") | |
| 145 | exit(1) | |
| 146 | return | |
| 147 | ||
| 148 | def makeifnotexist(self): | |
| 149 | '''Method makeifnotexist() creates directory if it does not exist.''' | |
| 150 | if(self.exists()==0): | |
| 151 | self.make() | |
| 152 | return True | |
| 153 | else: | |
| 154 | return False | |
| 155 | ||
| 156 | def remove(self): | |
| 157 | '''Method remove() removes directory recursively. WARNING! No questions asked.''' | |
| 158 | if(self.exists()): | |
| 159 | try: | |
| 160 | os.rmdir(self.fullpath()) | |
| 161 | except: | |
| 162 | print("Cannot remove directory "+self.fullpath()+ "\n") | |
| 163 | exit(1) | |
| 164 | return | |
| 165 | ||
| 166 | def goto(self): | |
| 167 | ''' | |
| 168 | Method goto() moves current directory to the one specified by fullpath(). WARNING: when using the relative paths, do not call this function multiple times. | |
| 169 | ''' | |
| 170 | try: | |
| 171 | os.chdir(self.fullpath()) | |
| 172 | except: | |
| 173 | print("Cannot go to directory "+self.fullpath()+"\n") | |
| 174 | return | |
| 175 | ||
| 176 | ||
| 177 | class Statistics: | |
| 178 | ''' | |
| 179 | Class that deals with the statistics file from the simulations. | |
| 180 | File is generally large and not all data is needed, so it is dealt with in a specific way. | |
| 181 | ''' | |
| 182 | ||
| 183 | def __init__(self,path,filename="statistics.csv"): | |
| 184 | ''' | |
| 185 | At the initialization call it receives optional filename parameter specifying the path and filename of the statistics file. | |
| 186 | ||
| 187 | The local variables path, filename, fullname (joined path and filename) and private check if the file exists are stored. | |
| 188 | ''' | |
| 189 | self.path=path | |
| 190 | self.filename=filename | |
| 191 | self.fullname=os.path.join(path,filename) | |
| 192 | return | |
| 193 | ||
| 194 | def exists(self): | |
| 195 | '''Method check if the statistics file exists.''' | |
| 196 | if(os.path.isfile(self.fullname)): | |
| 197 | return True | |
| 198 | else: | |
| 199 | return False | |
| 200 | ||
| 5795ac | 201 | def lineCount(self): |
| 8ab985 | 202 | ''' |
| SP | 203 | Internal method for determining the number of the lines in the most efficient way. Is it really the most efficient? |
| 204 | ''' | |
| 205 | f = open(self.fullname, "r+") | |
| 206 | try: | |
| 207 | buf = mmap.mmap(f.fileno(), 0) | |
| 208 | lines = 0 | |
| 209 | readline = buf.readline | |
| 210 | while readline(): | |
| 211 | lines += 1 | |
| 212 | f.close() | |
| 213 | except: | |
| 214 | lines=0 | |
| 215 | f.close() | |
| 216 | return lines | |
| 217 | ||
| 5795ac | 218 | def tail(self): |
| SP | 219 | with open(self.fullname,'r') as myfile: |
| 8ab985 | 220 | lines=myfile.readlines() |
| SP | 221 | return [lines[len(lines)-2].replace('\n',''),lines[len(lines)-1].replace('\n','')] |
| 222 | ||
| 5795ac | 223 | def checkFileValidity(self): |
| 8ab985 | 224 | try: |
| 5795ac | 225 | lines=self.tail() |
| 8ab985 | 226 | except: |
| SP | 227 | return(False) |
| 228 | if len(lines)<2: | |
| 229 | return(False) | |
| 5795ac | 230 | return(True) |
| SP | 231 | |
| 232 | def getSimulationDeltaTime(self): | |
| 233 | try: | |
| 234 | lines=self.tail() | |
| 235 | except: | |
| 236 | return 0 | |
| 237 | ||
| 8ab985 | 238 | fields=shlex.split(lines[0]) |
| SP | 239 | epoch1=fields[0] |
| 240 | n1=fields[1] | |
| 241 | ||
| 242 | fields=shlex.split(lines[1]) | |
| 243 | epoch2=fields[0] | |
| 244 | n2=fields[1] | |
| 245 | try: | |
| 5795ac | 246 | dT=int(epoch2)-int(epoch1) |
| 8ab985 | 247 | except: |
| 5795ac | 248 | return 0 |
| SP | 249 | return dT |
| 250 | ||
| 251 | def getLastIterationInStatistics(self): | |
| 252 | try: | |
| 253 | lines=self.tail() | |
| 254 | except: | |
| 255 | return 0 | |
| 256 | ||
| 257 | fields=shlex.split(lines[0]) | |
| 258 | epoch1=fields[0] | |
| 259 | n1=fields[1] | |
| 260 | ||
| 261 | fields=shlex.split(lines[1]) | |
| 262 | epoch2=fields[0] | |
| 263 | return (fields[1]) | |
| 99bb43 | 264 | |
| SP | 265 | def getColumn(self,n=0): |
| 266 | lines=self.readText().splitlines() | |
| 267 | col=[] | |
| 268 | name=lines[0].split()[n] | |
| 269 | for line in lines: | |
| 270 | col.append(line.split()[n]) | |
| 271 | return col[2:],name | |
| 272 | ||
| 273 | def getTable(self): | |
| 274 | lines=self.readText().splitlines() | |
| 275 | keys=lines[0].split() | |
| 276 | table={} | |
| 277 | def num(s): | |
| 278 | try: | |
| 279 | return int(s) | |
| 280 | except ValueError: | |
| 281 | return float(s) | |
| 282 | for key in keys: | |
| 283 | table[key]=[] | |
| 284 | for line in lines: | |
| 285 | fields=line.split() | |
| f0131d | 286 | for i in range(0,len(keys)): |
| 99bb43 | 287 | try: |
| SP | 288 | value=num(fields[i]) |
| 289 | table[keys[i]].append(value) | |
| 290 | except: | |
| 291 | pass | |
| 292 | return table | |
| 5795ac | 293 | |
| 8ab985 | 294 | |
| SP | 295 | def readText(self): |
| 296 | with open(self.fullname, 'r+') as fin: | |
| 297 | cont=fin.read() | |
| 298 | return cont | |
| 299 | ||
| 300 | def __str__(self): | |
| 301 | ''' | |
| 302 | Prints the full path with filename of the statistics.csv file | |
| 303 | ''' | |
| 304 | return(str(self.fullname)) | |
| 305 | ||
| 306 | ||
| 307 | ||
| 308 | class Runner: | |
| 309 | ''' | |
| 310 | Class Runner consists of a single running or terminated instance of the trisurf. It manages starting, stopping, verifying the running process and printing the reports of the configured instances. | |
| 311 | ''' | |
| 312 | ||
| 313 | @property | |
| 314 | def Dir(self): | |
| 315 | return Directory(maindir=self.maindir,simdir=self.subdir) | |
| 316 | ||
| 317 | ||
| 318 | @property | |
| 319 | def Statistics(self): | |
| 320 | return Statistics(self.Dir.fullpath(), "statistics.csv") | |
| 321 | ||
| 322 | def __init__(self, subdir='run0', tape=None, snapshot=None, runArgs=[]): | |
| 323 | self.subdir=subdir | |
| 324 | self.runArgs=runArgs | |
| 325 | self.isFromSnapshot=False | |
| 326 | if(tape!=None): | |
| 327 | self.initFromTape(tape) | |
| 328 | if(snapshot!=None): | |
| 329 | self.initFromSnapshot(snapshot) | |
| 330 | return | |
| 331 | ||
| 332 | ||
| 333 | def initFromTape(self, tape): | |
| 334 | self.Tape=Tape() | |
| 335 | self.Tape.readTape(tape) | |
| 336 | self.tapeFilename=tape | |
| 337 | ||
| 338 | def initFromSnapshot(self, snapshotfile): | |
| 339 | try: | |
| 340 | tree = ET.parse(snapshotfile) | |
| 341 | except: | |
| 342 | print("Error reading snapshot file") | |
| 343 | exit(1) | |
| 344 | self.isFromSnapshot=True | |
| 345 | self.snapshotFile=snapshotfile | |
| 346 | root = tree.getroot() | |
| 347 | tapetxt=root.find('tape') | |
| 348 | version=root.find('trisurfversion') | |
| 349 | self.Tape=Tape() | |
| 350 | self.Tape.setTape(tapetxt.text) | |
| 351 | ||
| 352 | def getPID(self): | |
| 353 | try: | |
| 354 | fp = open(os.path.join(self.Dir.fullpath(),'.lock')) | |
| 355 | except IOError as e: | |
| 356 | return 0 #file probably does not exist. e==2?? | |
| 357 | pid=fp.readline() | |
| 358 | fp.close() | |
| 359 | return int(pid) | |
| 360 | ||
| 361 | def getLastIteration(self): | |
| 362 | try: | |
| 363 | fp = open(os.path.join(self.Dir.fullpath(),'.status')) | |
| 364 | except IOError as e: | |
| 365 | return -1 #file probably does not exist. e==2?? | |
| 366 | status=fp.readline() | |
| 367 | fp.close() | |
| 368 | return int(status) | |
| 369 | ||
| 370 | def isCompleted(self): | |
| 371 | if int(self.Tape.getValue("iterations"))+int(self.Tape.getValue("inititer"))==self.getLastIteration()+1: | |
| 372 | return True | |
| 373 | else: | |
| 374 | return False | |
| 5795ac | 375 | |
| SP | 376 | |
| 377 | def getStartTime(self): | |
| 378 | try: | |
| 379 | return os.path.getmtime(os.path.join(self.Dir.fullpath(),'.lock')) | |
| 380 | except: | |
| 381 | return -1 | |
| 8ab985 | 382 | |
| SP | 383 | def getStatus(self): |
| 384 | pid=self.getPID() | |
| 385 | if(self.isCompleted()): | |
| 386 | return TS_COMPLETED | |
| 387 | if(pid==0): | |
| 388 | return TS_NOLOCK | |
| 389 | if(psutil.pid_exists(int(pid))): | |
| 390 | proc= psutil.Process(int(pid)) | |
| 391 | #psutil.__version__ == '3.4.2' requires name() and status(), some older versions reguire name, status | |
| 392 | if(psutil.__version__>='2.0.0'): | |
| 393 | procname=proc.name() | |
| 394 | procstat=proc.status() | |
| 395 | else: | |
| 396 | procname=proc.name | |
| 397 | procstat=proc.status | |
| 398 | if procname=="trisurf": | |
| 399 | if procstat=="stopped": | |
| 400 | return TS_STOPPED | |
| 401 | else: | |
| 402 | return TS_RUNNING | |
| 403 | else: | |
| 404 | return TS_NONEXISTANT | |
| 405 | else: | |
| 406 | return TS_NONEXISTANT | |
| 407 | ||
| 408 | def start(self): | |
| 409 | if(self.getStatus()==0 or self.getStatus()==TS_COMPLETED): | |
| 410 | #check if executable exists | |
| 411 | if(shutil.which('trisurf')==None): | |
| 412 | print("Error. Trisurf executable not found in PATH. Please install trisurf prior to running trisurf manager.") | |
| 413 | exit(1) | |
| 414 | #Symlinks tape file to the directory or create tape file from snapshot in the direcory... | |
| 415 | if(self.Dir.makeifnotexist()): | |
| 416 | if(self.isFromSnapshot==False): | |
| 417 | try: | |
| 418 | os.symlink(os.path.abspath(self.tapeFilename), self.Dir.fullpath()+"/tape") | |
| 419 | except: | |
| 420 | print("Error while symlinking "+os.path.abspath(self.tapeFilename)+" to "+self.Dir.fullpath()+"/tape") | |
| 421 | exit(1) | |
| 422 | else: | |
| 423 | try: | |
| 424 | with open (os.path.join(self.Dir.fullpath(),"tape"), "w") as myfile: | |
| 425 | #myfile.write("#This is automatically generated tape file from snapshot") | |
| 426 | myfile.write(str(self.Tape.rawText)) | |
| 427 | except: | |
| 428 | print("Error -- cannot make tapefile "+ os.path.join(self.Dir.fullpath(),"tape")+" from the snapshot in the running directory") | |
| 429 | exit(1) | |
| 430 | try: | |
| 431 | os.symlink(os.path.abspath(self.snapshotFile), os.path.join(self.Dir.fullpath(),"initial_snapshot.vtu")) | |
| 432 | except: | |
| 433 | print("Error while symlinking "+os.path.abspath(self.snapshotFile)+" to "+os.path.join(self.Dir.fullpath(),self.snapshotFile)) | |
| 434 | ||
| 435 | #check if the simulation has been completed. in this case notify user and stop executing. | |
| 436 | if(self.isCompleted() and ("--force-from-tape" not in self.runArgs) and ("--reset-iteration-count" not in self.runArgs)): | |
| 437 | print("The simulation was completed. Not starting executable in "+self.Dir.fullpath()) | |
| 438 | return | |
| 439 | ||
| 440 | cwd=Directory(maindir=os.getcwd()) | |
| 441 | lastVTU=self.getLastVTU() #we get last VTU file in case we need to continue the simulation from last snapshot. Need to be done before the Dir.goto() call. | |
| 442 | self.Dir.goto() | |
| 443 | print("Starting trisurf-ng executable in "+self.Dir.fullpath()) | |
| 444 | if(self.isFromSnapshot==True): | |
| 445 | #here we try to determine whether we should continue the simulation or start from last known VTU snapshot. | |
| 446 | if(lastVTU==None): | |
| 447 | initSnap="initial_snapshot.vtu" | |
| 448 | else: | |
| 449 | initSnap=lastVTU | |
| 450 | print("WARNING: Not using initial snapshot as starting point, but selecting "+initSnap+" as a starting vesicle") | |
| 451 | params=["trisurf", "--restore-from-vtk",initSnap]+self.runArgs | |
| 452 | print("InitSnap is: "+initSnap) | |
| 453 | else: | |
| 454 | #veify if dump exists. If not it is a first run and shoud be run with --force-from-tape | |
| 455 | if(os.path.isfile("dump.bin")==False): | |
| 456 | self.runArgs.append("--force-from-tape") | |
| 457 | params=["trisurf"]+self.runArgs | |
| 458 | subprocess.Popen (params, stdout=subprocess.DEVNULL) | |
| 459 | cwd.goto() | |
| 460 | else: | |
| 461 | print("Process in "+self.Dir.fullpath()+" already running. Not starting.") | |
| 462 | return | |
| 463 | ||
| 464 | ||
| 465 | def setMaindir(self,prefix,variables): | |
| 466 | maindir="" | |
| 467 | for p,v in zip(prefix,variables): | |
| 84450d | 468 | tv=str(self.Tape.config[v]) |
| 8ab985 | 469 | maindir=maindir+p+tv |
| SP | 470 | self.maindir=maindir |
| 471 | return | |
| 472 | ||
| 473 | def setSubdir(self, subdir="run0"): | |
| 474 | self.subdir=subdir | |
| 475 | return | |
| 476 | ||
| 477 | def getStatistics(self, statfile="statistics.csv"): | |
| 478 | self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment")) | |
| 479 | pid=self.getPID() | |
| 480 | status=self.getStatus() | |
| 5795ac | 481 | if(self.Statistics.checkFileValidity()): |
| SP | 482 | ETA=str(datetime.timedelta(microseconds=(int(self.Tape.config['iterations'])-int(self.Statistics.getLastIterationInStatistics()))*self.Statistics.getSimulationDeltaTime())*1000000) |
| 8ab985 | 483 | if(status==TS_NONEXISTANT or status==TS_NOLOCK): |
| SP | 484 | statustxt="Not running" |
| 485 | pid="" | |
| 486 | ETA="" | |
| 487 | elif status==TS_STOPPED: | |
| 488 | statustxt="Stopped" | |
| 489 | ETA="N/A" | |
| 490 | elif status==TS_COMPLETED: | |
| 491 | statustxt="Completed" | |
| 492 | pid="" | |
| 493 | ETA="" | |
| 494 | else: | |
| 495 | statustxt="Running" | |
| 496 | ||
| 5795ac | 497 | if(self.Statistics.checkFileValidity()): |
| SP | 498 | report=[time.strftime('%Y-%m-%d %H:%M:%S', time.localtime(int(self.getStartTime()))),ETA, statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()] |
| 8ab985 | 499 | else: |
| SP | 500 | report=["N/A","N/A",statustxt, pid, str(self.Dir.fullpath()), self.Comment.getText()] |
| 501 | return report | |
| 502 | ||
| 503 | ||
| 504 | def stop(self): | |
| 505 | try: | |
| 506 | p=psutil.Process(self.getPID()) | |
| 507 | p.kill() | |
| 508 | except: | |
| 509 | print("Could not stop the process. Is the process running? Do you have sufficient privileges?") | |
| 510 | ||
| 511 | ||
| 512 | def writeComment(self, data, mode='w'): | |
| 513 | self.Comment=FileContent(os.path.join(self.Dir.fullpath(),".comment")) | |
| 514 | self.Comment.writefile(data,mode=mode) | |
| 515 | ||
| 516 | ||
| f49271 | 517 | def getLastVTUold(self): |
| 8ab985 | 518 | vtuidx=self.getLastIteration()-int(self.Tape.getValue("inititer")) |
| SP | 519 | if vtuidx<0: |
| 520 | return None | |
| 521 | else: | |
| 522 | return 'timestep_{:06d}.vtu'.format(vtuidx) | |
| 523 | ||
| f49271 | 524 | def getLastVTU(self): |
| SP | 525 | flist=[] |
| 526 | for file in os.listdir(self.Dir.fullpath()): | |
| 527 | if file.endswith(".vtu"): | |
| 528 | flist.append(file) | |
| 0d561c | 529 | flist.sort() |
| SP | 530 | if(len(flist)==0): |
| 531 | return(-1) | |
| 532 | else: | |
| 533 | return(flist[-1]) | |
| f49271 | 534 | |
| 8ab985 | 535 | def __str__(self): |
| SP | 536 | if(self.getStatus()==0): |
| 537 | str=" not running." | |
| 538 | else: | |
| 539 | str=" running." | |
| 540 | return(self.Dir.fullpath()+str) | |
| 541 | ||
| 57b1a6 | 542 | def __repr__(self): |
| SP | 543 | return("Instance of trisurf in "+self.Dir.fullpath()) |
